Human Gene SNRPD2 (ENST00000342669.8_6) from GENCODE V45lift37
  Description: Plays a role in pre-mRNA splicing as a core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (PubMed:11991638, PubMed:18984161, PubMed:19325628, PubMed:23333303, PubMed:25555158, PubMed:26912367, PubMed:28502770, PubMed:28781166, PubMed:28076346, PubMed:32494006). Component of both the pre-catalytic spliceosome B complex and activated spliceosome C complexes (PubMed:11991638, PubMed:28502770, PubMed:28781166, PubMed:28076346). As a component of the minor spliceosome, involved in the splicing of U12-type introns in pre-mRNAs (PubMed:15146077). (from UniProt P62316)
RefSeq Summary (NM_004597): The protein encoded by this gene belongs to the small nuclear ribonucleoprotein core protein family. It is required for pre-mRNA splicing and small nuclear ribonucleoprotein biogenesis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009].
Gencode Transcript: ENST00000342669.8_6
Gencode Gene: ENSG00000125743.11_9
Transcript (Including UTRs)
   Position: hg19 chr19:46,190,718-46,195,211 Size: 4,494 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr19:46,190,811-46,195,146 Size: 4,336 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2024-04-24 11:59:55

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:46,190,718-46,195,211)mRNA (may differ from genome)Protein (118 aa)
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-  Comments and Description Text from UniProtKB
  ID: SMD2_HUMAN
DESCRIPTION: RecName: Full=Small nuclear ribonucleoprotein Sm D2; Short=Sm-D2; AltName: Full=snRNP core protein D2;
FUNCTION: Plays a role in pre-mRNA splicing as a core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (PubMed:11991638, PubMed:18984161, PubMed:19325628, PubMed:23333303, PubMed:25555158, PubMed:26912367, PubMed:28502770, PubMed:28781166, PubMed:28076346, PubMed:32494006). Component of both the pre-catalytic spliceosome B complex and activated spliceosome C complexes (PubMed:11991638, PubMed:28502770, PubMed:28781166, PubMed:28076346). As a component of the minor spliceosome, involved in the splicing of U12-type introns in pre-mRNAs (PubMed:15146077).
SUBUNIT: Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (PubMed:11991638, PubMed:19325628, PubMed:21516107, PubMed:25555158, PubMed:26912367, PubMed:28502770, PubMed:28781166, PubMed:28076346, PubMed:32494006, PubMed:36797247). Most spliceosomal snRNPs contain a common set of Sm proteins, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP (PubMed:10025403, PubMed:19325628, PubMed:21516107, PubMed:25555158, PubMed:26912367, PubMed:28502770, PubMed:28781166, PubMed:28076346). Component of the U1 snRNP (PubMed:19325628, PubMed:25555158). The U1 snRNP is composed of the U1 snRNA and the 7 core Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG, and at least three U1 snRNP-specific proteins SNRNP70/U1-70K, SNRPA/U1-A and SNRPC/U1-C (PubMed:19325628, PubMed:25555158). Component of the U4/U6-U5 tri-snRNP complex 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). Component of the minor spliceosome, which splices U12-type introns (PubMed:15146077, PubMed:33509932). 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 (PubMed:16314521). 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. Interacts with SMN1; the interaction is direct (PubMed:21816274). Interacts with GEMIN2; the interaction is direct (PubMed:21816274, PubMed:31799625). Interacts with SNRPD1; the interaction is direct (PubMed:21816274, PubMed:31799625). Interacts with SNRPF; the interaction is direct (PubMed:21816274, PubMed:31799625).
INTERACTION: P62316; P54253: ATXN1; NbExp=3; IntAct=EBI-297993, EBI-930964; P62316; Q8NHQ1: CEP70; NbExp=3; IntAct=EBI-297993, EBI-739624; P62316; Q9BW66: CINP; NbExp=3; IntAct=EBI-297993, EBI-739784; P62316; P54105: CLNS1A; NbExp=11; IntAct=EBI-297993, EBI-724693; P62316; P42858: HTT; NbExp=3; IntAct=EBI-297993, EBI-466029; P62316; Q9Y333: LSM2; NbExp=3; IntAct=EBI-297993, EBI-347416; P62316; P62312: LSM6; NbExp=3; IntAct=EBI-297993, EBI-373310; P62316; P62314: SNRPD1; NbExp=3; IntAct=EBI-297993, EBI-372177; P62316; P62306: SNRPF; NbExp=11; IntAct=EBI-297993, EBI-356900; P62316; Q5MJ10: SPANXN2; NbExp=3; IntAct=EBI-297993, EBI-12023934;
SUBCELLULAR LOCATION: Cytoplasm, cytosol Nucleus te=SMN-mediated assembly into core snRNPs occurs in the cytosol before SMN-mediated transport to the nucleus to be included in spliceosomes.
MISCELLANEOUS: In the autoimmune disease systemic lupus erythematosus, antinuclear antibodies are developed with Sm specificity.
SIMILARITY: Belongs to the snRNP core protein family.

-  Primer design for this transcript
 

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-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 133.98 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 2675.92 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -14.8065-0.228 Picture PostScript Text
3' UTR -19.8093-0.213 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR010920 - LSM_dom_sf
IPR047575 - Sm
IPR027248 - Sm_D2
IPR001163 - Sm_dom_euk/arc

Pfam Domains:
PF01423 - LSM domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1B34 - X-ray 3CW1 - X-ray 3JCR - EM 3PGW - X-ray 4F7U - X-ray 4PJO - X-ray 4V98 - X-ray 4WZJ - X-ray 5MQF - EM 5O9Z - EM 5XJC - EM 5XJL - X-ray 5XJQ - X-ray 5XJR - X-ray 5XJS - X-ray 5XJT - X-ray 5XJU - X-ray 5YZG - EM 5Z56 - EM 5Z57 - EM 5Z58 - EM 6AH0 - EM 6AHD - EM 6FF7 - EM 6ICZ - EM 6ID0 - EM 6ID1 - EM 6QDV - EM 6QW6 - EM 6QX9 - EM 6Y53 - EM 6Y5Q - EM 7A5P - EM 7ABG - EM 7ABI - EM 7B0Y - EM 7DVQ - EM 7EVO - EM 7QTT - EM 7VPX - EM 7W59 - EM 7W5A - EM 7W5B - EM 8C6J - EM 8CH6 - EM 8HK1 - EM


ModBase Predicted Comparative 3D Structure on P62316
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0000245 spliceosomal complex assembly
GO:0000387 spliceosomal snRNP assembly
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0051170 nuclear import

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005682 U5 snRNP
GO:0005685 U1 snRNP
GO:0005686 U2 snRNP
GO:0005687 U4 snRNP
GO:0005689 U12-type spliceosomal complex
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0030532 small nuclear ribonucleoprotein complex
GO:0034709 methylosome
GO:0034715 pICln-Sm protein complex
GO:0034719 SMN-Sm protein complex
GO:0046540 U4/U6 x U5 tri-snRNP complex
GO:0070062 extracellular exosome
GO:0071005 U2-type precatalytic spliceosome
GO:0071007 U2-type catalytic step 2 spliceosome
GO:0071013 catalytic step 2 spliceosome


-  Descriptions from all associated GenBank mRNAs
  AK291912 - Homo sapiens cDNA FLJ76568 complete cds, highly similar to Homo sapiens small nuclear ribonucleoprotein D2 polypeptide 16.5kDa (SNRPD2), transcript variant 1, mRNA.
BC001930 - Homo sapiens small nuclear ribonucleoprotein D2 polypeptide 16.5kDa, mRNA (cDNA clone MGC:3995 IMAGE:2819767), complete cds.
BC000486 - Homo sapiens small nuclear ribonucleoprotein D2 polypeptide 16.5kDa, mRNA (cDNA clone MGC:8353 IMAGE:2819767), complete cds.
U15008 - Human SnRNP core protein Sm D2 mRNA, complete cds.
DQ891246 - Synthetic construct clone IMAGE:100003876; FLH176228.01X; RZPDo839A12122D small nuclear ribonucleoprotein D2 polypeptide 16.5kDa (SNRPD2) gene, encodes complete protein.
KJ892177 - Synthetic construct Homo sapiens clone ccsbBroadEn_01571 SNRPD2 gene, encodes complete protein.
DQ894432 - Synthetic construct Homo sapiens clone IMAGE:100008892; FLH176224.01L; RZPDo839A12121D small nuclear ribonucleoprotein D2 polypeptide 16.5kDa (SNRPD2) gene, encodes complete protein.
AB464218 - Synthetic construct DNA, clone: pF1KB6775, Homo sapiens SNRPD2 gene for small nuclear ribonucleoprotein D2 polypeptide, without stop codon, in Flexi system.
JD438018 - Sequence 419042 from Patent EP1572962.
JD185179 - Sequence 166203 from Patent EP1572962.
JD147545 - Sequence 128569 from Patent EP1572962.
JD418799 - Sequence 399823 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P62316 (Reactome details) participates in the following event(s):

R-HSA-191790 Loading and methylation of Sm proteins onto SMN Complexes
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-72107 Formation of the Spliceosomal E complex
R-HSA-75083 ATAC spliceosome mediated 3' splice site cleavage, exon ligation
R-HSA-75080 Formation of AT-AC A complex
R-HSA-75079 Formation of AT-AC C complex
R-HSA-191830 snRNP nuclear import and release
R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-191786 snRNP complex assembly
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-75081 Formation of AT-AC B Complex
R-HSA-75082 ATAC spliceosome mediated Lariat formation,5' splice site cleavage
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-191763 snRNP:Snurportin complex formation
R-HSA-191784 snRNA Cap hypermethylation
R-HSA-191859 snRNP Assembly
R-HSA-194441 Metabolism of non-coding RNA
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72165 mRNA Splicing - Minor Pathway
R-HSA-8953854 Metabolism of RNA
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA

-  Other Names for This Gene
  Alternate Gene Symbols: A8K797, ENST00000342669.1, ENST00000342669.2, ENST00000342669.3, ENST00000342669.4, ENST00000342669.5, ENST00000342669.6, ENST00000342669.7, NM_001384647, P43330, P62316, SMD2_HUMAN, SNRPD1, uc317wko.1
UCSC ID: ENST00000342669.8_6
RefSeq Accession: NM_004597
Protein: P62316 (aka SMD2_HUMAN)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.