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Carf calcium responsive transcription factor [ Rattus norvegicus (Norway rat) ]

Gene ID: 301446, updated on 5-Mar-2024

Summary

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Official Symbol
Carfprovided by RGD
Official Full Name
calcium responsive transcription factorprovided by RGD
Primary source
RGD:1306822
See related
Ensembl:ENSRNOG00000017491 AllianceGenome:RGD:1306822
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
Also known as
Als2cr8
Summary
Enables DNA binding activity and DNA-binding transcription factor activity. Involved in positive regulation of transcription from RNA polymerase II promoter in response to calcium ion. Located in nucleus. Orthologous to human CARF (calcium responsive transcription factor). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Kidney (RPKM 50.4), Brain (RPKM 47.6) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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Location:
9q32
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (68996419..69046480)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (61502368..61552433)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (66878526..66928658)

Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 117, member B Neighboring gene uncharacterized LOC120094801 Neighboring gene islet cell autoantigen 1-like Neighboring gene WD repeat domain 12 Neighboring gene basic proline-rich protein-like Neighboring gene neurobeachin-like 1 Neighboring gene peptidyl-prolyl cis-trans isomerase NIMA-interacting 4-like Neighboring gene ATP synthase membrane subunit c locus 2, pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Regulation of brain-derived neurotrophic factor exon IV transcription through calcium responsive elements in cortical neurons. Zheng F, et al. PLoS One, 2011. PMID 22174809, Free PMC Article
  2. A calcium-responsive transcription factor, CaRF, that regulates neuronal activity-dependent expression of BDNF. Tao X, et al. Neuron, 2002 Jan 31. PMID 11832226
  3. CARF is a novel protein that cooperates with mouse p19ARF (human p14ARF) in activating p53. Hasan MK, et al. J Biol Chem, 2002 Oct 4. PMID 12154087
  4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription activator activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in cellular response to calcium ion IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to calcium ion IEA
Inferred from Electronic Annotation
more info
  
involved_in cellular response to calcium ion ISO
Inferred from Sequence Orthology
more info
  
involved_in cellular response to calcium ion ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in granular component IEA
Inferred from Electronic Annotation
more info
  
located_in granular component ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
calcium-responsive transcription factor
Names
amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 8
amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8 protein
calcium-response factor

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_001106915.1 → NP_001100385.1  calcium-responsive transcription factor

    See identical proteins and their annotated locations for NP_001100385.1

    Status: PROVISIONAL

    Source sequence(s)
    CH473965
    UniProtKB/Swiss-Prot
    D4A7U2
    Related
    ENSRNOP00000023536.4, ENSRNOT00000023536.7
    Conserved Domains (1) summary
    pfam15299
    Location:119 → 349
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086027.1 Reference GRCr8

    Range
    68996419..69046480
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039083318.2 → XP_038939246.1  calcium-responsive transcription factor isoform X2

    Conserved Domains (1) summary
    pfam15299
    Location:316 → 543
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  2. XM_006244971.4 → XP_006245033.2  calcium-responsive transcription factor isoform X1

    Conserved Domains (1) summary
    pfam15299
    Location:316 → 543
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  3. XM_039083319.2 → XP_038939247.1  calcium-responsive transcription factor isoform X3

    UniProtKB/TrEMBL
    A0A0G2K3E6
    Conserved Domains (1) summary
    pfam15299
    Location:203 → 430
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  4. XM_006244974.5 → XP_006245036.1  calcium-responsive transcription factor isoform X5

    Conserved Domains (1) summary
    pfam15299
    Location:231 → 461
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  5. XM_039083321.2 → XP_038939249.1  calcium-responsive transcription factor isoform X4

    Conserved Domains (1) summary
    pfam15299
    Location:1 → 197
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  6. XM_039083320.2 → XP_038939248.1  calcium-responsive transcription factor isoform X4

    Conserved Domains (1) summary
    pfam15299
    Location:1 → 197
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  7. XM_017596367.3 → XP_017451856.1  calcium-responsive transcription factor isoform X4

    Conserved Domains (1) summary
    pfam15299
    Location:1 → 197
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
D4A7U2.1 GenPept UniProtKB/Swiss-Prot:D4A7U2

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