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Protein

U6 snRNA-associated Sm-like protein LSm4

Gene

LSM4

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Plays 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).2 Publications

GO - Molecular functioni

  • PH domain binding Source: CAFA
  • RNA binding Source: UniProtKB
  • U6 snRNA binding Source: GO_Central

GO - Biological processi

Keywordsi

Molecular functionRibonucleoprotein, RNA-binding
Biological processmRNA processing, mRNA splicing

Enzyme and pathway databases

ReactomeiR-HSA-430039 mRNA decay by 5' to 3' exoribonuclease
R-HSA-72163 mRNA Splicing - Major Pathway

Names & Taxonomyi

Protein namesi
Recommended name:
U6 snRNA-associated Sm-like protein LSm4
Alternative name(s):
Glycine-rich protein
Short name:
GRP
Gene namesi
Name:LSM4
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 19

Organism-specific databases

EuPathDBiHostDB:ENSG00000130520.10
HGNCiHGNC:17259 LSM4
MIMi607284 gene
neXtProtiNX_Q9Y4Z0

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

DisGeNETi25804
OpenTargetsiENSG00000130520
PharmGKBiPA134906569

Polymorphism and mutation databases

BioMutaiLSM4
DMDMi10720082

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001255641 – 139U6 snRNA-associated Sm-like protein LSm4Add BLAST139

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionine1 Publication1
Cross-linki80Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources

Keywords - PTMi

Acetylation, Isopeptide bond, Ubl conjugation

Proteomic databases

EPDiQ9Y4Z0
MaxQBiQ9Y4Z0
PaxDbiQ9Y4Z0
PeptideAtlasiQ9Y4Z0
PRIDEiQ9Y4Z0
ProteomicsDBi86267

PTM databases

iPTMnetiQ9Y4Z0
PhosphoSitePlusiQ9Y4Z0
SwissPalmiQ9Y4Z0

Expressioni

Gene expression databases

BgeeiENSG00000130520 Expressed in 234 organ(s), highest expression level in vagina
CleanExiHS_LSM4
ExpressionAtlasiQ9Y4Z0 baseline and differential
GenevisibleiQ9Y4Z0 HS

Organism-specific databases

HPAiHPA040932

Interactioni

Subunit structurei

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:28781166, PubMed:26912367). 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).3 Publications

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi117336, 65 interactors
CORUMiQ9Y4Z0
DIPiDIP-31209N
IntActiQ9Y4Z0, 27 interactors
MINTiQ9Y4Z0
STRINGi9606.ENSP00000469468

Structurei

3D structure databases

ProteinModelPortaliQ9Y4Z0
SMRiQ9Y4Z0
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the snRNP Sm proteins family.Curated

Phylogenomic databases

eggNOGiKOG3293 Eukaryota
ENOG4111TZU LUCA
GeneTreeiENSGT00610000086173
HOGENOMiHOG000182713
HOVERGENiHBG000486
InParanoidiQ9Y4Z0
KOiK12623
OMAiLVNCDNW
PhylomeDBiQ9Y4Z0
TreeFamiTF315027

Family and domain databases

CDDicd01723 LSm4, 1 hit
InterProiView protein in InterPro
IPR034101 Lsm4
IPR027141 LSm4/Sm_D1/D3
IPR001163 LSM_dom_euk/arc
IPR010920 LSM_dom_sf
PANTHERiPTHR23338 PTHR23338, 1 hit
PfamiView protein in Pfam
PF01423 LSM, 1 hit
SMARTiView protein in SMART
SM00651 Sm, 1 hit
SUPFAMiSSF50182 SSF50182, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

This entry has 1 described isoform and 3 potential isoforms that are computationally mapped.Show allAlign All

Q9Y4Z0-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MLPLSLLKTA QNHPMLVELK NGETYNGHLV SCDNWMNINL REVICTSRDG
60 70 80 90 100
DKFWRMPECY IRGSTIKYLR IPDEIIDMVK EEVVAKGRGR GGLQQQKQQK
110 120 130
GRGMGGAGRG VFGGRGRGGI PGTGRGQPEK KPGRQAGKQ
Length:139
Mass (Da):15,350
Last modified:November 1, 1999 - v1
Checksum:iBCEFB20247335A1B
GO

Computationally mapped potential isoform sequencesi

There are 3 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
U3KQK1U3KQK1_HUMAN
U6 snRNA-associated Sm-like protein...
LSM4
125Annotation score:
V9GZ56V9GZ56_HUMAN
U6 snRNA-associated Sm-like protein...
LSM4
238Annotation score:
M0QXB0M0QXB0_HUMAN
U6 snRNA-associated Sm-like protein...
LSM4
69Annotation score:

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ238096 mRNA Translation: CAB45867.1
AF182290 mRNA Translation: AAD56228.1
AF117235 mRNA Translation: AAF17216.1
AF251218 mRNA Translation: AAF90055.1
BC000387 mRNA Translation: AAH00387.1
BC003652 mRNA Translation: AAH03652.1
BC022198 mRNA Translation: AAH22198.1
BC023665 mRNA Translation: AAH23665.1
CCDSiCCDS12374.1
RefSeqiNP_036453.1, NM_012321.4
UniGeneiHs.515255

Genome annotation databases

EnsembliENST00000593829; ENSP00000469468; ENSG00000130520
GeneIDi25804
KEGGihsa:25804
UCSCiuc002niq.4 human

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ238096 mRNA Translation: CAB45867.1
AF182290 mRNA Translation: AAD56228.1
AF117235 mRNA Translation: AAF17216.1
AF251218 mRNA Translation: AAF90055.1
BC000387 mRNA Translation: AAH00387.1
BC003652 mRNA Translation: AAH03652.1
BC022198 mRNA Translation: AAH22198.1
BC023665 mRNA Translation: AAH23665.1
CCDSiCCDS12374.1
RefSeqiNP_036453.1, NM_012321.4
UniGeneiHs.515255

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JCRelectron microscopy7.0041-139[»]
5O9Zelectron microscopy4.50q1-139[»]
ProteinModelPortaliQ9Y4Z0
SMRiQ9Y4Z0
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi117336, 65 interactors
CORUMiQ9Y4Z0
DIPiDIP-31209N
IntActiQ9Y4Z0, 27 interactors
MINTiQ9Y4Z0
STRINGi9606.ENSP00000469468

PTM databases

iPTMnetiQ9Y4Z0
PhosphoSitePlusiQ9Y4Z0
SwissPalmiQ9Y4Z0

Polymorphism and mutation databases

BioMutaiLSM4
DMDMi10720082

Proteomic databases

EPDiQ9Y4Z0
MaxQBiQ9Y4Z0
PaxDbiQ9Y4Z0
PeptideAtlasiQ9Y4Z0
PRIDEiQ9Y4Z0
ProteomicsDBi86267

Protocols and materials databases

DNASUi25804
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000593829; ENSP00000469468; ENSG00000130520
GeneIDi25804
KEGGihsa:25804
UCSCiuc002niq.4 human

Organism-specific databases

CTDi25804
DisGeNETi25804
EuPathDBiHostDB:ENSG00000130520.10
GeneCardsiLSM4
HGNCiHGNC:17259 LSM4
HPAiHPA040932
MIMi607284 gene
neXtProtiNX_Q9Y4Z0
OpenTargetsiENSG00000130520
PharmGKBiPA134906569
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3293 Eukaryota
ENOG4111TZU LUCA
GeneTreeiENSGT00610000086173
HOGENOMiHOG000182713
HOVERGENiHBG000486
InParanoidiQ9Y4Z0
KOiK12623
OMAiLVNCDNW
PhylomeDBiQ9Y4Z0
TreeFamiTF315027

Enzyme and pathway databases

ReactomeiR-HSA-430039 mRNA decay by 5' to 3' exoribonuclease
R-HSA-72163 mRNA Splicing - Major Pathway

Miscellaneous databases

ChiTaRSiLSM4 human
GeneWikiiLSM4
GenomeRNAii25804
PROiPR:Q9Y4Z0
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000130520 Expressed in 234 organ(s), highest expression level in vagina
CleanExiHS_LSM4
ExpressionAtlasiQ9Y4Z0 baseline and differential
GenevisibleiQ9Y4Z0 HS

Family and domain databases

CDDicd01723 LSm4, 1 hit
InterProiView protein in InterPro
IPR034101 Lsm4
IPR027141 LSm4/Sm_D1/D3
IPR001163 LSM_dom_euk/arc
IPR010920 LSM_dom_sf
PANTHERiPTHR23338 PTHR23338, 1 hit
PfamiView protein in Pfam
PF01423 LSM, 1 hit
SMARTiView protein in SMART
SM00651 Sm, 1 hit
SUPFAMiSSF50182 SSF50182, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiLSM4_HUMAN
AccessioniPrimary (citable) accession number: Q9Y4Z0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: November 1, 1999
Last modified: November 7, 2018
This is version 167 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. Human chromosome 19
    Human chromosome 19: entries, gene names and cross-references to MIM
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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Main funding by: National Institutes of Health

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