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P62312

- LSM6_HUMAN

UniProt

P62312 - LSM6_HUMAN

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Protein
U6 snRNA-associated Sm-like protein LSm6
Gene
LSM6
Organism
Homo sapiens (Human)
Status
Reviewed - 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.

GO - Molecular functioni

  1. poly(A) RNA binding Source: UniProtKB
  2. protein binding Source: IntAct

GO - Biological processi

  1. RNA metabolic process Source: Reactome
  2. RNA splicing Source: UniProtKB
  3. exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay Source: Reactome
  4. gene expression Source: Reactome
  5. mRNA metabolic process Source: Reactome
  6. mRNA processing Source: UniProtKB-KW
  7. nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay Source: Reactome
  8. rRNA processing Source: UniProtKB-KW
  9. tRNA processing Source: UniProtKB-KW
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: Chromosome 4

Organism-specific databases

HGNCiHGNC:17017. LSM6.

Subcellular locationi

Cytoplasm. Nucleus By similarity 1 Publication

GO - Cellular componenti

  1. cytosol Source: Reactome
  2. extracellular vesicular exosome Source: UniProt
  3. small nuclear ribonucleoprotein complex Source: UniProtKB
  4. spliceosomal complex Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA128394584.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 8080U6 snRNA-associated Sm-like protein LSm6
PRO_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.
GenevestigatoriP62312.

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
LSM3P623103EBI-373310,EBI-348239
LSM5Q9Y4Y94EBI-373310,EBI-373007
LSM7Q9UK454EBI-373310,EBI-348372

Protein-protein interaction databases

BioGridi116328. 22 interactions.
DIPiDIP-31128N.
IntActiP62312. 15 interactions.
MINTiMINT-4100591.
STRINGi9606.ENSP00000296581.

Structurei

3D structure databases

ProteinModelPortaliP62312.
SMRiP62312. Positions 7-74.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG1958.
HOVERGENiHBG052369.
InParanoidiP62312.
KOiK12625.
OMAiEMETENM.
OrthoDBiEOG7HXCTK.
PhylomeDBiP62312.
TreeFamiTF313751.

Family and domain databases

InterProiIPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
[Graphical view]
PfamiPF01423. LSM. 1 hit.
[Graphical view]
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.

Sequencei

Sequence statusi: Complete.

P62312-1 [UniParc]FASTAAdd to Basket

« Hide

MSLRKQTPSD FLKQIIGRPV VVKLNSGVDY RGVLACLDGY MNIALEQTEE   50
YVNGQLKNKY GDAFIRGNNV LYISTQKRRM 80
Length:80
Mass (Da):9,128
Last modified:July 5, 2004 - v1
Checksum:i21167891FDE804F1
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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.

Polymorphism databases

DMDMi61227727.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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 .
CCDSi CCDS3767.1.
RefSeqi NP_009011.1. NM_007080.2.
UniGenei Hs.190520.

3D structure databases

ProteinModelPortali P62312.
SMRi P62312. Positions 7-74.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 116328. 22 interactions.
DIPi DIP-31128N.
IntActi P62312. 15 interactions.
MINTi MINT-4100591.
STRINGi 9606.ENSP00000296581.

PTM databases

PhosphoSitei P62312.

Polymorphism databases

DMDMi 61227727.

Proteomic databases

MaxQBi P62312.
PaxDbi P62312.
PeptideAtlasi P62312.
PRIDEi P62312.

Protocols and materials databases

DNASUi 11157.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000296581 ; ENSP00000296581 ; ENSG00000164167 .
ENST00000502781 ; ENSP00000422392 ; ENSG00000164167 .
ENST00000504181 ; ENSP00000420929 ; ENSG00000164167 .
ENST00000515311 ; ENSP00000427036 ; ENSG00000164167 .
GeneIDi 11157.
KEGGi hsa:11157.
UCSCi uc003ikq.4. human.

Organism-specific databases

CTDi 11157.
GeneCardsi GC04P147097.
HGNCi HGNC:17017. LSM6.
HPAi HPA045079.
MIMi 607286. gene.
neXtProti NX_P62312.
PharmGKBi PA128394584.
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG1958.
HOVERGENi HBG052369.
InParanoidi P62312.
KOi K12625.
OMAi EMETENM.
OrthoDBi EOG7HXCTK.
PhylomeDBi P62312.
TreeFami TF313751.

Enzyme and pathway databases

Reactomei REACT_20518. mRNA decay by 5' to 3' exoribonuclease.

Miscellaneous databases

GeneWikii LSM6.
GenomeRNAii 11157.
NextBioi 42433.
PROi P62312.
SOURCEi Search...

Gene expression databases

Bgeei P62312.
CleanExi HS_LSM6.
Genevestigatori P62312.

Family and domain databases

InterProi IPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
[Graphical view ]
Pfami PF01423. LSM. 1 hit.
[Graphical view ]
SMARTi SM00651. Sm. 1 hit.
[Graphical view ]
SUPFAMi SSF50182. SSF50182. 1 hit.
ProtoNeti Search...

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: September 3, 2014
This is version 97 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

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