PaperBLAST
PaperBLAST Hits for mRNA_3004 (85 a.a., MASTILPLEL...)
Show query sequence
>mRNA_3004
MASTILPLELVDRAIGSKVWVIMKTEREFTGTLVGFDDYVNMVLEDVTEYETTAEGRKSS
KLGQTLLNGNNIAMIVPGRGPEDEQ
Running BLASTp...
Found 46 similar proteins in the literature:
LSM5_ARATH / Q9FKB0 Sm-like protein LSM5; AtLSM5; Protein SUPERSENSITIVE TO ABA AND DROUGHT 1; AtSAD1; U6 snRNA-associated Sm-like protein LSM5 from Arabidopsis thaliana (Mouse-ear cress) (see 5 papers)
NP_199698 Small nuclear ribonucleoprotein family protein from Arabidopsis thaliana
AT5G48870 SAD1 (SUPERSENSITIVE TO ABA AND DROUGHT 1); RNA binding from Arabidopsis thaliana
70% identity, 92% coverage
- function: Component of LSM protein complexes, which are involved in RNA processing. Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation by promoting decapping and leading to accurate 5'-3' mRNA decay. The cytoplasmic LSM1-LSM7 complex regulates developmental gene expression by the decapping of specific development- related transcripts. Component of the nuclear LSM2-LSM8 complex which is involved splicing nuclear mRNAs. LSM2-LSM8 binds directly to the U6 small nuclear RNAs (snRNAs) and is essential for accurate splicing of selected development-related mRNAs through the stabilization of the spliceosomal U6 snRNA. Plays a critical role in the regulation of development-related gene expression (PubMed:23221597, PubMed:23620288). Involved in the control of plant sensitivity to abscisic acid (ABA) and drought (PubMed:11740939). Functions with ABH1 as negative regulator of ABA signaling in guard cells (PubMed:12427994). Required for regulation of splicing efficiency of many stress-responsive genes under stress conditions (PubMed:24393432).
subunit: Component of the heptameric LSM1-LSM7 complex that forms a seven-membered ring structure with a donut shape. The LSM subunits are arranged in the order LSM1, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4. Component of the heptameric LSM2-LSM8 complex that forms a seven- membered ring structure with a donut shape. The LSM subunits are arranged in the order LSM8, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4 (PubMed:23221597, PubMed:23620288). LSM2 subunit interacts only with its two neighboring subunits, LSM6A or LSM6B and LSM7 (PubMed:23221597).
disruption phenotype: Embryonic lethality when homozygous. - Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis.
Cui, Genome biology 2014 - GeneRIF: Overexpression of SAD1 in Arabidopsis improves salt tolerance in transgenic plants, which correlates with an increase in splicing accuracy and efficiency for stress-responsive genes.
- Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...NP_013543 DDB0233378 LSm4 (Lsm4p) LSM4 NP_036453 NP_001027236 NP_198124 NP_011037 DDB0233383 LSm5 (Lsm5p) LSM5 NP_036454 NP_648022 NP_199698 NP_011073 DDB0233198 LSm6 (Lsm6p) LSM6 NP_009011 NP_611528 NP_181909 NP_010666 DDB0233196 LSm7 (Lsm7p) LSM7 NP_057283 NP_609807 NP_178480 NP_014252 DDB0233384 LSm8 (Lsm8p) NAA38 NP_057284 NP_647660 NP_176747 NP_012556 DDB0302415 d SmE (Sme1p) SNRPE...”
- ZmNF-YB10, a maize NF-Y transcription factor, positively regulates drought and salt stress response in Arabidopsis thaliana
Wang, GM crops & food 2025 - “...gene phosphatase-like protein FRY1( AtFRY1 , AT5G63980), small nuclear ribonucleoprotein family protein ( AtSAD1 , AT5G48870), and protein kinase superfamily protein ( AtSOS2 , AT5G35410). It was found that the expression of AtSAG13 , AtCOR15 , AtDREB2A , AtFRY1 , AtSAD1 , and AtSOS2 in Arabidopsis...”
- Dissection of figured wood trait in curly birch (Betula pendula Roth var. carelica (Mercklin) Hämet-Ahti) using high-throughput genotyping
Gubaev, Scientific reports 2024 - “...that the homolog of the candidate gene Bpev01.c0000.g0081 in Arabidopsis (Sm-like protein ( SAD1 ), AT5G48870) affects both ABA sensitivity and drought-induced ABA biosynthesis: ABA-deficiency was detected in sad1 mutant plants 31 . The authors proposed a critical role for the SAD 1 gene in RNA...”
- Warming-induced changes of broccoli head to cauliflower-like curd in Brassica oleracea are regulated by DNA methylation as revealed by methylome and transcriptome co-profiling
Yao, Molecular horticulture 2022 - “...shoot apex inflorescence: LOC106336011 ( AT5G02960 , a ribosomal protein S12/S23 family protein), LOC106316876 ( AT5G48870 , SAD1 , a polypeptide similar to multifunctional Sm-like snRNP proteins that are required for mRNA splicing, export, and degradation), LOC106315720 ( AT5G20920 , the protein synthesis initiation factor eIF2...”
- The FLA4-FEI Pathway: A Unique and Mysterious Signaling Module Related to Cell Wall Structure and Stress Signaling
Seifert, Genes 2021 - “...0.09 0.12 AT1G74800 GALT5 AGP biosynt. D + [ 47 ] Golgi 0.02 0.13 0.00 AT5G48870 SAD1 ABA signaling (neg. regulator) I [ 65 ] cytosol, nuc. 0.16 0.39 0.01 AT4G21670 CPL1 ABA signaling (neg. regulator) I [ 65 ] nuc. 0.22 -0.26 0.31 AT1G24180 IAR4...”
- Genome-wide identification and expression analyses of Sm genes reveal their involvement in early somatic embryogenesis in Dimocarpus longan Lour
Li, PloS one 2020 - “...150 16135.20 10.14 No Dlo_031761.1 DlLSm4c AT5G27720 AtLSm4 scaffold845:311468:313948 150 16135.20 10.14 No Dlo_023673.1 DlLSm5a AT5G48870 AtLSm5 scaffold52:850634:851892 120 13777.51 5.54 No Dlo_012057.1 DlLSm5b AT5G48870 AtLSm5 scaffold224:406385:407477 87 9599.07 4.50 No Dlo_032946.1 DlLSm6 AT2G43810 AtLSm6b scaffold908:10301:13180 91 9794.13 9.13 No Dlo_028712.1 DlLSm7a AT2G03870 AtLSm7 Scaffold70:1068910:1071695 99...”
- Importin-β From the Recretohalophyte Limonium bicolor Enhances Salt Tolerance in Arabidopsis thaliana by Reducing Root Hair Development and Abscisic Acid Sensitivity
Xu, Frontiers in plant science 2020 - “...DROUGHT 2 ( AT2G31660 , AtSAD2 ), SUPER SENSITIVE TO ABA AND DROUGHT 1 ( AT5G48870 , AtSAD1 ), GLABRA3 ( AT5G41315 , AtGL3 ), ENHANCER OF GLABRA3 ( AT1G63650 , AtEGL 3), CAPRICE ( AT2G46410 , AtCPC ), and TRYPTICHON ( AT5G53200 , AtTRY ),...”
- Drought Stress Causes Specific Changes to the Spliceosome and Stress Granule Components
Marondedze, Frontiers in molecular biosciences 2019 - “...X AT3G13570 SC35-like splicing factor 30A X X AT3G26560 ATP-dependent RNA helicase, putative X X AT5G48870 Small nuclear ribonucleoprotein family protein X X AT1G09770 Cell division cycle 5 X AT4G02840 Small nuclear ribonucleoprotein family protein X AT4G30330 Small nuclear ribonucleoprotein family protein X AT4G38780 Pre-mRNA-processing-splicing factor...”
- Improvement of Drought Tolerance in Rice (Oryza sativa L.): Genetics, Genomic Tools, and the WRKY Gene Family
Sahebi, BioMed research international 2018 - “...thaliana Stomatal Movement, Ion and Osmotic Homeostasis, Regulatory Proteins, Hormone Signaling [ 84 ] SAD1 AT5G48870 Arabidopsis thaliana Stomatal Movement, Ion and Osmotic Homeostasis [ 85 ] HARDY AT2G36450 Arabidopsis thaliana Regulatory Proteins, Transcription Factors, AP2-Domain [ 78 ] OST2 AT2G18960 Arabidopsis thaliana Stomatal Movement, Ion...”
- More
LSM5_HUMAN / Q9Y4Y9 U6 snRNA-associated Sm-like protein LSm5 from Homo sapiens (Human) (see 3 papers)
P62322 U6 snRNA-associated Sm-like protein LSm5 from Mus musculus
NP_036454 U6 snRNA-associated Sm-like protein LSm5 isoform a from Homo sapiens
65% identity, 88% coverage
- function: Plays a role in pre-mRNA splicing as component of the U4/U6- U5 tri-snRNP complex that is involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex) (PubMed:28781166). The heptameric LSM2-8 complex binds specifically to the 3'-terminal U-tract of U6 snRNA (PubMed:10523320).
subunit: Component of the precatalytic spliceosome (spliceosome B complex) (PubMed:28781166). Component of the U4/U6-U5 tri-snRNP complex, a building block of the precatalytic spliceosome (spliceosome B complex) (PubMed:10523320, PubMed:26912367, PubMed:28781166). The U4/U6-U5 tri-snRNP complex is composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, SNRNP40, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39, plus LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8 (PubMed:26912367). LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8 form a heptameric, ring-shaped subcomplex (the LSM2-8 complex) that is part of the U4/U6-U5 tri-snRNP complex and the precatalytic spliceosome (PubMed:10523320, PubMed:26912367, PubMed:28781166). - In utero and lactational 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) exposure exacerbates urinary dysfunction in hormone-treated C57BL/6J mice through a non-malignant mechanism involving proteomic changes in the prostate that differ from those elicited by testosterone and estradiol
Turco, American journal of clinical and experimental urology 2020 (secret) - Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...NP_732931 NP_177812 NP_013543 DDB0233378 LSm4 (Lsm4p) LSM4 NP_036453 NP_001027236 NP_198124 NP_011037 DDB0233383 LSm5 (Lsm5p) LSM5 NP_036454 NP_648022 NP_199698 NP_011073 DDB0233198 LSm6 (Lsm6p) LSM6 NP_009011 NP_611528 NP_181909 NP_010666 DDB0233196 LSm7 (Lsm7p) LSM7 NP_057283 NP_609807 NP_178480 NP_014252 DDB0233384 LSm8 (Lsm8p) NAA38 NP_057284 NP_647660 NP_176747 NP_012556 DDB0302415 d SmE...”
- B Cell Lymphocytes as a Potential Source of Breast Carcinoma Marker Candidates
Tkáčiková, International journal of molecular sciences 2024 - “...10 10 31.3 Q7L2H7 Eukaryotic translation initiation factor 3 subunit M 51 15 15 42.5 Q9Y4Y9 U6 snRNA-associated Sm-like protein LSm5 56 6 6 9.9 ijms-25-07351-t004_Table 4 Table 4 A total of 17 down- and upregulated proteins identified in luminal A, luminal B, TNBC, and benign...”
- “...I3L4N8 0.187 157.77 0.243 77.41 0.571 83.21 0.262 88.8 U6 snRNA-associated Sm-like protein LSm5 LSM5 Q9Y4Y9 0.228 207.85 0.395 71.81 0.498 78.14 0.208 117.05 Complement component 1 Q subcomponent-binding protein, mitochondrial C1QBP Q07021 0.296 168.91 0.412 84.96 0.699 41.6 0.51 89.27 Nucleosome assembly protein 1-like 1,...”
- Life and Death of mRNA Molecules in Entamoeba histolytica.
Valdés-Flores, Frontiers in cellular and infection microbiology 2018 - “...Q9Y333 EHI_068580 EhLsm2 C4LU49 Lsm3 P62310 EHI_151310 EhLsm3 C4LSH4 Lsm4 Q9Y4Z0 EHI_049370 EhLsm4 C4LUD9 Lsm5 Q9Y4Y9 EHI_076840 EhLsm5 B1N3I3 Lsm6 P62312 EHI_188130 EhLsm6 C4M187 Lsm7 Q9UK45 EHI_025840 EhLsm7 C4M939 Edc3 Q96F86 EHI_198940 Ehedc3 C4LWU0 Dhh1 P26196 EHI_093900 Ehdhh1 C4LYI1 XRN2 Q9H0D6 EHI_133330 EhXRN2 C4MB40 DEADENYLATION FACTORS...”
- Structure and RNA-binding properties of the bacterial LSm protein Hfq
Sauer, RNA biology 2013 - “...proteins: LSm1, (O15116); LSm2, (Q9Y333); LSm4, (Q9Y4Z0); LSm5, (Q9Y4Y9); LSm6, (P62312); LSm8, (O95777). The RNA Binding Properties of Hfq and the Initial sRNA...”
- Inhibition of Raf-MEK-ERK and hypoxia pathways by Phyllanthus prevents metastasis in human lung (A549) cancer cell line
Lee, BMC complementary and alternative medicine 2013 - “...-0.78 -0.27 P15515 MASCOT;UNIPROT KB/SWISS-PROT;COGS 15 U6 snRNA-associated Sm-like protein LSm5 -0.33 -0.57 -0.19 -0.54 Q9Y4Y9 MASCOT;UNIPROT KB/SWISS-PROT;COGS 16 Bcl-2-like protein 11 -0.25 -1.00 -1.00 -0.70 O43521 MASCOT;UNIPROT KB/SWISS-PROT;COGS 17 Contactin-2 precursor -0.29 -0.60 -0.42 -0.39 Q02246 MASCOT;UNIPROT KB/SWISS-PROT;COGS 18 Bis(5-adenosyl)-triphosphatase -1.00 -1.00 N/A -1.00 P49789...”
- Intact mass detection, interpretation, and visualization to automate Top-Down proteomics on a large scale.
Durbin, Proteomics 2010 - “...having a THRASH inferred MW of 9980.06 Da and an unmodified MW at 9900.07 Da (Q9Y4Y9). The detected precursor containing a methylation ( m = +14) in the (bottom middle, Fig. 5 ) had a MW of 9703.99 Da, with an unmodified mass of 9689.98 Da...”
LOC106316876 sm-like protein LSM5 from Brassica oleracea var. oleracea
68% identity, 91% coverage
- Warming-induced changes of broccoli head to cauliflower-like curd in Brassica oleracea are regulated by DNA methylation as revealed by methylome and transcriptome co-profiling
Yao, Molecular horticulture 2022 - “...in the shoot apex inflorescence: LOC106336011 ( AT5G02960 , a ribosomal protein S12/S23 family protein), LOC106316876 ( AT5G48870 , SAD1 , a polypeptide similar to multifunctional Sm-like snRNP proteins that are required for mRNA splicing, export, and degradation), LOC106315720 ( AT5G20920 , the protein synthesis initiation...”
- “...2021 ), and highly expressed in proliferating tissues (Pontvianne et al. 2007 ). SAD1 ( LOC106316876 ) encodes a polypeptide similar to multifunctional Sm-like snRNP proteins that control splice-site recognition and contributes to stress tolerance in Arabidopsis (Cui et al. 2014 ). RPS10B ( LOC106298457 ),...”
NP_648022 uncharacterized protein, isoform A from Drosophila melanogaster
64% identity, 84% coverage
LOC725641 U6 snRNA-associated Sm-like protein LSm5 from Apis mellifera
66% identity, 84% coverage
- ame-miR-5119-<i>Eth</i> axis modulates larval-pupal transition of western honeybee worker
Dong, Frontiers in physiology 2024 - “...3 fluorescent quantitative PCR system (ABI Company, Tampa, FL, United States). U 6 (GenBank ID: LOC725641) was used as the internal reference of ame-miR-5119 and actin (GenBank ID: NM001185145) was used as the internal reference of Eth, Ethr, Jhamt, and Kr-h 1 genes. The reaction system...”
- First Characterization and Regulatory Function of piRNAs in the Apis mellifera Larval Response to Ascosphaera apis Invasion
Sun, International journal of molecular sciences 2023 - “...used as templates for the PCR of the reference gene snRNA U 6 (GenBank ID: LOC725641), which was conducted on a T100 thermocycler (Bio-Rad, Hercules, CA, USA) under the following conditions: pre-denaturation at 95 C for 5 min, 40 amplification cycles of denaturation at 95 C...”
- ame-miR-34 Modulates the Larval Body Weight and Immune Response of Apis mellifera Workers to Ascosphara apis Invasion
Wu, International journal of molecular sciences 2023 - “...a QuantStudio 3 fluorescent quantitative PCR system (ABI Company, Tampa, FL, USA). AmU6 (GenBank ID: LOC725641) was used as the internal reference. The reaction system (20 L) included 10 L of Hifair qPCR SYBR Green Master Mix (Low Rox Plus) (Yeasen, Shanghai, China), 1 L of...”
- “...ame-miR-34-targeted genes and the internal reference genes actin (GenBank ID: NM001185145) and AmU6 (GenBank ID: LOC725641). RT-qPCR was performed to determine the effects of overexpression and knockdown of ame-miR-34 following the method described in Section 4.4 . The experiment was performed three times using three independent...”
AFUA_7G04280 small nuclear ribonucleoprotein (LSM5), putative from Aspergillus fumigatus Af293
61% identity, 95% coverage
LSM5_SCHPO / O42978 U6 snRNA-associated Sm-like protein LSm5 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see paper)
NP_596373 U6 snRNP-associated protein Lsm5 from Schizosaccharomyces pombe
62% identity, 96% coverage
- function: Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. LSm5 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA (By similarity).
subunit: LSm subunits form a heteromer with a doughnut shape. - Crystal structures of Lsm3, Lsm4 and Lsm5/6/7 from Schizosaccharomyces pombe.
Wu, PloS one 2012 - GeneRIF: Analysis of the inter-subunit interactions in Lsm5/6/7 reveals the organization order among Lsm5, Lsm6 and Lsm7
FGSG_06819 hypothetical protein from Fusarium graminearum PH-1
58% identity, 92% coverage
3swnA / O42978 Structure of the lsm657 complex: an assembly intermediate of the lsm1 7 and lsm2 8 rings (see paper)
63% identity, 92% coverage
NP_001124182 U6 snRNA-associated Sm-like protein LSm5 isoform b from Homo sapiens
69% identity, 71% coverage
PF3D7_1443300 U6 snRNA-associated Sm-like protein LSm5, putative from Plasmodium falciparum 3D7
55% identity, 79% coverage
- A bioinformatic survey of RNA-binding proteins in Plasmodium
Reddy, BMC genomics 2015 - “...PVX_091835 PY17X_0925900 LSM2 PF3D7_0520300 PVX_080230 PY17X_1238500 LSM3 PF3D7_0819900 PVX_089370 PY17X_0711100 LSM4 PF3D7_1107000 PVX_091025 PY17X_0942400 LSM5 PF3D7_1443300 PVX_118325 PY17X_1311000 LSM6 PF3D7_1325000 PVX_116625 PY17X_1344900 LSM7 PF3D7_1209200 PVX_084490 PY17X_0610100 Pab1 PF3D7_1224300 PVX_123845 PY17X_1441700 Rpb4 PF3D7_1404000 PVX_086235 PY17X_1040500 Rbp7 PF3D7_1104700.1, PVX_090915 PY17X_0944700 PF3D7_1104700.2 Sbp1 PF3D7_0501300 PVX_097583 Upf1 PF3D7_1005500 PVX_094465 PY17X_1206900...”
PY17X_1311000 U6 snRNA-associated Sm-like protein LSm5, putative from Plasmodium yoelii
55% identity, 79% coverage
- A bioinformatic survey of RNA-binding proteins in Plasmodium
Reddy, BMC genomics 2015 - “...LSM2 PF3D7_0520300 PVX_080230 PY17X_1238500 LSM3 PF3D7_0819900 PVX_089370 PY17X_0711100 LSM4 PF3D7_1107000 PVX_091025 PY17X_0942400 LSM5 PF3D7_1443300 PVX_118325 PY17X_1311000 LSM6 PF3D7_1325000 PVX_116625 PY17X_1344900 LSM7 PF3D7_1209200 PVX_084490 PY17X_0610100 Pab1 PF3D7_1224300 PVX_123845 PY17X_1441700 Rpb4 PF3D7_1404000 PVX_086235 PY17X_1040500 Rbp7 PF3D7_1104700.1, PVX_090915 PY17X_0944700 PF3D7_1104700.2 Sbp1 PF3D7_0501300 PVX_097583 Upf1 PF3D7_1005500 PVX_094465 PY17X_1206900 Upf2 PF3D7_0925800...”
PVX_118325 U6 snRNA-associated Sm-like protein LSm5, putative from Plasmodium vivax
55% identity, 79% coverage
- A bioinformatic survey of RNA-binding proteins in Plasmodium
Reddy, BMC genomics 2015 - “...PY17X_0925900 LSM2 PF3D7_0520300 PVX_080230 PY17X_1238500 LSM3 PF3D7_0819900 PVX_089370 PY17X_0711100 LSM4 PF3D7_1107000 PVX_091025 PY17X_0942400 LSM5 PF3D7_1443300 PVX_118325 PY17X_1311000 LSM6 PF3D7_1325000 PVX_116625 PY17X_1344900 LSM7 PF3D7_1209200 PVX_084490 PY17X_0610100 Pab1 PF3D7_1224300 PVX_123845 PY17X_1441700 Rpb4 PF3D7_1404000 PVX_086235 PY17X_1040500 Rbp7 PF3D7_1104700.1, PVX_090915 PY17X_0944700 PF3D7_1104700.2 Sbp1 PF3D7_0501300 PVX_097583 Upf1 PF3D7_1005500 PVX_094465 PY17X_1206900 Upf2...”
LSM5_YEAST / P40089 U6 snRNA-associated Sm-like protein LSm5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 10 papers)
NP_011073, YER146W Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA from Saccharomyces cerevisiae
48% identity, 80% coverage
- function: Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved in degradation of nuclear pre-mRNA by targeting them for decapping. LSM5 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM5, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM5 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.
subunit: Component of the heptameric LSM1-LSM7 complex that forms a seven-membered ring structure with a doughnut shape. The LSm subunits are arranged in the order LSM1, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4. Except for LSM1, where a C-terminal helix crosses the ring structure to form additional interactions with LSM3 and LSM6, each subunit interacts only with its two neighboring subunits. The LSM1-LSM7 complex interacts with PAT1; within the complex PAT1 has direct interactions with LSM2 and LSM3. Component of the heptameric LSM2-LSM8 complex that forms a seven-membered ring structure with a doughnut shape; an RNA strand can pass through the hole in the center of the ring structure. The LSm subunits are arranged in the order LSM8, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4. LSM2-LSM8 associates with PAT1 and XRN1. A complex comprising LSM2-LSM7 without LSM1 or LSM8 may exist. Component of the spliceosome U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRP3, PRP4, PRP6, PRP8, PRP18, PRP31, PRP38, SNU13, SNU23, SNU66, SNU114, SPP381, SMB1, SMD1, SMD2, SMD3, SMX2, SMX3, LSM2, LSM3, LSM4, LSM5, LSM6, LSM7, LSM8, BRR2 and DIB1. Interacts with PAT1. - Proteomic analysis revealed the roles of YRR1 deletion in enhancing the vanillin resistance of Saccharomyces cerevisiae
Cao, Microbial cell factories 2021 - “...ends 1.31 YLR150W Stm1 Protein required for optimal translation under nutrient stress 1.42 rRNA processing YER146W Lsm5 Possibly involved in processing tRNA, snoRNA, and rRNA 1.31 YDL208W Nhp2 snoRNA-binding protein NHP2 rRNA processing 1.42 YGL029W Cgr1 Protein involved in processing of pre-rRNA 1.60 YGR159C Nsr1 Pre-rRNA...”
- Protein functional module identification method combining topological features and gene expression data
Zhao, BMC genomics 2021 - “...YHR027C, YHR200W, YKL145W,YLR421C, YMR314W, YOR117W, YOR259C, YOR261C, YPR108W 6.86e-17 YBL026W, YCR077C, YDR378C, YER112W, spliceosomal mRNA YER146W, YGL173C, YJL124C, YJR022W, tri-snRNP processing YKL173W, YLR147C,YLR275W, YMR268C, complex YNL118C, YPR178W, YOL149W, YNL147W, YLR438C-A 2.77e-27 YAL043C, YDR195W, YDR228C, YDR301W, mRNA cleavage mRNA YER133W, YGR156W, YJL033W, YJR093C, factor complex polyadenylation YKL018W,...”
- Dynamic identifying protein functional modules based on adaptive density modularity in protein-protein interaction networks
Shen, BMC bioinformatics 2015 - “...genes, 91.7% mRNA metabolic process ybl026w ybr055c ybr152w ycr077c ydl098c ydl160c ydr037w ydr378c ydr473c yer112w yer146w ygl173c ygr075c ygr091w yjl124c yjr022w ylr438c-a ymr080c ymr268c ynl147w ynl256w yor308c ypr082c ypr178w 1.43e-31 20 out of 24 genes, 83.3% mRNA splicing, via spliceosome ybr119w ydl087c ydr235w ydr240c yer029c yfl017w-a...”
- “...mRNA metabolic process ybl026w ybl098w ybr055c ycr077c ydl085c-a ydl121c ydl160c ydr055w ydr378c ydr473c yel015w yer112w yer146w yer172c ygl068w ygl173c ygr091w yhr019c yhr140w yjl013c yjl035c yjl124c yjr022w ykl173w ylr419w ylr438c-a ymr268c ynl092w ynl118c ynl147w ynl240c ynr011c yor308c ypr058w ypr178w Conclusions Protein functional module is a fundamental unit...”
- Malleable ribonucleoprotein machine: protein intrinsic disorder in the Saccharomyces cerevisiae spliceosome
Coelho, PeerJ 2013 - “...0.23 0.28 0.16 LSm8 LSm2 YBL026W P38203 11.2 95 0.23 0.10 0.29 0.11 LSm2 LSm5 YER146W P40089 10.4 93 0.33 0.45 0.14 0.00 LSm5 LSm3 YLR438C P57743 10.0 89 0.32 0.52 0.38 0.09 LSm3 3BW1 (1-89) LSm6 YDR378C Q06406 9.38 86 0.21 0.20 0.00 0.27 LSm6...”
- Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...DDB0233378 LSm4 (Lsm4p) LSM4 NP_036453 NP_001027236 NP_198124 NP_011037 DDB0233383 LSm5 (Lsm5p) LSM5 NP_036454 NP_648022 NP_199698 NP_011073 DDB0233198 LSm6 (Lsm6p) LSM6 NP_009011 NP_611528 NP_181909 NP_010666 DDB0233196 LSm7 (Lsm7p) LSM7 NP_057283 NP_609807 NP_178480 NP_014252 DDB0233384 LSm8 (Lsm8p) NAA38 NP_057284 NP_647660 NP_176747 NP_012556 DDB0302415 d SmE (Sme1p) SNRPE NP_003085...”
- Deletion of a subgroup of ribosome-related genes minimizes hypoxia-induced changes and confers hypoxia tolerance
Shah, Physiological genomics 2011 - “...YIL041W YDL223C YBL032W YNL031C YER057C YDR225W YDL181W YER146W YPL004C YDL131W YGL106W YNL074C YER009W YIR006C YGR193C YBL030C YGR086C YEL037C YJL173C YOL005C...”
- Modifying the DPClus algorithm for identifying protein complexes based on new topological structures
Li, BMC bioinformatics 2008 - “...provides a cluster which is composed of ten proteins: YGL173c, YOL149w, YBL026w, YCR077c, YJR022w, YER112w, YER146w, YDR378c, YNL147w, and YLR438c-a. The functional annotations for each protein in the cluster are listed in this file. Click here for file Acknowledgements The authors would like to thank Md...”
- Biological context networks: a mosaic view of the interactome
Rachlin, Molecular systems biology 2006 - “...Spliceosome assembly, exocytosis CDC6 YJL194W 11 7 14.8 3.6 Pre-replicative complex formation and maintenance LSM5 YER146W 37 16 17.2 3.6 Nuclear mRNA splicing, via spliceosome, mRNA catabolism, rRNA processing SKP1 YDR328C 42 17 11.1 3.5 Vacuolar acidification, protein ubiquitination, G1/S transition of mitotic cell cycle, protein...”
- More
- Malleable ribonucleoprotein machine: protein intrinsic disorder in the Saccharomyces cerevisiae spliceosome
Coelho, PeerJ 2013 - “...0.28 0.16 LSm8 LSm2 YBL026W P38203 11.2 95 0.23 0.10 0.29 0.11 LSm2 LSm5 YER146W P40089 10.4 93 0.33 0.45 0.14 0.00 LSm5 LSm3 YLR438C P57743 10.0 89 0.32 0.52 0.38 0.09 LSm3 3BW1 (1-89) LSm6 YDR378C Q06406 9.38 86 0.21 0.20 0.00 0.27 LSm6 RES...”
- A Sm-like protein complex that participates in mRNA degradation
Bouveret, The EMBO journal 2000 - “...allowed independently the identification of Lsm5p (SwissProt P40089, hypothetical 10.4 kDa protein). One of the peptides identified and the corresponding...”
B1N3I3 Sm domain-containing protein from Entamoeba histolytica (strain ATCC 30459 / HM-1:IMSS / ABRM)
EHI_076840 uncharacterized protein from Entamoeba histolytica HM-1:IMSS
38% identity, 86% coverage
- Life and Death of mRNA Molecules in Entamoeba histolytica
Valdés-Flores, Frontiers in cellular and infection microbiology 2018 - “...snRNP F EHI_060400 C4M6J5 LSm2 U6 snRNA-associated Sm-like LSm2 EHI_068580 C4LU49 LSm5 hypothetical protein EHI_076840 B1N3I3 U1 snRNP U1-related No U1 snRNA U1A, HA-tag U1 snRNP-specific protein EHI_050780 C4LTU8 U1-70K U1 snRNP subunit EHI_153670 C4LSE9 p68 A-B (U1-5'ss) EhDEAD20 EHI_096390 C4LWF2 TIA-1/TIAR RNA-binding protein TIA-1 EHI_056660...”
- “...C4LU49 Lsm3 P62310 EHI_151310 EhLsm3 C4LSH4 Lsm4 Q9Y4Z0 EHI_049370 EhLsm4 C4LUD9 Lsm5 Q9Y4Y9 EHI_076840 EhLsm5 B1N3I3 Lsm6 P62312 EHI_188130 EhLsm6 C4M187 Lsm7 Q9UK45 EHI_025840 EhLsm7 C4M939 Edc3 Q96F86 EHI_198940 Ehedc3 C4LWU0 Dhh1 P26196 EHI_093900 Ehdhh1 C4LYI1 XRN2 Q9H0D6 EHI_133330 EhXRN2 C4MB40 DEADENYLATION FACTORS CAF1 Q9UIV1 EHI_...”
- Life and Death of mRNA Molecules in Entamoeba histolytica
Valdés-Flores, Frontiers in cellular and infection microbiology 2018 - “...SmF snRNP F EHI_060400 C4M6J5 LSm2 U6 snRNA-associated Sm-like LSm2 EHI_068580 C4LU49 LSm5 hypothetical protein EHI_076840 B1N3I3 U1 snRNP U1-related No U1 snRNA U1A, HA-tag U1 snRNP-specific protein EHI_050780 C4LTU8 U1-70K U1 snRNP subunit EHI_153670 C4LSE9 p68 A-B (U1-5'ss) EhDEAD20 EHI_096390 C4LWF2 TIA-1/TIAR RNA-binding protein TIA-1...”
- “...EHI_068580 EhLsm2 C4LU49 Lsm3 P62310 EHI_151310 EhLsm3 C4LSH4 Lsm4 Q9Y4Z0 EHI_049370 EhLsm4 C4LUD9 Lsm5 Q9Y4Y9 EHI_076840 EhLsm5 B1N3I3 Lsm6 P62312 EHI_188130 EhLsm6 C4M187 Lsm7 Q9UK45 EHI_025840 EhLsm7 C4M939 Edc3 Q96F86 EHI_198940 Ehedc3 C4LWU0 Dhh1 P26196 EHI_093900 Ehdhh1 C4LYI1 XRN2 Q9H0D6 EHI_133330 EhXRN2 C4MB40 DEADENYLATION FACTORS CAF1...”
H3BKC5 LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated (Fragment) from Mus musculus
57% identity, 44% coverage
PHS042 small nucleoprotein from Pyrococcus horikoshii OT3
35% identity, 84% coverage
1lojC / O26745 Crystal structure of a methanobacterial sm-like archaeal protein (smap1) bound to uridine-5'-monophosphate (ump) (see paper)
37% identity, 86% coverage
O29386 Putative snRNP Sm-like protein from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)
AF0875 snRNP, putative from Archaeoglobus fulgidus DSM 4304
36% identity, 89% coverage
7abgj / P62304 pre-Bact-1 spliceosome (see paper)
32% identity, 81% coverage
RUXE_HUMAN / P62304 Small nuclear ribonucleoprotein E; snRNP-E; Sm protein E; Sm-E; SmE from Homo sapiens (Human) (see 21 papers)
P62305 Small nuclear ribonucleoprotein E from Mus musculus
NP_003085 small nuclear ribonucleoprotein E isoform 1 from Homo sapiens
32% identity, 75% coverage
- function: Plays a role in pre-mRNA splicing as a core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (PubMed:11991638, PubMed:18984161, PubMed:19325628, PubMed:23246290, PubMed:23333303, PubMed:25555158, PubMed:26912367, PubMed:28076346, PubMed:28502770, PubMed:28781166, PubMed:32494006). Component of both the pre-catalytic spliceosome B complex and activated spliceosome C complexes (PubMed:11991638, PubMed:28076346, PubMed:28502770, PubMed:28781166). As a component of the minor spliceosome, involved in the splicing of U12-type introns in pre-mRNAs (PubMed:15146077). As part of the U7 snRNP it is involved in histone 3'-end processing (PubMed:12975319).
subunit: Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (PubMed:11991638, PubMed:19325628, PubMed:21516107, PubMed:23246290, PubMed:25555158, PubMed:26912367, PubMed:28076346, PubMed:28502770, PubMed:28781166, PubMed:32494006, PubMed:36797247). Most spliceosomal snRNPs contain a common set of Sm proteins, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP (PubMed:19325628, PubMed:21516107, PubMed:25555158, PubMed:26912367, PubMed:28076346, PubMed:28502770, PubMed:28781166). Component of the U1 snRNP (PubMed:19325628, PubMed:25555158). The U1 snRNP is composed of the U1 snRNA and the 7 core Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG, and at least three U1 snRNP-specific proteins SNRNP70/U1-70K, SNRPA/U1-A and SNRPC/U1-C (PubMed:19325628, PubMed:25555158). Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, SNRNP40, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39, plus LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8 (PubMed:26912367). Component of the U7 snRNP complex, or U7 Sm protein core complex, that is composed of the U7 snRNA and at least LSM10, LSM11, SNRPB, SNRPD3, SNRPE, SNRPF and SNRPG; the complex does not contain SNRPD1 and SNRPD2 (PubMed:11574479). Component of the minor spliceosome, which splices U12-type introns (PubMed:15146077, PubMed:33509932). Part of the SMN-Sm complex that contains SMN1, GEMIN2/SIP1, DDX20/GEMIN3, GEMIN4, GEMIN5, GEMIN6, GEMIN7, GEMIN8, STRAP/UNRIP and the Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG; catalyzes core snRNPs assembly (PubMed:16314521, PubMed:18984161). Forms a 6S pICln-Sm complex composed of CLNS1A/pICln, SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG; ring-like structure where CLNS1A/pICln mimics additional Sm proteins and which is unable to assemble into the core snRNP (PubMed:18984161, PubMed:23333303). Interacts with SMN1; the interaction is direct (PubMed:10500148). Interacts with GEMIN2 (via N-terminus); the interaction is direct (PubMed:21816274, PubMed:31799625). Interacts with SNRPF; the interaction is direct (PubMed:21816274, PubMed:31799625). Interacts with SNRPG; the interaction is direct (PubMed:21816274, PubMed:31799625). - Protein composition of catalytically active U7-dependent processing complexes assembled on histone pre-mRNA containing biotin and a photo-cleavable linker.
Skrajna, Nucleic acids research 2018 - “...Q80X82 Symplekin 4 2.1 10 P62320 SmD3 3 1.7 11 P62309 SmG 2 1.4 12 P62305 SmE 3 1.1 14 Q9D824 Fip1 4 0.7 15 Q9EPU4 CPSF160 3 0.5 16 Q9WUF3 *FLASH 4 0.5 22 Q8K4P0 WDR33 4 0.2 The hierarchy is based on the value...”
- Saikosaponins induced hepatotoxicity in mice via lipid metabolism dysregulation and oxidative stress: a proteomic study.
Li, BMC complementary and alternative medicine 2017 - “...1.49 2 Splicing factor, arginine/serine-rich 7 Ptbp1 P17225 1.59 2 Polypyrimidine tract-binding protein 1 Ruxe P62305 -1.38 24 Small nuclear ribonucleoprotein E Smd2 P62317 -1.17 2 Small nuclear ribonucleoprotein Sm D2 Npm1 Q61937 -1.09 8 Nucleophosmin Rps16 P14131 -2.29 8 40S ribosomal protein S16 Rpsa P14206...”
- Reconstructing genome-wide protein-protein interaction networks using multiple strategies with homologous mapping
Lo, PloS one 2015 - “...number: P62304), has 92 amino acids and a single homologous protein (Snrpe; UniProt accession number: P62305 and E -value is 4 10 49 ) in M. musculus using BLASTP even though the sequence identity is 100% between these two proteins. Therefore, we cannot infer homologous PPIs...”
- Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...NP_178480 NP_014252 DDB0233384 LSm8 (Lsm8p) NAA38 NP_057284 NP_647660 NP_176747 NP_012556 DDB0302415 d SmE (Sme1p) SNRPE NP_003085 NP_609162 NP_567844 NP_014802 2B. U1 snRNP-specific proteins DDB0233134 U1-70K (Snp1p) SNRP70 NP_003080 NP_477205 NP_190636 NP_012203 DDB0233514 CROP (Luc7p) LUC7L3 NP_006098 NP_572337 NP_199954 NP_010196 DDB0233135-b U1 A (na) SNRPA NP_004587 NP_511045...”
- The mitotic surveillance pathway requires PLK1-dependent 53BP1 displacement from kinetochores
Burigotto, 2023 - Peptidomic changes in human serous colorectal cancer patients.
Xu, Journal of gastrointestinal oncology 2023 - “...0.02286 Antibiotic,antimicrobial,DNA-binding,heparin-binding,Hydrolase,protease,serine protease RPL37A P61513 60S ribosomal protein L37a AGGAWTYNTT 2.98 0.02583 Ribonucleoprotein,ribosomal protein SNRPE P62304 Small nuclear ribonucleoprotein E TLLQSVSN 2.23 0.00000 Ribonucleoprotein,RNA-binding Down-regulated peptides P0DOX7 Immunoglobulin kappa light chain DSTYSLSSTLTLSK 0.60 0.01802 Disulfide bond IGKV2-30 P06310 Immunoglobulin kappa variable 2-30 DVVMTQSPLSLPV 0.60 0.01501 Adaptive...”
- Blood Proteome Profiling Reveals Biomarkers and Pathway Alterations in Fragile X PM at Risk for Developing FXTAS.
Zafarullah, International journal of molecular sciences 2023 - “...family member A 137 Q9H3G5 CPVL 0.39 13.61 0.002079 0.032871 Probable serine carboxypeptidase CPVL 138 P62304 SNRPE 0.43 12.95 0.002122 0.033305 Small nuclear ribonucleoprotein E 139 P02749 APOH 0.78 14.82 0.002154 0.033305 Beta-2-glycoprotein 1 140 Q8N5M9 JAGN1 0.44 13.09 0.002171 0.033305 Protein jagunal homolog 1 141...”
- 6-Hydroxydopamine Induces Neurodegeneration in Terminally Differentiated SH-SY5Y Neuroblastoma Cells via Enrichment of the Nucleosomal Degradation Pathway: a Global Proteomics Approach
Magalingam, Journal of molecular neuroscience : MN 2022 - “...Q06830 Peroxiredoxin-1 PRDX1 44,220 3.01E-04 -0.411 P07195 L-lactate dehydrogenase B chain LDHB 73,278 2.98E-02 -0.383 P62304 Small nuclear ribonucleoprotein E SNRPE 21,608 2.24E-02 -0.383 Q13263 Transcription intermediary factor 1-beta TRIM28 177,100 1.22E-03 -0.351 Q12905 Interleukin enhancer-binding factor 2 ILF2 86,124 8.24E-03 -0.342 P06733 Alpha-enolase ENO1 94,338...”
- Unravelling the neuroprotective mechanisms of carotenes in differentiated human neural cells: Biochemical and proteomic approaches
Magalingam, Food chemistry. Molecular sciences 2022 - “...Prohibitin PHB 59,608 2.24E-02 0.767 P09936 Ubiquitin carboxyl-terminal hydrolase isozyme L1 UCHL1 49,648 1.03E-03 0.783 P62304 Small nuclear ribonucleoprotein E SNRPE 21,608 1.22E-03 0.784 P62318 Small nuclear ribonucleoprotein Sm D3 SNRPD3 27,832 8.24E-03 0.789 P06576 ATP synthase subunit beta mitochondrial ATP5F1B 113,120 7.24E-04 0.792 Q99714 3-hydroxyacyl-CoA...”
- Characterization of the Secretome, Transcriptome, and Proteome of Human β Cell Line EndoC-βH1.
Ryaboshapkina, Molecular & cellular proteomics : MCP 2022 - “...P00352 ALDH1A1 75 P16870 CPE 125 Q9Y3C8 UFC1 26 P02766 TTR 76 P41567 EIF1 126 P62304 SNRPE 27 Q96FJ2 DYNLL2 77 P01859 IGHG2 127 O43598 DNPH1 28 P10599 TXN 78 P01034 CST3 128 Q00688 FKBP3 29 Q9H3M0 KCNF1 79 P63261 ACTG1 129 Q99729 HNRNPAB 30 P20674...”
- The Protective Action of Metformin against Pro-Inflammatory Cytokine-Induced Human Islet Cell Damage and the Mechanisms Involved.
Giusti, Cells 2022 - “...1 (PTHR23105:SF38) SNU13 23.22 51.02 Q9UI30 MULTIFUNCTIONAL METHYLTRANSFERASE SUBUNIT TRM112-LIKE PROTEIN (PTHR12773:SF2) TRMT112 51.09 50.85 P62304 SMALL NUCLEAR RIBONUCLEOPROTEIN E (PTHR11193:SF9) SNRPE 51.39 50.61 Q9Y6K5 2-5-OLIGOADENYLATE SYNTHASE 3 (PTHR11258:SF4) OAS3 52.63 52.68 translation factor Q53EL6 PROGRAMMED CELL DEATH PROTEIN 4 (PTHR12626:SF3) PDCD4 0.32 0.32 P06730 EUKARYOTIC...”
- Partners in crime: Proteins implicated in RNA repeat expansion diseases.
Baud, Wiley interdisciplinary reviews. RNA 2022 - “...(Mankodi, 2001 ) CCUG hnRNP core protein and snRNP Sm antigen Small nuclear ribonucleoprotein E P62304 (human) Colocalized with RNA foci in DM2 patients (Perdoni et al., 2009 ) CCUG RBFOX1 RNA binding protein fox1 homolog Q9NWB1 (human) Colocalized with RNA foci in DM2 patients (Sellier...”
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D3ZSP1 Small nuclear ribonucleoprotein E from Rattus norvegicus
32% identity, 75% coverage
1m8vA / Q9V0Y8 Structure of pyrococcus abyssii sm protein in complex with a uridine heptamer (see paper)
34% identity, 84% coverage
- Ligands: rna; uridine-5'-monophosphate (1m8vA)
Q9V0Y8 Putative snRNP Sm-like protein from Pyrococcus abyssi (strain GE5 / Orsay)
34% identity, 84% coverage
1i5lC / O29386 Crystal structure of an sm-like protein (af-sm1) from archaeoglobus fulgidus complexed with short poly-u RNA (see paper)
35% identity, 85% coverage
8xi2e / A8IYZ2 Cryo-em structure of the chlamydomonas c Complex (see paper)
34% identity, 81% coverage
TK0976 snRNP component, Sm-like protein from Thermococcus kodakaraensis KOD1
31% identity, 84% coverage
NP_001291393 small nuclear ribonucleoprotein E isoform 2 from Homo sapiens
34% identity, 68% coverage
- Oncofetal SNRPE promotes HCC tumorigenesis by regulating the FGFR4 expression through alternative splicing.
Wu, British journal of cancer 2024 - GeneRIF: Oncofetal SNRPE promotes HCC tumorigenesis by regulating the FGFR4 expression through alternative splicing.
- A missense mutation in SNRPE linked to non-syndromal microcephaly interferes with U snRNP assembly and pre-mRNA splicing.
Chen, PLoS genetics 2019 - GeneRIF: Study reports de novo heterozygous missense mutation within the SNRPE gene disturbing appropriate spatiotemporal gene expression in the brain through aberrant mRNA splicing, and likely to cause the microcephaly phenotype.
- Mutations in SNRPE, which encodes a core protein of the spliceosome, cause autosomal-dominant hypotrichosis simplex.
Pasternack, American journal of human genetics 2013 - GeneRIF: Mutations in SNRPE, which encodes a core protein of the spliceosome, cause autosomal-dominant hypotrichosis simplex
- Targeting the deregulated spliceosome core machinery in cancer cells triggers mTOR blockade and autophagy.
Quidville, Cancer research 2013 (PubMed)- GeneRIF: Overexpression of SNRPE is associated with highly aggressive breast cancers.
- Spliceosomal protein E regulates neoplastic cell growth by modulating expression of cyclin E/CDK2 and G2/M checkpoint proteins.
Li, Journal of cellular and molecular medicine 2008 - GeneRIF: growth arrest by SmE directly correlates with the reduction of cyclin E, CDK2, CDC25C and CDC2 expression, and up-regulation of p27Kip
- Branchpoint selection in the splicing of U12-dependent introns in vitro.
McConnell, RNA (New York, N.Y.) 2002 - GeneRIF: In the SME intron, the position of the branchpoint A residue within the region base paired with U12 differs from that in P120 and XTF.
PF1542 small nuclear ribonucleoprotein, putative from Pyrococcus furiosus DSM 3638
32% identity, 84% coverage
- Production and Application of a Soluble Hydrogenase from Pyrococcus furiosus
Wu, Archaea (Vancouver, B.C.) 2015 - “...tag Ni-free trimeric SHI; (f) lane 4, native SHI; lane 5, 9x-His tag dimeric SHI (PF1542 is an unrelated protein that is a persistent contaminant that copurified with dimeric SHI). The SDS PAGE gel data were modified from [ 11 13 ]. Figure 2 Genetic strategy...”
- Homologous expression of a subcomplex of Pyrococcus furiosus hydrogenase that interacts with pyruvate ferredoxin oxidoreductase
Hopkins, PloS one 2011 - “...be separated from OE-SHI Dimer ( Figure 1b ). MALDI-TOF/TOF analysis revealed this to be PF1542, a gene annotated as snRNP (small nuclear ribonucleoprotein) that functions to mediate RNA-RNA interactions [26] . Size exclusion analysis of OE-SHI Dimer using a calibrated Superdex S200 column indicated the...”
- “...apparent M r of 88,000 daltons, in agreement with the trimer weight of PF0893-0894 and PF1542 ( Table 3 ). As shown in Table 3 , the OE-SHI Dimer was much less thermostable and more sensitive to oxygen exposure. As expected in the absence of the...”
AT4G30330 small nuclear ribonucleoprotein E, putative / snRNP-E, putative / Sm protein E, putative from Arabidopsis thaliana
NP_567844 Small nuclear ribonucleoprotein family protein from Arabidopsis thaliana
32% identity, 80% coverage
- Drought Stress Causes Specific Changes to the Spliceosome and Stress Granule Components
Marondedze, Frontiers in molecular biosciences 2019 - “...X X AT1G09770 Cell division cycle 5 X AT4G02840 Small nuclear ribonucleoprotein family protein X AT4G30330 Small nuclear ribonucleoprotein family protein X AT4G38780 Pre-mRNA-processing-splicing factor X AT5G16780 SART-1 family X AT5G61140 U5 small nuclear ribonucleoprotein helicase X AT1G09140 Serine/Arginine protein 30 X AT1G71310 cobalt ion binding...”
- Early Responses to Severe Drought Stress in the Arabidopsis thaliana Cell Suspension Culture Proteome
Alqurashi, Proteomes 2018 - “...N -acetylmuramoyl- l -alanyl- d -glutamate-2,6-diaminopimelate ligase 0.5563 AT1G16740 Ribosomal protein L20 Protein B 0.6690 AT4G30330 Small nuclear ribonucleoprotein family protein 0.6363 AT2G19720 Ribosomal protein S15A B 0.6255 AT5G61130 Plasmodesmata callose-binding protein 1 0.6135 AT4G00810 60S acidic ribosomal protein family 0.6094 AT3G06680 Ribosomal L29e protein family...”
- The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing
Wang, Genome biology 2004 - “...1 9 >1-1c Sm, 1 atSmD3-b At1g20580 1 7 >1-1c Sm, 1 SmE SmE atSmE-a At4g30330 4 2 >2-4b Sm, 1 atSmE-b At2g18740 2 10 AltA (1); >2-4b Sm, 1 SmF SmF atSmF At4g30220 4 6 Sm, 1 SmG SmG atSmG-a At2g23930 2 13 Sm, 1...”
- Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...DDB0233384 LSm8 (Lsm8p) NAA38 NP_057284 NP_647660 NP_176747 NP_012556 DDB0302415 d SmE (Sme1p) SNRPE NP_003085 NP_609162 NP_567844 NP_014802 2B. U1 snRNP-specific proteins DDB0233134 U1-70K (Snp1p) SNRP70 NP_003080 NP_477205 NP_190636 NP_012203 DDB0233514 CROP (Luc7p) LUC7L3 NP_006098 NP_572337 NP_199954 NP_010196 DDB0233135-b U1 A (na) SNRPA NP_004587 NP_511045 NP_180585 No...”
NP_732931 uncharacterized protein from Drosophila melanogaster
Q8IMX8 U6 snRNA-associated Sm-like protein LSm3 from Drosophila melanogaster
47% identity, 48% coverage
RUXE_DROME / Q9VLV5 Probable small nuclear ribonucleoprotein E; snRNP-E; Sm protein E; Sm-E; SmE from Drosophila melanogaster (Fruit fly) (see paper)
NP_609162 small ribonucleoprotein particle protein SmE from Drosophila melanogaster
33% identity, 73% coverage
- function: Plays a role in pre-mRNA splicing as a core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome.
subunit: Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (By similarity). Interacts with the SMN complex (PubMed:18621711). - Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...NP_014252 DDB0233384 LSm8 (Lsm8p) NAA38 NP_057284 NP_647660 NP_176747 NP_012556 DDB0302415 d SmE (Sme1p) SNRPE NP_003085 NP_609162 NP_567844 NP_014802 2B. U1 snRNP-specific proteins DDB0233134 U1-70K (Snp1p) SNRP70 NP_003080 NP_477205 NP_190636 NP_012203 DDB0233514 CROP (Luc7p) LUC7L3 NP_006098 NP_572337 NP_199954 NP_010196 DDB0233135-b U1 A (na) SNRPA NP_004587 NP_511045 NP_180585...”
AT2G18740 small nuclear ribonucleoprotein E, putative / snRNP-E, putative / Sm protein E, putative from Arabidopsis thaliana
32% identity, 80% coverage
- The Arabidopsis spliceosomal protein SmEb modulates ABA responses by maintaining proper alternative splicing of HAB1
Hong, Stress biology 2021 - “...and smeb-2 mutants have T-DNA insertions in the second exon and fourth intron of the At2g18740 gene, respectively (Fig. 1 b). Quantitative reverse transcription-PCR (qRT-PCR) analysis determined that the transcript level of SmEb was nearly undetectable in smeb-1 and smeb-2 mutants (Fig. 1 c). Phenotyping of...”
- “...website of Arabidopsis Information Resource ( www.arabidopsis.org ) under the following accession numbers: SmEb , At2g18740; HAB1 , At1g72770; ABI3 , At3g24650; ABI4 , At2g40220; ABI5 , At2g36270; TUB8 , At5g23860. Authors contributions H.S. and Z.W. designed the experiments; Y.H., H.S., and Z.W. analyzed the data;...”
- Genome-wide identification and expression analyses of Sm genes reveal their involvement in early somatic embryogenesis in Dimocarpus longan Lour
Li, PloS one 2020 - “...105 12063.15 9.74 No Dlo_038407.1 DlSmD3 AT1G20580 AtSmD3b scaffold69:954276:957329 No termination codon No Dlo_015839.1 DlSmEa AT2G18740 AtSmEb Scaffold3:469665:469951 79 9194.89 9.89 No Dlo_019122.2 DlSmEb AT2G18740 AtSmEb Scaffold38:1862876:1865058 79 9167.82 9.82 No Dlo_021780.1 DlSmF AT4G30220 AtSmF(AtSmFa) scaffold46:632326:633944 88 9910.28 4.43 No Dlo_009662.1 DlSmG AT2G23930 AtSmGa scaffold19:1245388:1247149 80...”
- PORCUPINE regulates development in response to temperature through alternative splicing
Capovilla, Nature plants 2018 (PubMed)- “...ribonucleoprotein family protein containing a Like-Sm (LSM) domain, At2g18740, to which we refer here as PORCUPINE (PCP) because of the striking `spiky'...”
- “...AT1G17130 AT2G16600 AT4G08350 AT1G60170 AT3G57290 AT2G18740 AT2G24590 AT3G12580 AT2G37340 AT1G07350 AT1G55310 AT1G51380 AT1G21190 AT1G76300 AT1G09660 AT1G23860...”
- A Microsomal Proteomics View of H₂O₂- and ABA-Dependent Responses
Alqurashi, Proteomes 2017 - “...2.9 7.1 3. Cell growth/division AT5G43070 WPP domain protein 1 0.042 0.4 0.2 4. Transcription AT2G18740 Small nuclear ribonucleoprotein 0.02 7.7 4.3 AT5G40480 Embryo defective 3012 0.0084 5.6 7.9 AT1G14850 Nucleoporin 155 0.0058 0.1 0.2 5. Protein synthesis AT1G08360 Ribosomal protein L1p/L10e 0.037 3.1 ns AT4G10450...”
- Identification of genes involved in wild crucifer Rorippa indica resistance response on mustard aphid Lipaphis erysimi challenge
Bandopadhyay, PloS one 2013 - “...family protein AT5G13810 Oxidative stress RI13 JK034082 203 2e-38 Repressed Small nuclear ribonucleoprotein family protein AT2G18740 Structural RI14 JK034065 89 5e-27 Repressed HSPRO2, Ortholog of sugar beet, HS1 PRO-1 AT2G40000 Signalling RI15 JK034066 223 1e-48 Induced Ribulose bisphosphate carboxylase small chain 1A AT1G67090 Photosynthesis RI16 JK034067...”
- “...in the time course study. Among the up regulated structural TDFs were small nuclear ribonucleoprotein (AT2G18740) (up regulated to 1.63 fold at 12 hpi) and chloroplast inner envelope Tic22 like family protein (AT5G62650) (up regulated to 2.35 fold at 48 hpi) involved in import of nuclear...”
- Global protein interactome exploration through mining genome-scale data in Arabidopsis thaliana
Xu, BMC genomics 2010 - “...interactions with at least two other splicing factors. Among these 31 proteins, eleven proteins, like AT2G18740, and AT3G53570, are annotated as small nuclear ribonucleoproteins, which are the components of spliceosome. These consistencies not only validate the composition of the spliceosome but also reflect the biological applications...”
- Statistical evaluation of transcriptomic data generated using the Affymetrix one-cycle, two-cycle and IVT-Express RNA labelling protocols with the Arabidopsis ATH1 microarray
Holman, Plant methods 2010 - “...pyrophosphorylase-related. 265443_at 6.4 6.7 3.0 AT2G20750 ATEXPB1 (ARABIDOPSIS THALIANA EXPANSIN B1). 266074_at 5.1 8.1 1.7 AT2G18740 Small nuclear ribonucleoprotein E, putative/snRNP-E, putative/Sm protein E, putative. 266125_at 6.9 6.3 1.8 AT2G45050 Zinc finger (GATA type) family protein. 267064_at 6.8 7.9 2.9 AT2G41110 CAM2 (CALMODULIN-2); calcium ion binding....”
- The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing
Wang, Genome biology 2004 - “...1 7 >1-1c Sm, 1 SmE SmE atSmE-a At4g30330 4 2 >2-4b Sm, 1 atSmE-b At2g18740 2 10 AltA (1); >2-4b Sm, 1 SmF SmF atSmF At4g30220 4 6 Sm, 1 SmG SmG atSmG-a At2g23930 2 13 Sm, 1 atSmG-b At3g11500 3 9 Sm, 1 LSM2...”
P57670 Putative snRNP Sm-like protein from Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)
27% identity, 92% coverage
MM2383 Small nuclear riboprotein-like protein from Methanosarcina mazei Goe1
38% identity, 86% coverage
E1ZJG0 Small nuclear ribonucleoprotein E from Chlorella variabilis
30% identity, 80% coverage
- Impacts of Endocrine Disruptor di-n-Butyl Phthalate Ester on Microalga Chlorella vulgaris Verified by Approaches of Proteomics and Gene Ontology
Liao, Molecules (Basel, Switzerland) 2020 - “...Function A0A2P6TB75 Small nuclear ribonucleoprotein E 2,360,960.93 690,303.1496 3.42 U2 snRNP (GO:0005686) U4 snRNP (GO:0005687) E1ZJG0 Small nuclear ribonucleoprotein E 2,360,960.93 690,303.1496 3.42 U2 snRNP (GO:0005686) U4 snRNP (GO:0005687) E1Z2X3 Histone H2A 1,447,145,818 528,512,569.9 2.74 nucleosome (GO:0000786) E1ZGZ5 Histone H2A 1,447,145,818 528,512,569.9 2.74 nucleosome (GO:0000786) E1Z345...”
LSM3A_ARATH / Q9LMN4 Sm-like protein LSM3A; AtLSM3A; U6 snRNA-associated Sm-like protein LSM3A from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT1G21190 small nuclear ribonucleoprotein, putative / snRNP, putative / Sm protein, putative from Arabidopsis thaliana
41% identity, 51% coverage
- function: Component of LSM protein complexes, which are involved in RNA processing. Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation by promoting decapping and leading to accurate 5'-3' mRNA decay. The cytoplasmic LSM1-LSM7 complex regulates developmental gene expression by the decapping of specific development- related transcripts. Component of the nuclear LSM2-LSM8 complex which is involved splicing nuclear mRNAs. LSM2-LSM8 binds directly to the U6 small nuclear RNAs (snRNAs) and is essential for accurate splicing of selected development-related mRNAs through the stabilization of the spliceosomal U6 snRNA. Plays a critical role in the regulation of development-related gene expression.
subunit: Component of the heptameric LSM1-LSM7 complex that forms a seven-membered ring structure with a donut shape. The LSM subunits are arranged in the order LSM1, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4. Component of the heptameric LSM2-LSM8 complex that forms a seven- membered ring structure with a donut shape. The LSM subunits are arranged in the order LSM8, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4 (PubMed:23221597, PubMed:23620288). LSM3A subunit interacts only with its two neighboring subunits, LSM2 and LSM6A or LSM6B (PubMed:23221597). - Searching for G-Quadruplex-Binding Proteins in Plants: New Insight into Possible G-Quadruplex Regulation
Volná, Biotech (Basel (Switzerland)) 2021 - “...searching results. Motif Protein Full Name AN Length E-Value Query Cover NIQI Hypothetical protein AXX17 AT1G21190 OAP13840.1 265 4 10 6 100 Unnamed protein product AAN60302.1 272 4 10 6 100 Unnamed protein product CAA0224497.1 312 4 10 6 100 Alba DNA/RNA binding protein NP_564108.1 315...”
- Arabidopsis thaliana LSM proteins function in mRNA splicing and degradation
Golisz, Nucleic acids research 2013 - “...71 67 74 92 AtLSM2 At1g03330 76 67 78 92 86 78 86 98 AtLSM3a At1g21190 80 43 75 90 94 65 94 99 AtLSM3b At1g76860 80 48 78 94 92 67 92 98 AtLSM4 At5g27720 87 40 77 79 96 58 87 82 AtLSM5 At5g48870...”
- “...mRNA processing At1g03330 Small nuclear RNP family protein AtLSM2 3 mRNA processing & mRNA splicing At1g21190 Small nuclear RNP family protein AtLSM3a 3 mRNA processing & mRNA splicing At1g76860 Small nuclear RNP family protein AtLSM3b 3 mRNA processing & mRNA splicing At5g27720 Small nuclear RNP family...”
- The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing
Wang, Genome biology 2004 - “...3 9 Sm, 1 LSM2 LSm2 atLSM2 At1g03330 1 7 Sm, 1 LSM3 LSm3 atLSM3a At1g21190 1 6 >1-1c Sm, 1 atLSM3b At1g76860 1 16 >1-1c Sm, 1 LSM4 LSm4 atLSM4 At5g27720 5 13 Sm, 1 LSM5 LSm5 atLSM5 /SAD1 At5g48870 5 7 AltA (1); Sm,...”
I3KZX4 U6 snRNA-associated Sm-like protein LSm3 from Oreochromis niloticus
31% identity, 70% coverage
NP_502579 U6 snRNA-associated Sm-like protein LSm3 from Caenorhabditis elegans
43% identity, 48% coverage
6qw663 / P62310 6qw663 (see paper)
31% identity, 84% coverage
LSM3_HUMAN / P62310 U6 snRNA-associated Sm-like protein LSm3 from Homo sapiens (Human) (see 4 papers)
NP_055278 U6 snRNA-associated Sm-like protein LSm3 from Homo sapiens
31% identity, 70% coverage
- function: Plays a role in pre-mRNA splicing as component of the U4/U6- U5 tri-snRNP complex that is involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex) (PubMed:28781166). The heptameric LSM2-8 complex binds specifically to the 3'-terminal U-tract of U6 snRNA (PubMed:10523320).
subunit: Component of the precatalytic spliceosome (spliceosome B complex) (PubMed:11991638, PubMed:28781166). Component of the U4/U6-U5 tri-snRNP complex, a building block of the precatalytic spliceosome (spliceosome B complex) (PubMed:10523320, PubMed:26912367, PubMed:28781166). The U4/U6-U5 tri-snRNP complex is composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, SNRNP40, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39, plus LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8 (PubMed:26912367). LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8 form a heptameric, ring-shaped subcomplex (the LSM2-8 complex) that is part of the U4/U6-U5 tri-snRNP complex and the precatalytic spliceosome (PubMed:10523320, PubMed:26912367, PubMed:28781166). - LIF Inhibits Proliferation of Esophageal Squamous Carcinoma Cells by Radiation Mediated Through JAK-STAT Signaling Pathway
Luo, Journal of Cancer 2023 - “...HMGCS1 57.30 111.35 75.65 -0.5577 0.0491 12 Q15651 HMGN3 10.70 116.95 79.45 -0.5578 0.0489 13 P62310 LSM3 11.80 111.30 75.6 -0.5580 0.0486 14 P29401 TKT 67.80 105.20 71.45 -0.5581 0.0484 15 P15018 LIF 22.01 100.09 67.9 -0.5598 0.0483 16 P84243 H3-3A 15.32 134.35 91.1 -0.5605 0.0472...”
- Blood Proteome Profiling Reveals Biomarkers and Pathway Alterations in Fragile X PM at Risk for Developing FXTAS.
Zafarullah, International journal of molecular sciences 2023 - “...0.499658 7 Q9Y3B2 EXOSC1 Exosome complex component CSL4 0.9398573 0.0000276 0.0450991 0.91006 0.009782 0.8639569 8 P62310 LSM3 U6 snRNA-associated Sm-like protein LSm3 0.0135975 0.0000349 0.4197721 0.342944 9.16 10 5 0.8092159 9 Q92769 HDAC2 Histone deacetylase 2 0.5817782 0.0015861 0.002199 0.421168 0.055764 0.3596959 10 P42025 ACTR1B Beta-centractin...”
- “...Q9Y3B2 EXOSC1 0.85 12.98 6.37 10 8 2.76 10 5 Exosome complex component CSL4 6 P62310 LSM3 1.09 13.49 9.67 10 8 3.49 10 5 U6 snRNA-associated Sm-like protein LSm3 7 P55957 BID 1.59 13.87 5.27 10 7 0.00016297 BH3-interacting domain death agonist 8 Q15370 ELOB...”
- Neurodevelopmental signatures of narcotic and neuropsychiatric risk factors in 3D human-derived forebrain organoids.
Notaras, Molecular psychiatry 2021 - “...SUPT6H Q7KZ85 APLP2 Q06481 USP7 Q93009 TIMM21 Q9BVV7 APMAP Q9HDC9 SRP19 P09132 RPS27L Q71UM5 LSM3 P62310 TNPO3 Q9Y5L0 SAP30BP Q9UHR5 APLP2 Q06481 TMEM209 Q96SK2 RPL36 Q9Y3U8 RPS13 P62277 CDC42BPB Q9Y5S2 FMNL2 Q96PY5 HDHD5 Q9BXW7 ZFYVE1 Q9HBF4 ARMCX1 Q9P291 DHTKD1 Q96HY7 Because each of our treatment groups...”
- The Protective Effect of Liquiritin in Hypoxia/Reoxygenation-Induced Disruption on Blood Brain Barrier.
Li, Frontiers in pharmacology 2021 - “...alpha O95777 LSM8 U6 snRNA-associated Sm-like protein LSm8 P61769 B2M Beta-2-microglobulin P02647 APOA1 Apolipoprotein A-I P62310 LSM3 U6 snRNA-associated Sm-like protein LSm3 Q9NX14 NDUFB11 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 11, mitochondrial Q9H3P7 ACBD3 Golgi resident protein GCP60 Q494V2 CFAP100 Cilia- and flagella-associated protein 100...”
- HMGB1 and Caveolin-1 related to RPE cell senescence in age-related macular degeneration.
Sun, Aging 2019 - “...SNX25 17.23254402 0.000304062 Q14240 EIF4A2 15.7087038 0.402011 J3KSW2 POLI 13.22929896 0.0174629 E7EX17 EIF4B 12.53696128 0.106437 P62310 LSM3 11.81044422 0.0147819 Q03135 CAV1 0.810928595 0.289982 P42224 STAT1 4.42761394 0.000198283 P05362 ICAM1 2.45723684 0.00874002 Upregulation and translocation of HMGB1 in ARPE-19 cells after A2E treatment To determine the optimized...”
- Life and Death of mRNA Molecules in Entamoeba histolytica.
Valdés-Flores, Frontiers in cellular and infection microbiology 2018 - “...et al., 2012 Lsm1 O15116 EHI_188020 EhLsm 1 B1N3A8 Lsm2 Q9Y333 EHI_068580 EhLsm2 C4LU49 Lsm3 P62310 EHI_151310 EhLsm3 C4LSH4 Lsm4 Q9Y4Z0 EHI_049370 EhLsm4 C4LUD9 Lsm5 Q9Y4Y9 EHI_076840 EhLsm5 B1N3I3 Lsm6 P62312 EHI_188130 EhLsm6 C4M187 Lsm7 Q9UK45 EHI_025840 EhLsm7 C4M939 Edc3 Q96F86 EHI_198940 Ehedc3 C4LWU0 Dhh1 P26196...”
- Over-expressed Testis-specific Protein Y-encoded 1 as a novel biomarker for male hepatocellular carcinoma.
Li, PloS one 2014 - “...kinase 1 0.01 0.0199 2.27 Q9Y2Q3 GSTK1 Glutathione S-transferase kappa 1 1 0.01 0.0185 2.27 P62310 LSM3 U6 snRNA-associated Sm-like protein LSm3 2 0.01 0.0181 2.25 P04632 CPNS1 Calpain small subunit 1 1 0.01 0.0191 2.27 P84090 ERH Enhancer of rudimentary homolog 2 0.01 0.0181 2.27...”
- Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...NP_476921 NP_199263 NP_010946 DDB0233376 LSm2 (Lsm2p) LSM2 NP_067000 NP_648570 NP_563682 NP_009527 DDB0233377 LSm3 (Lsm3p) LSM3 NP_055278 NP_732931 NP_177812 NP_013543 DDB0233378 LSm4 (Lsm4p) LSM4 NP_036453 NP_001027236 NP_198124 NP_011037 DDB0233383 LSm5 (Lsm5p) LSM5 NP_036454 NP_648022 NP_199698 NP_011073 DDB0233198 LSm6 (Lsm6p) LSM6 NP_009011 NP_611528 NP_181909 NP_010666 DDB0233196 LSm7 (Lsm7p)...”
- The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci.
Ingelfinger, RNA (New York, N.Y.) 2002 - GeneRIF: LSm1-7 proteins colocalize with DCP1,DCP2 and Xrn1 in cytoplasmic foci
LSM3B_ARATH / Q9C6K5 Sm-like protein LSM3B; AtLSM3B; U6 snRNA-associated Sm-like protein LSM3B from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT1G76860 small nuclear ribonucleoprotein, putative / snRNP, putative / Sm protein, putative from Arabidopsis thaliana
NP_177812 Small nuclear ribonucleoprotein family protein from Arabidopsis thaliana
39% identity, 50% coverage
- function: Component of LSM protein complexes, which are involved in RNA processing. Component of the cytoplasmic LSM1-LSM7 complex which is involved in mRNA degradation by promoting decapping and leading to accurate 5'-3' mRNA decay. The cytoplasmic LSM1-LSM7 complex regulates developmental gene expression by the decapping of specific development- related transcripts. Component of the nuclear LSM2-LSM8 complex which is involved splicing nuclear mRNAs. LSM2-LSM8 binds directly to the U6 small nuclear RNAs (snRNAs) and is essential for accurate splicing of selected development-related mRNAs through the stabilization of the spliceosomal U6 snRNA. Plays a critical role in the regulation of development-related gene expression.
subunit: Component of the heptameric LSM1-LSM7 complex that forms a seven-membered ring structure with a donut shape. The LSM subunits are arranged in the order LSM1, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4. Component of the heptameric LSM2-LSM8 complex that forms a seven- membered ring structure with a donut shape. The LSM subunits are arranged in the order LSM8, LSM2, LSM3, LSM6, LSM5, LSM7 and LSM4 (PubMed:23221597, PubMed:23620288). LSM3B subunit interacts only with its two neighboring subunits, LSM2 and LSM6A or LSM6B (PubMed:23221597). - Genome-wide identification and expression analyses of Sm genes reveal their involvement in early somatic embryogenesis in Dimocarpus longan Lour
Li, PloS one 2020 - “...125 14179.59 5.26 No Dlo_024845.1 DlLSm2 AT1G03330 AtLSm2 scaffold556:163264:167575 377 42539.65 9.16 No Dlo_009273.1 DlLSm3 AT1G76860 AtLSm3b scaffold185:484650:485838 74 8682.79 4.45 No Dlo_014195.1 DlLSm4a AT5G27720 AtLSm4 scaffold263:327344:329240 146 15843.89 10.01 No Dlo_021351.1 DlLSm4b AT5G27720 AtLSm4 scaffold449:612750:615216 150 16135.20 10.14 No Dlo_031761.1 DlLSm4c AT5G27720 AtLSm4 scaffold845:311468:313948 150...”
- Drought Stress Causes Specific Changes to the Spliceosome and Stress Granule Components
Marondedze, Frontiers in molecular biosciences 2019 - “...small nuclear ribonucleoprotein helicase X AT1G09140 Serine/Arginine protein 30 X AT1G71310 cobalt ion binding X AT1G76860 Small nuclear ribonucleoprotein X AT4G14342 Splicing factor 3B subunit 5 X AT5G44200 CAP-binding protein 20 X AT1G03330 Small nuclear ribonucleoprotein X c X c AT4G35785 RNA-binding (RRM/RBD/RNP motifs) X c...”
- A Genetic Screen Identifies PRP18a, a Putative Second Step Splicing Factor Important for Alternative Splicing and a Normal Phenotype in Arabidopsis thaliana
Kanno, G3 (Bethesda, Md.) 2018 - “...At1g14650 SF3a120, SAP114 17S U2 snRNP At1g60900 U2AF65B Splice site selection Park et al. 2017 At1g76860 Lsm3B small nuclear ribonucleoprotein Golisz et al. 2013 At2g16940 fSAP59, CC1-like splicing factor recruited prior to B* At2g29210 SRm160 SR-related protein At2g40650 PRP38 U4/U6.U5 tri-snRNP At2g43370 U11/U12-35K U11/U12-specific Lorkovic et...”
- An unbiased nuclear proteomics approach reveals novel nuclear protein components that participates in MAMP-triggered immunity
Fakih, Plant signaling & behavior 2016 - “...Q8L716 AT1G60900 Small nuclear ribonucleoprotein Q9SUM2 AT4G30220 Small nuclear ribonucleoprotein family protein, mRNA splicing Q9C6K5 AT1G76860 nuclear cap-binding protein, mRNA metabolism Q9XFD1 AT5G44200 RNA-binding protein-related F4JM55 AT4G28990 We also analyzed the proteins common between Col-0 and cerk1 nuclei after chitosan treatment (presented at the intersection in...”
- Arabidopsis thaliana LSM proteins function in mRNA splicing and degradation
Golisz, Nucleic acids research 2013 - “...86 78 86 98 AtLSM3a At1g21190 80 43 75 90 94 65 94 99 AtLSM3b At1g76860 80 48 78 94 92 67 92 98 AtLSM4 At5g27720 87 40 77 79 96 58 87 82 AtLSM5 At5g48870 75 45 70 94 88 67 86 95 AtLSM6a At2g43810...”
- “...mRNA splicing At1g21190 Small nuclear RNP family protein AtLSM3a 3 mRNA processing & mRNA splicing At1g76860 Small nuclear RNP family protein AtLSM3b 3 mRNA processing & mRNA splicing At5g27720 Small nuclear RNP family protein AtLSM4 3 mRNA processing & mRNA splicing At5g48870 Small nuclear RNP family...”
- The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing
Wang, Genome biology 2004 - “...At1g03330 1 7 Sm, 1 LSM3 LSm3 atLSM3a At1g21190 1 6 >1-1c Sm, 1 atLSM3b At1g76860 1 16 >1-1c Sm, 1 LSM4 LSm4 atLSM4 At5g27720 5 13 Sm, 1 LSM5 LSm5 atLSM5 /SAD1 At5g48870 5 7 AltA (1); Sm, 1 [47] LSM6 LSm6 atLSM6a At3g59810 3...”
- Spliceosomal genes in the D. discoideum genome: a comparison with those in H. sapiens, D. melanogaster, A. thaliana and S. cerevisiae
Yu, Protein & cell 2011 - “...NP_010946 DDB0233376 LSm2 (Lsm2p) LSM2 NP_067000 NP_648570 NP_563682 NP_009527 DDB0233377 LSm3 (Lsm3p) LSM3 NP_055278 NP_732931 NP_177812 NP_013543 DDB0233378 LSm4 (Lsm4p) LSM4 NP_036453 NP_001027236 NP_198124 NP_011037 DDB0233383 LSm5 (Lsm5p) LSM5 NP_036454 NP_648022 NP_199698 NP_011073 DDB0233198 LSm6 (Lsm6p) LSM6 NP_009011 NP_611528 NP_181909 NP_010666 DDB0233196 LSm7 (Lsm7p) LSM7 NP_057283...”
- An unbiased nuclear proteomics approach reveals novel nuclear protein components that participates in MAMP-triggered immunity
Fakih, Plant signaling & behavior 2016 - “...pre-mRNA Q8L716 AT1G60900 Small nuclear ribonucleoprotein Q9SUM2 AT4G30220 Small nuclear ribonucleoprotein family protein, mRNA splicing Q9C6K5 AT1G76860 nuclear cap-binding protein, mRNA metabolism Q9XFD1 AT5G44200 RNA-binding protein-related F4JM55 AT4G28990 We also analyzed the proteins common between Col-0 and cerk1 nuclei after chitosan treatment (presented at the intersection...”
6ppqF / Q9UUI1 Structure of s. Pombe lsm1-7 with RNA, polyuridine with 3' adenosine (see paper)
30% identity, 81% coverage
NP_594380 U6 snRNP-associated protein Lsm6 from Schizosaccharomyces pombe
30% identity, 81% coverage
PAAG_00101 small nuclear ribonucleoprotein from Paracoccidioides lutzii Pb01
34% identity, 64% coverage
- Transcriptional and proteomic responses to carbon starvation in Paracoccidioides
Lima, PLoS neglected tropical diseases 2014 - “...control PAAG_08234 transcription factor RfeF * transcription control PAAG_01733 28 kDa ribonucleoprotein * transcriptional control PAAG_00101 small nuclear ribonucleoprotein * splicing PAAG_01630 small nuclear ribonucleoprotein LSM2 * splicing PAAG_02329 U2 small nuclear ribonucleoprotein A * splicing PAAG_07983 ribonuclease H * RNA processing PAAG_06966 RNA methyltransferase *...”
4wzjMM / P62306 4wzjMM (see paper)
34% identity, 100% coverage
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory