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Protein

U6 snRNA-associated Sm-like protein LSm6

Gene

LSM6

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). Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner, facilitating the efficient association of RNA processing factors with their substrates. Component of the cytoplasmic LSM1-LSM7 complex, which is thought to be involved in mRNA degradation by activating the decapping step in the 5'-to-3' mRNA decay pathway (Probable).1 Publication2 Publications

GO - Molecular functioni

GO - Biological processi

Keywordsi

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

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 LSm6
Gene namesi
Name:LSM6
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 4

Organism-specific databases

EuPathDBiHostDB:ENSG00000164167.9
HGNCiHGNC:17017 LSM6
MIMi607286 gene
neXtProtiNX_P62312

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

Cytoplasm, Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

DisGeNETi11157
OpenTargetsiENSG00000164167
PharmGKBiPA128394584

Chemistry databases

DrugBankiDB04272 Citric Acid
DB02745 Uridine
DB03685 Uridine-5'-Monophosphate

Polymorphism and mutation databases

BioMutaiLSM6
DMDMi61227727

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001255751 – 80U6 snRNA-associated Sm-like protein LSm6Add BLAST80

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei59N6-acetyllysineCombined sources1

Keywords - PTMi

Acetylation

Proteomic databases

EPDiP62312
PaxDbiP62312
PeptideAtlasiP62312
PRIDEiP62312
ProteomicsDBi57390
TopDownProteomicsiP62312

PTM databases

iPTMnetiP62312
PhosphoSitePlusiP62312

Expressioni

Gene expression databases

BgeeiENSG00000164167 Expressed in 228 organ(s), highest expression level in leukocyte
CleanExiHS_LSM6
GenevisibleiP62312 HS

Organism-specific databases

HPAiHPA045079

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). Component of the heptameric LSM1-LSM7 complex, which consists of LSM1, LSM2, LSM3, LSM4, LSM5, LSM6 and LSM7 (PubMed:12515382).4 Publications

Binary interactionsi

Protein-protein interaction databases

BioGridi116328, 50 interactors
CORUMiP62312
DIPiDIP-31128N
IntActiP62312, 17 interactors
MINTiP62312
STRINGi9606.ENSP00000296581

Structurei

3D structure databases

ProteinModelPortaliP62312
SMRiP62312
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiKOG1783 Eukaryota
COG1958 LUCA
GeneTreeiENSGT00730000110856
HOVERGENiHBG052369
InParanoidiP62312
KOiK12625
OMAiVMYISAD
OrthoDBiEOG091G13K2
PhylomeDBiP62312
TreeFamiTF313751

Family and domain databases

InterProiView protein in InterPro
IPR016487 Lsm6/sSmF
IPR001163 LSM_dom_euk/arc
IPR010920 LSM_dom_sf
PANTHERiPTHR11021 PTHR11021, 1 hit
PfamiView protein in Pfam
PF01423 LSM, 1 hit
PIRSFiPIRSF006609 snRNP_SmF, 1 hit
SMARTiView protein in SMART
SM00651 Sm, 1 hit
SUPFAMiSSF50182 SSF50182, 1 hit

Sequencei

Sequence statusi: Complete.

P62312-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSLRKQTPSD FLKQIIGRPV VVKLNSGVDY RGVLACLDGY MNIALEQTEE
60 70 80
YVNGQLKNKY GDAFIRGNNV LYISTQKRRM
Length:80
Mass (Da):9,128
Last modified:July 5, 2004 - v1
Checksum:i21167891FDE804F1
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ238098 mRNA Translation: CAB45869.1
AF182292 mRNA Translation: AAD56230.1
AK312126 mRNA Translation: BAG35062.1
AC097372 Genomic DNA Translation: AAY41032.1
CH471056 Genomic DNA Translation: EAX05029.1
CH471056 Genomic DNA Translation: EAX05030.1
CH471056 Genomic DNA Translation: EAX05031.1
BC016026 mRNA Translation: AAH16026.1
CCDSiCCDS3767.1
RefSeqiNP_009011.1, NM_007080.2
XP_016863161.1, XM_017007672.1
XP_016863162.1, XM_017007673.1
UniGeneiHs.190520

Genome annotation databases

EnsembliENST00000296581; ENSP00000296581; ENSG00000164167
ENST00000502781; ENSP00000422392; ENSG00000164167
ENST00000504181; ENSP00000420929; ENSG00000164167
ENST00000515311; ENSP00000427036; ENSG00000164167
GeneIDi11157
KEGGihsa:11157
UCSCiuc003ikq.5 human

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ238098 mRNA Translation: CAB45869.1
AF182292 mRNA Translation: AAD56230.1
AK312126 mRNA Translation: BAG35062.1
AC097372 Genomic DNA Translation: AAY41032.1
CH471056 Genomic DNA Translation: EAX05029.1
CH471056 Genomic DNA Translation: EAX05030.1
CH471056 Genomic DNA Translation: EAX05031.1
BC016026 mRNA Translation: AAH16026.1
CCDSiCCDS3767.1
RefSeqiNP_009011.1, NM_007080.2
XP_016863161.1, XM_017007672.1
XP_016863162.1, XM_017007673.1
UniGeneiHs.190520

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3JCRelectron microscopy7.0061-80[»]
5O9Zelectron microscopy4.50s1-80[»]
ProteinModelPortaliP62312
SMRiP62312
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116328, 50 interactors
CORUMiP62312
DIPiDIP-31128N
IntActiP62312, 17 interactors
MINTiP62312
STRINGi9606.ENSP00000296581

Chemistry databases

DrugBankiDB04272 Citric Acid
DB02745 Uridine
DB03685 Uridine-5'-Monophosphate

PTM databases

iPTMnetiP62312
PhosphoSitePlusiP62312

Polymorphism and mutation databases

BioMutaiLSM6
DMDMi61227727

Proteomic databases

EPDiP62312
PaxDbiP62312
PeptideAtlasiP62312
PRIDEiP62312
ProteomicsDBi57390
TopDownProteomicsiP62312

Protocols and materials databases

DNASUi11157
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000296581; ENSP00000296581; ENSG00000164167
ENST00000502781; ENSP00000422392; ENSG00000164167
ENST00000504181; ENSP00000420929; ENSG00000164167
ENST00000515311; ENSP00000427036; ENSG00000164167
GeneIDi11157
KEGGihsa:11157
UCSCiuc003ikq.5 human

Organism-specific databases

CTDi11157
DisGeNETi11157
EuPathDBiHostDB:ENSG00000164167.9
GeneCardsiLSM6
HGNCiHGNC:17017 LSM6
HPAiHPA045079
MIMi607286 gene
neXtProtiNX_P62312
OpenTargetsiENSG00000164167
PharmGKBiPA128394584
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1783 Eukaryota
COG1958 LUCA
GeneTreeiENSGT00730000110856
HOVERGENiHBG052369
InParanoidiP62312
KOiK12625
OMAiVMYISAD
OrthoDBiEOG091G13K2
PhylomeDBiP62312
TreeFamiTF313751

Enzyme and pathway databases

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

Miscellaneous databases

GeneWikiiLSM6
GenomeRNAii11157
PROiPR:P62312
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000164167 Expressed in 228 organ(s), highest expression level in leukocyte
CleanExiHS_LSM6
GenevisibleiP62312 HS

Family and domain databases

InterProiView protein in InterPro
IPR016487 Lsm6/sSmF
IPR001163 LSM_dom_euk/arc
IPR010920 LSM_dom_sf
PANTHERiPTHR11021 PTHR11021, 1 hit
PfamiView protein in Pfam
PF01423 LSM, 1 hit
PIRSFiPIRSF006609 snRNP_SmF, 1 hit
SMARTiView protein in SMART
SM00651 Sm, 1 hit
SUPFAMiSSF50182 SSF50182, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiLSM6_HUMAN
AccessioniPrimary (citable) accession number: P62312
Secondary accession number(s): Q4W5J5, Q9Y4Y8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 5, 2004
Last sequence update: July 5, 2004
Last modified: October 10, 2018
This is version 136 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. Human chromosome 4
    Human chromosome 4: entries, gene names and cross-references to MIM
  2. SIMILARITY comments
    Index of protein domains and families
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
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