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Protein

Small nuclear ribonucleoprotein Sm D1

Gene

Snrpd1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in an heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. May act as a charged protein scaffold to promote snRNP assembly or strengthen snRNP-snRNP interactions through nonspecific electrostatic contacts with RNA (By similarity).By similarity

GO - Molecular functioni

  1. poly(A) RNA binding Source: MGI

GO - Biological processi

  1. spliceosomal snRNP assembly Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein

Keywords - Biological processi

mRNA processing, mRNA splicing

Enzyme and pathway databases

ReactomeiREACT_206812. snRNP Assembly.
REACT_235610. mRNA Splicing - Minor Pathway.
REACT_260226. mRNA Splicing - Major Pathway.

Names & Taxonomyi

Protein namesi
Recommended name:
Small nuclear ribonucleoprotein Sm D1
Short name:
Sm-D1
Alternative name(s):
Sm-D autoantigen
snRNP core protein D1
Gene namesi
Name:Snrpd1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 18

Organism-specific databases

MGIiMGI:98344. Snrpd1.

Subcellular locationi

Cytoplasmcytosol By similarity. Nucleus By similarity
Note: SMN-mediated assembly into core snRNPs occurs in the cytosol before SMN-mediated transport to the nucleus to be included in spliceosomes.By similarity

GO - Cellular componenti

  1. catalytic step 2 spliceosome Source: MGI
  2. cytoplasm Source: MGI
  3. cytosol Source: UniProtKB
  4. methylosome Source: UniProtKB
  5. nucleus Source: MGI
  6. pICln-Sm protein complex Source: UniProtKB
  7. SMN-Sm protein complex Source: UniProtKB
  8. U12-type spliceosomal complex Source: MGI
  9. U1 snRNP Source: UniProtKB
  10. U4 snRNP Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus, Spliceosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 119119Small nuclear ribonucleoprotein Sm D1PRO_0000122202Add
BLAST

Post-translational modificationi

Methylated on arginine residues by PRMT5 and PRMT7; probable asymmetric dimethylation which is required for assembly and biogenesis of snRNPs.By similarity

Keywords - PTMi

Methylation

Proteomic databases

MaxQBiP62315.
PaxDbiP62315.
PRIDEiP62315.

PTM databases

PhosphoSiteiP62315.

Expressioni

Gene expression databases

BgeeiP62315.
CleanExiMM_SNRPD1.
GenevestigatoriP62315.

Interactioni

Subunit structurei

U1 snRNP is for instance composed of the 7 core Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in an heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP, and at least three U1 snRNP-specific proteins SNRNP70/U1-70K, SNRPA/U1-A and SNRPC/U1-C. Component of the U11/U12 snRNPs that are part of the U12-type spliceosome. 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. 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 (By similarity).By similarity

Protein-protein interaction databases

BioGridi203379. 2 interactions.
IntActiP62315. 3 interactions.
MINTiMINT-124808.
STRINGi10090.ENSMUSP00000002551.

Structurei

3D structure databases

ProteinModelPortaliP62315.
SMRiP62315. Positions 1-96.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 8080Sufficient for interaction with CLNS1ABy similarityAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi86 – 11934Arg/Lys-rich (basic)Add
BLAST

Sequence similaritiesi

Belongs to the snRNP core protein family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG1958.
GeneTreeiENSGT00510000047245.
HOGENOMiHOG000182713.
HOVERGENiHBG061491.
InParanoidiP62315.
KOiK11087.
OMAiQMNTALR.
OrthoDBiEOG7BZVWB.
PhylomeDBiP62315.
TreeFamiTF314224.

Family and domain databases

InterProiIPR027141. LSm4/Sm_D1/D3.
IPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
[Graphical view]
PANTHERiPTHR23338. PTHR23338. 1 hit.
PfamiPF01423. LSM. 1 hit.
[Graphical view]
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.

Sequencei

Sequence statusi: Complete.

P62315-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKLVRFLMKL SHETVTIELK NGTQVHGTIT GVDVSMNTHL KAVKMTLKNR
60 70 80 90 100
EPVQLETLSI RGNNIRYFIL PDSLPLDTLL VDVEPKVKSK KREAVAGRGR
110
GRGRGRGRGR GRGRGGPRR
Length:119
Mass (Da):13,282
Last modified:July 5, 2004 - v1
Checksum:i0C81C94BF98E0810
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M58558 mRNA. Translation: AAA96493.1.
AK005517 mRNA. Translation: BAB24092.1.
AK007674 mRNA. Translation: BAB25178.1.
AK011455 mRNA. Translation: BAB27628.1.
AK013075 mRNA. Translation: BAB28635.1.
AK134582 mRNA. Translation: BAE22192.1.
AK135979 mRNA. Translation: BAE22759.1.
BC024875 mRNA. Translation: AAH24875.1.
CCDSiCCDS29056.1.
RefSeqiNP_033252.1. NM_009226.4.
UniGeneiMm.603.

Genome annotation databases

EnsembliENSMUST00000002551; ENSMUSP00000002551; ENSMUSG00000002477.
GeneIDi20641.
KEGGimmu:20641.
UCSCiuc008eaz.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M58558 mRNA. Translation: AAA96493.1.
AK005517 mRNA. Translation: BAB24092.1.
AK007674 mRNA. Translation: BAB25178.1.
AK011455 mRNA. Translation: BAB27628.1.
AK013075 mRNA. Translation: BAB28635.1.
AK134582 mRNA. Translation: BAE22192.1.
AK135979 mRNA. Translation: BAE22759.1.
BC024875 mRNA. Translation: AAH24875.1.
CCDSiCCDS29056.1.
RefSeqiNP_033252.1. NM_009226.4.
UniGeneiMm.603.

3D structure databases

ProteinModelPortaliP62315.
SMRiP62315. Positions 1-96.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi203379. 2 interactions.
IntActiP62315. 3 interactions.
MINTiMINT-124808.
STRINGi10090.ENSMUSP00000002551.

PTM databases

PhosphoSiteiP62315.

Proteomic databases

MaxQBiP62315.
PaxDbiP62315.
PRIDEiP62315.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000002551; ENSMUSP00000002551; ENSMUSG00000002477.
GeneIDi20641.
KEGGimmu:20641.
UCSCiuc008eaz.1. mouse.

Organism-specific databases

CTDi6632.
MGIiMGI:98344. Snrpd1.

Phylogenomic databases

eggNOGiCOG1958.
GeneTreeiENSGT00510000047245.
HOGENOMiHOG000182713.
HOVERGENiHBG061491.
InParanoidiP62315.
KOiK11087.
OMAiQMNTALR.
OrthoDBiEOG7BZVWB.
PhylomeDBiP62315.
TreeFamiTF314224.

Enzyme and pathway databases

ReactomeiREACT_206812. snRNP Assembly.
REACT_235610. mRNA Splicing - Minor Pathway.
REACT_260226. mRNA Splicing - Major Pathway.

Miscellaneous databases

ChiTaRSiSnrpd1. mouse.
NextBioi25835.
PROiP62315.
SOURCEiSearch...

Gene expression databases

BgeeiP62315.
CleanExiMM_SNRPD1.
GenevestigatoriP62315.

Family and domain databases

InterProiIPR027141. LSm4/Sm_D1/D3.
IPR010920. LSM_dom.
IPR001163. Ribonucl_LSM.
IPR006649. Ribonucl_LSM_euk/arc.
[Graphical view]
PANTHERiPTHR23338. PTHR23338. 1 hit.
PfamiPF01423. LSM. 1 hit.
[Graphical view]
SMARTiSM00651. Sm. 1 hit.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The murine Sm-D autoantigen: multiple genes, genetic polymorphism, evolutionary conservation and lack of intervening sequences in the coding region."
    Mitsuda T., Eisenberg R.A., Cohen P.L.
    J. Autoimmun. 5:277-287(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: BALB/c.
    Tissue: Lymphoma.
  2. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Egg, Medulla oblongata, Pancreas and Placenta.
  3. "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].
    Strain: Czech II.
    Tissue: Mammary gland.

Entry informationi

Entry nameiSMD1_MOUSE
AccessioniPrimary (citable) accession number: P62315
Secondary accession number(s): P13641, Q3UYM0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 5, 2004
Last sequence update: July 5, 2004
Last modified: February 4, 2015
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

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. 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.