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Snapc3 small nuclear RNA activating complex, polypeptide 3 [ Mus musculus (house mouse) ]

Gene ID: 77634, updated on 2-Nov-2024

Summary

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Official Symbol
Snapc3provided by MGI
Official Full Name
small nuclear RNA activating complex, polypeptide 3provided by MGI
Primary source
MGI:MGI:1916338
See related
Ensembl:ENSMUSG00000028483 AllianceGenome:MGI:1916338
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
1810020H02Rik; 4930558A07Rik; 5031401C21Rik; E030018J20Rik
Summary
Predicted to enable RNA polymerase III type 3 promoter sequence-specific DNA binding activity and bent DNA binding activity. Predicted to contribute to RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and core promoter sequence-specific DNA binding activity. Predicted to be involved in snRNA transcription by RNA polymerase II and snRNA transcription by RNA polymerase III. Predicted to be located in nuclear body and nucleolus. Predicted to be part of snRNA-activating protein complex. Is expressed in several structures, including nervous system and sensory organ. Orthologous to human SNAPC3 (small nuclear RNA activating complex polypeptide 3). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in CNS E11.5 (RPKM 14.7), CNS E14 (RPKM 14.0) and 22 other tissues See more
Orthologs
human all
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Genomic context

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See Snapc3 in Genome Data Viewer
Location:
4 C3; 4 39.46 cM
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (83333948..83391256)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (83415711..83473019)

Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer mm9_chr4:82969964-82970265 Neighboring gene STARR-seq mESC enhancer starr_10639 Neighboring gene predicted gene, 42306 Neighboring gene predicted gene 11413 Neighboring gene predicted gene 11184 Neighboring gene STARR-seq mESC enhancer starr_10641 Neighboring gene STARR-positive B cell enhancer mm9_chr4:83063359-83063659 Neighboring gene STARR-seq mESC enhancer starr_10644 Neighboring gene PC4 and SFRS1 interacting protein 1 Neighboring gene ribosomal protein L34 pseudogene Neighboring gene predicted gene, 42308

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Disruption of Ledgf/Psip1 results in perinatal mortality and homeotic skeletal transformations. Sutherland HG, et al. Mol Cell Biol, 2006 Oct. PMID 16980622, Free PMC Article
  2. Characterization of an exchangeable gene trap using pU-17 carrying a stop codon-beta geo cassette. Taniwaki T, et al. Dev Growth Differ, 2005 Apr. PMID 15840001
  3. Exchangeable gene trap using the Cre/mutated lox system. Araki K, et al. Cell Mol Biol (Noisy-le-grand), 1999 Jul. PMID 10512203
  4. EUCOMM--the European conditional mouse mutagenesis program. Friedel RH, et al. Brief Funct Genomic Proteomic, 2007 Sep. PMID 17967808
  5. Cell-Type-Specific Gene Expression in Developing Mouse Neocortex: Intermediate Progenitors Implicated in Axon Development. Bedogni F, et al. Front Mol Neurosci, 2021. PMID 34321999, Free PMC Article

See all (24) citations in PubMed

GeneRIFs: Gene References Into Functions

Pathways from PubChem

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General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
contributes_to RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase III type 3 promoter sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables bent DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
contributes_to core promoter sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in snRNA transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in snRNA transcription by RNA polymerase III IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in nuclear body IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear body ISO
Inferred from Sequence Orthology
more info
  
located_in nucleolus IEA
Inferred from Electronic Annotation
more info
  
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
part_of snRNA-activating protein complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
snRNA-activating protein complex subunit 3
Names
SNAPc subunit 3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001358795.1 → NP_001345724.1  snRNA-activating protein complex subunit 3 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks alternate 3' coding exons and differs in the 3' coding region and 3' UTR compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AK016168, AK049933, BE993334
    Consensus CDS
    CCDS89770.1
    UniProtKB/TrEMBL
    Q9CQB0
    Related
    ENSMUSP00000102842.2, ENSMUST00000071544.11
    Conserved Domains (1) summary
    pfam12251
    Location:198 → 269
    zf-SNAP50_C; snRNA-activating protein of 50kDa MW C terminal

  2. NM_029949.4 → NP_084225.1  snRNA-activating protein complex subunit 3 isoform 1

    See identical proteins and their annotated locations for NP_084225.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AK049933, BC048713
    Consensus CDS
    CCDS38792.1
    UniProtKB/Swiss-Prot
    Q8C0A5, Q9D2C9
    Related
    ENSMUSP00000030206.4, ENSMUST00000030206.10
    Conserved Domains (1) summary
    pfam12251
    Location:198 → 399
    zf-SNAP50_C; snRNA-activating protein of 50kDa MW C terminal

RNA

  1. NR_152448.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains additional 3' exons compared to variant 1. This variant is represented as non-coding because use of the 5' expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AK019863, AK049933, BX682545

  2. NR_152449.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains an alternate internal exon and additional 3' exons compared to variant 1. This variant is represented as non-coding because use of the 5' expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL670851, BX682545

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000070.7 Reference GRCm39 C57BL/6J

    Range
    83333948..83391256
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011250134.3 → XP_011248436.1  snRNA-activating protein complex subunit 3 isoform X2

    See identical proteins and their annotated locations for XP_011248436.1

    UniProtKB/Swiss-Prot
    Q8C0A5, Q9D2C9
    Conserved Domains (1) summary
    pfam12251
    Location:198 → 399
    zf-SNAP50_C; snRNA-activating protein of 50kDa MW C terminal

  2. XM_006538369.4 → XP_006538432.1  snRNA-activating protein complex subunit 3 isoform X2

    See identical proteins and their annotated locations for XP_006538432.1

    UniProtKB/Swiss-Prot
    Q8C0A5, Q9D2C9
    Conserved Domains (1) summary
    pfam12251
    Location:198 → 399
    zf-SNAP50_C; snRNA-activating protein of 50kDa MW C terminal

  3. XM_006538370.4 → XP_006538433.1  snRNA-activating protein complex subunit 3 isoform X2

    See identical proteins and their annotated locations for XP_006538433.1

    UniProtKB/Swiss-Prot
    Q8C0A5, Q9D2C9
    Related
    ENSMUSP00000124181.2, ENSMUST00000124856.8
    Conserved Domains (1) summary
    pfam12251
    Location:198 → 399
    zf-SNAP50_C; snRNA-activating protein of 50kDa MW C terminal

  4. XM_017320455.2 → XP_017175944.1  snRNA-activating protein complex subunit 3 isoform X2

    UniProtKB/Swiss-Prot
    Q8C0A5, Q9D2C9
    Conserved Domains (1) summary
    pfam12251
    Location:198 → 399
    zf-SNAP50_C; snRNA-activating protein of 50kDa MW C terminal

  5. XM_030253911.1 → XP_030109771.1  snRNA-activating protein complex subunit 3 isoform X2

    UniProtKB/Swiss-Prot
    Q8C0A5, Q9D2C9
    Related
    ENSMUSP00000123793.2, ENSMUST00000143533.8
    Conserved Domains (1) summary
    pfam12251
    Location:198 → 399
    zf-SNAP50_C; snRNA-activating protein of 50kDa MW C terminal

  6. XM_036164546.1 → XP_036020439.1  snRNA-activating protein complex subunit 3 isoform X1

    UniProtKB/TrEMBL
    V9H0W7
    Conserved Domains (5) summary
    cd07557
    Location:880 → 967
    trimeric_dUTPase; Trimeric dUTP diphosphatases
    cd03715
    Location:18 → 225
    RT_ZFREV_like; A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or ...
    pfam00665
    Location:692 → 788
    rve; Integrase core domain
    pfam17919
    Location:309 → 387
    RT_RNaseH_2; RNase H-like domain found in reverse transcriptase
    cl14782
    Location:480 → 617
    RNase_H_like; Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8

  7. XM_036164547.1 → XP_036020440.1  snRNA-activating protein complex subunit 3 isoform X1

    UniProtKB/TrEMBL
    V9H0W7
    Conserved Domains (5) summary
    cd07557
    Location:880 → 967
    trimeric_dUTPase; Trimeric dUTP diphosphatases
    cd03715
    Location:18 → 225
    RT_ZFREV_like; A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or ...
    pfam00665
    Location:692 → 788
    rve; Integrase core domain
    pfam17919
    Location:309 → 387
    RT_RNaseH_2; RNase H-like domain found in reverse transcriptase
    cl14782
    Location:480 → 617
    RNase_H_like; Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8

  8. XM_030253916.2 → XP_030109776.1  snRNA-activating protein complex subunit 3 isoform X4

    Conserved Domains (1) summary
    pfam12251
    Location:198 → 268
    zf-SNAP50_C; snRNA-activating protein of 50kDa MW C terminal

  9. XM_030253915.2 → XP_030109775.1  snRNA-activating protein complex subunit 3 isoform X4

    Conserved Domains (1) summary
    pfam12251
    Location:198 → 268
    zf-SNAP50_C; snRNA-activating protein of 50kDa MW C terminal

  10. XM_036164548.1 → XP_036020441.1  snRNA-activating protein complex subunit 3 isoform X5

    Conserved Domains (1) summary
    pfam12251
    Location:198 → 220
    zf-SNAP50_C; snRNA-activating protein of 50kDa MW C terminal

  11. XM_030253914.2 → XP_030109774.1  snRNA-activating protein complex subunit 3 isoform X4

    Conserved Domains (1) summary
    pfam12251
    Location:198 → 268
    zf-SNAP50_C; snRNA-activating protein of 50kDa MW C terminal

  12. XM_030253913.2 → XP_030109773.1  snRNA-activating protein complex subunit 3 isoform X3

    Conserved Domains (1) summary
    pfam12251
    Location:198 → 269
    zf-SNAP50_C; snRNA-activating protein of 50kDa MW C terminal
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9D2C9.2 GenPept UniProtKB/Swiss-Prot:Q9D2C9

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