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Protein

U6 snRNA-associated Sm-like protein LSm6

Gene

LSM6

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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. 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 di-snRNP, spliceosomal U4/U6.U5 tri-snRNP, and free U6 snRNP). It binds directly to the 3'-terminal U-tract of U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. LSM2-LSM8 probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping, and in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA (By similarity).By similarity

GO - Molecular functioni

  • poly(A) RNA binding Source: UniProtKB

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Biological processi

mRNA processing, mRNA splicing, rRNA processing, tRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiREACT_20518. mRNA decay by 5' to 3' exoribonuclease.

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
ProteomesiUP000005640 Componenti: Chromosome 4

Organism-specific databases

HGNCiHGNC:17017. LSM6.

Subcellular locationi

  • Cytoplasm 1 Publication
  • Nucleus By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA128394584.

Polymorphism and mutation databases

BioMutaiLSM6.
DMDMi61227727.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 8080U6 snRNA-associated Sm-like protein LSm6PRO_0000125575Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei59 – 591N6-acetyllysine1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiP62312.
PaxDbiP62312.
PeptideAtlasiP62312.
PRIDEiP62312.

PTM databases

PhosphoSiteiP62312.

Expressioni

Gene expression databases

BgeeiP62312.
CleanExiHS_LSM6.
GenevisibleiP62312. HS.

Organism-specific databases

HPAiHPA045079.

Interactioni

Subunit structurei

Component of the heptameric LSM1-LSM7 complex, which consists of LSM1, LSM2, LSM3, LSM4, LSM5, LSM6 and LSM7. Component of the heptameric LSM2-LSM8 complex, which consists of LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8. The LSm subunits form a seven-membered ring structure with a doughnut shape.2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CLNS1AP541054EBI-373310,EBI-724693
LSM3P623106EBI-373310,EBI-348239
LSM5Q9Y4Y97EBI-373310,EBI-373007
LSM7Q9UK454EBI-373310,EBI-348372
SDCBPO005603EBI-373310,EBI-727004

Protein-protein interaction databases

BioGridi116328. 25 interactions.
DIPiDIP-31128N.
IntActiP62312. 16 interactions.
MINTiMINT-4100591.
STRINGi9606.ENSP00000296581.

Structurei

3D structure databases

ProteinModelPortaliP62312.
SMRiP62312. Positions 7-74.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG1958.
GeneTreeiENSGT00730000110856.
HOVERGENiHBG052369.
InParanoidiP62312.
KOiK12625.
OMAiEEYSNGQ.
OrthoDBiEOG7HXCTK.
PhylomeDBiP62312.
TreeFamiTF313751.

Family and domain databases

InterProiIPR016487. Lsm6/sSmF.
IPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
[Graphical view]
PfamiPF01423. LSM. 1 hit.
[Graphical view]
PIRSFiPIRSF006609. snRNP_SmF. 1 hit.
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
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.
UniGeneiHs.190520.

Genome annotation databases

EnsembliENST00000296581; ENSP00000296581; ENSG00000164167.
ENST00000502781; ENSP00000422392; ENSG00000164167.
ENST00000504181; ENSP00000420929; ENSG00000164167.
ENST00000515311; ENSP00000427036; ENSG00000164167.
GeneIDi11157.
KEGGihsa:11157.
UCSCiuc003ikq.4. human.

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.
UniGeneiHs.190520.

3D structure databases

ProteinModelPortaliP62312.
SMRiP62312. Positions 7-74.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116328. 25 interactions.
DIPiDIP-31128N.
IntActiP62312. 16 interactions.
MINTiMINT-4100591.
STRINGi9606.ENSP00000296581.

PTM databases

PhosphoSiteiP62312.

Polymorphism and mutation databases

BioMutaiLSM6.
DMDMi61227727.

Proteomic databases

MaxQBiP62312.
PaxDbiP62312.
PeptideAtlasiP62312.
PRIDEiP62312.

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.4. human.

Organism-specific databases

CTDi11157.
GeneCardsiGC04P147097.
HGNCiHGNC:17017. LSM6.
HPAiHPA045079.
MIMi607286. gene.
neXtProtiNX_P62312.
PharmGKBiPA128394584.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG1958.
GeneTreeiENSGT00730000110856.
HOVERGENiHBG052369.
InParanoidiP62312.
KOiK12625.
OMAiEEYSNGQ.
OrthoDBiEOG7HXCTK.
PhylomeDBiP62312.
TreeFamiTF313751.

Enzyme and pathway databases

ReactomeiREACT_20518. mRNA decay by 5' to 3' exoribonuclease.

Miscellaneous databases

GeneWikiiLSM6.
GenomeRNAii11157.
NextBioi42433.
PROiP62312.
SOURCEiSearch...

Gene expression databases

BgeeiP62312.
CleanExiHS_LSM6.
GenevisibleiP62312. HS.

Family and domain databases

InterProiIPR016487. Lsm6/sSmF.
IPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
[Graphical view]
PfamiPF01423. LSM. 1 hit.
[Graphical view]
PIRSFiPIRSF006609. snRNP_SmF. 1 hit.
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin."
    Salgado-Garrido J., Bragado-Nilsson E., Kandels-Lewis S., Seraphin B.
    EMBO J. 18:3451-3462(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "A doughnut-shaped heteromer of human Sm-like proteins binds to the 3'-end of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro."
    Achsel T., Brahms H., Kastner B., Bachi A., Wilm M., Luehrmann R.
    EMBO J. 18:5789-5802(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE, IDENTIFICATION IN THE LSM2-LSM8 COMPLEX.
  3. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  4. "Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
    Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H.
    , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
    Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Uterus.
  7. "The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci."
    Ingelfinger D., Arndt-Jovin D.J., Luehrmann R., Achsel T.
    RNA 8:1489-1501(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION, IDENTIFICATION IN THE LSM1-LSM7 COMPLEX.
  8. "Lysine acetylation targets protein complexes and co-regulates major cellular functions."
    Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
    Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-59, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiLSM6_HUMAN
AccessioniPrimary (citable) accession number: P62312
Secondary accession number(s): Q4W5J5, Q9Y4Y8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 5, 2004
Last sequence update: July 5, 2004
Last modified: July 22, 2015
This is version 108 of the entry and version 1 of the sequence. [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

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 4
    Human chromosome 4: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.