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Smarcc1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 301020, updated on 21-Jul-2018

Summary

Official Symbol
Smarcc1provided by RGD
Official Full Name
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 1provided by RGD
Primary source
RGD:1304850
See related
Ensembl:ENSRNOG00000020804
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Expression
Biased expression in Thymus (RPKM 136.8), Spleen (RPKM 109.5) and 9 other tissues See more
Orthologs

Genomic context

See Smarcc1 in Genome Data Viewer
Location:
8q32
Exon count:
30
Annotation release Status Assembly Chr Location
106 current Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (118206678..118326264)
104 previous assembly Rnor_5.0 (GCF_000001895.4) 8 NC_005107.3 (117561593..117677011)

Chromosome 8 - NC_005107.4Genomic Context describing neighboring genes Neighboring gene microtubule-associated protein 4 Neighboring gene DExH-box helicase 30 Neighboring gene uncharacterized LOC102547516 Neighboring gene chondroitin sulfate proteoglycan 5

Genomic regions, transcripts, and products

Expression

  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

Pathways from BioSystems

General gene information

Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
chromatin binding ISO
Inferred from Sequence Orthology
more info
 
molecular_function ND
No biological Data available
more info
 
protein N-terminus binding IEA
Inferred from Electronic Annotation
more info
 
protein N-terminus binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
ATP-dependent chromatin remodeling IEA
Inferred from Electronic Annotation
more info
 
animal organ morphogenesis IEA
Inferred from Electronic Annotation
more info
 
animal organ morphogenesis ISO
Inferred from Sequence Orthology
more info
 
chromatin remodeling ISO
Inferred from Sequence Orthology
more info
 
insulin receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
insulin receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
 
negative regulation of proteasomal ubiquitin-dependent protein catabolic process IEA
Inferred from Electronic Annotation
more info
 
negative regulation of proteasomal ubiquitin-dependent protein catabolic process ISO
Inferred from Sequence Orthology
more info
 
nucleosome disassembly IEA
Inferred from Electronic Annotation
more info
 
nucleosome disassembly ISO
Inferred from Sequence Orthology
more info
 
positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
positive regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
prostate gland development IEP
Inferred from Expression Pattern
more info
PubMed 
Component Evidence Code Pubs
SWI/SNF complex IEA
Inferred from Electronic Annotation
more info
 
SWI/SNF complex ISO
Inferred from Sequence Orthology
more info
 
XY body IEA
Inferred from Electronic Annotation
more info
 
XY body ISO
Inferred from Sequence Orthology
more info
 
cellular_component ND
No biological Data available
more info
 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
cytoplasm ISO
Inferred from Sequence Orthology
more info
 
intracellular ISO
Inferred from Sequence Orthology
more info
 
nBAF complex IEA
Inferred from Electronic Annotation
more info
 
nBAF complex ISO
Inferred from Sequence Orthology
more info
 
npBAF complex IEA
Inferred from Electronic Annotation
more info
 
npBAF complex ISO
Inferred from Sequence Orthology
more info
 
nucleoplasm IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
nucleus ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
SWI/SNF complex subunit SMARCC1

NCBI Reference Sequences (RefSeq)

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_001106861.1NP_001100331.1  SWI/SNF complex subunit SMARCC1

    See identical proteins and their annotated locations for NP_001100331.1

    Status: PROVISIONAL

    Source sequence(s)
    CH473954
    UniProtKB/TrEMBL
    D3ZJU5
    Related
    ENSRNOP00000060434.1, ENSRNOT00000064140.1
    Conserved Domains (5) summary
    COG5259
    Location:443709
    RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
    pfam04433
    Location:451536
    SWIRM; SWIRM domain
    pfam16495
    Location:882953
    SWIRM-assoc_1; SWIRM-associated region 1
    pfam16496
    Location:31444
    SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
    pfam16498
    Location:705769
    SWIRM-assoc_3; SWIRM-associated domain at the C-terminal

RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

Reference Rnor_6.0 Primary Assembly

Genomic

  1. NC_005107.4 Reference Rnor_6.0 Primary Assembly

    Range
    118206678..118326264
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006243770.3XP_006243832.1  SWI/SNF complex subunit SMARCC1 isoform X1

    See identical proteins and their annotated locations for XP_006243832.1

    Conserved Domains (5) summary
    COG5259
    Location:443709
    RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
    pfam04433
    Location:451536
    SWIRM; SWIRM domain
    pfam16495
    Location:882953
    SWIRM-assoc_1; SWIRM-associated region 1
    pfam16496
    Location:31444
    SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
    pfam16498
    Location:705769
    SWIRM-assoc_3; SWIRM-associated domain at the C-terminal
  2. XM_006243772.3XP_006243834.1  SWI/SNF complex subunit SMARCC1 isoform X3

    Conserved Domains (5) summary
    COG5259
    Location:443709
    RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
    pfam04433
    Location:451536
    SWIRM; SWIRM domain
    pfam16495
    Location:882953
    SWIRM-assoc_1; SWIRM-associated region 1
    pfam16496
    Location:31444
    SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
    pfam16498
    Location:705769
    SWIRM-assoc_3; SWIRM-associated domain at the C-terminal
  3. XM_006243771.3XP_006243833.1  SWI/SNF complex subunit SMARCC1 isoform X2

    UniProtKB/TrEMBL
    A0A0G2K9D6
    Related
    ENSRNOP00000074957.1, ENSRNOT00000082607.1
    Conserved Domains (5) summary
    COG5259
    Location:443709
    RSC8; RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
    pfam04433
    Location:451536
    SWIRM; SWIRM domain
    pfam16495
    Location:882953
    SWIRM-assoc_1; SWIRM-associated region 1
    pfam16496
    Location:31444
    SWIRM-assoc_2; SWIRM-associated domain at the N-terminal
    pfam16498
    Location:705769
    SWIRM-assoc_3; SWIRM-associated domain at the C-terminal

Alternate Rn_Celera

Genomic

  1. AC_000076.1 Alternate Rn_Celera

    Range
    109398958..109497187
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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