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Carf calcium response factor [ Mus musculus (house mouse) ]

Gene ID: 241066, updated on 5-Mar-2024

Summary

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Official Symbol
Carfprovided by MGI
Official Full Name
calcium response factorprovided by MGI
Primary source
MGI:MGI:2182269
See related
Ensembl:ENSMUSG00000026017 AllianceGenome:MGI:2182269
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
Als2cr8; ECBRC-FC1; ECBRC-FC2
Summary
Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Acts upstream of or within regulation of DNA-binding transcription factor activity. Located in granular component. Is expressed in several structures, including central nervous system; eye; genitourinary system; gut; and skeletal muscle tissue. Orthologous to human CARF (calcium responsive transcription factor). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis adult (RPKM 2.5), CNS E18 (RPKM 1.9) and 25 other tissues See more
Orthologs
human all
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Genomic context

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Location:
1 C2; 1 30.45 cM
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (60137380..60193112)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (60098221..60153953)

Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 117, member B Neighboring gene arginyl-tRNA synthetase 2, mitochondrial pseudogene Neighboring gene STARR-positive B cell enhancer mm9_chr1:60073097-60073398 Neighboring gene islet cell autoantigen 1-like Neighboring gene STARR-seq mESC enhancer starr_01058 Neighboring gene STARR-seq mESC enhancer starr_01059 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:60154934-60155145 Neighboring gene WD repeat domain 12 Neighboring gene predicted gene 15464 Neighboring gene STARR-seq mESC enhancer starr_01061 Neighboring gene neurobeachin like 1 Neighboring gene STARR-positive B cell enhancer mm9_chr1:60297214-60297515 Neighboring gene STARR-seq mESC enhancer starr_01062 Neighboring gene STARR-seq mESC enhancer starr_01063 Neighboring gene protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting, 4 (parvulin) pseudogene Neighboring gene STARR-seq mESC enhancer starr_01064 Neighboring gene STARR-seq mESC enhancer starr_01065 Neighboring gene cytochrome P450, family 20, subfamily a, polypeptide 1

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
  • 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. The transcription factor calcium-response factor limits NMDA receptor-dependent transcription in the developing brain. Lyons MR, et al. J Neurochem, 2016 Apr. PMID 26826701, Free PMC Article
  2. Acquisition of response thresholds for timed performance is regulated by a calcium-responsive transcription factor, CaRF. Agostino PV, et al. Genes Brain Behav, 2013 Aug. PMID 23848551
  3. Genome-wide identification of calcium-response factor (CaRF) binding sites predicts a role in regulation of neuronal signaling pathways. Pfenning AR, et al. PLoS One, 2010 May 27. PMID 20523734, Free PMC Article
  4. A calcium-responsive transcription factor, CaRF, that regulates neuronal activity-dependent expression of BDNF. Tao X, et al. Neuron, 2002 Jan 31. PMID 11832226
  5. CARF: an emerging regulator of p53 tumor suppressor and senescence pathway. Cheung CT, et al. Mech Ageing Dev, 2009 Jan-Feb. PMID 18555516

See all (25) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. This report that loss of CaRF leads to enhanced NMDAR-dependent induction of both Bdnf IV and the activity-regulated gene Arc, and we investigate potential mechanisms as well as biological consequences of this change in transcriptional regulation.
    Title: The transcription factor calcium-response factor limits NMDA receptor-dependent transcription in the developing brain.
  2. Carf(+/-) and Carf(-/-) mice were impaired in their ability to acquire timed response thresholds relative to Carf(+/+) mice.
    Title: Acquisition of response thresholds for timed performance is regulated by a calcium-responsive transcription factor, CaRF.
  3. These data strongly support the characterization of CaRF as a unique transcription factor and provide the first insight into the program of CaRF-regulated transcription in neurons.
    Title: Genome-wide identification of calcium-response factor (CaRF) binding sites predicts a role in regulation of neuronal signaling pathways.
  4. the data of this study reveal novel roles for CaRF in the organization and/or function of neural circuits that underlie essential aspects of learning and memory.
    Title: Reduced cortical BDNF expression and aberrant memory in Carf knock-out mice.
  5. Cloned as a calcium- and neural-selective transcriptional activator of the gene for Brain-Derived Neurotrophic Factor (BDNF).
    Title: A calcium-responsive transcription factor, CaRF, that regulates neuronal activity-dependent expression of BDNF.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
  
enables DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
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 IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cellular response to calcium ion ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within regulation of DNA-binding transcription factor activity IGI
Inferred from Genetic Interaction
more info
 PubMed 
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 IDA
Inferred from Direct Assay
more info
 PubMed 
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 chromosomal region candidate gene 8 protein homolog
calcium-response factor CaRF

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_001285463.1 → NP_001272392.1  calcium-responsive transcription factor isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has multiple differences compared to variant 1. These differences result in a distinct 5' UTR and cause translation initiation at an alternate start codon compared to variant 1. The encoded protein (isoform 2) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AC116581, AC138597, AK044738, BF456537
    Conserved Domains (1) summary
    pfam15299
    Location:108 → 338
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  2. NM_001285473.1 → NP_001272402.1  calcium-responsive transcription factor isoform 3

    See identical proteins and their annotated locations for NP_001272402.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) has a shorter 5' UTR and uses an alternate in-frame splice site in the 5' coding region compared to variant 1. The encoded protein (isoform 3) is shorter than isoform 1.
    Source sequence(s)
    AC138597, AF454947, BF456537, EU170502
    Consensus CDS
    CCDS78592.1
    UniProtKB/TrEMBL
    A8VI08
    Related
    ENSMUSP00000027171.6, ENSMUST00000027171.12
    Conserved Domains (1) summary
    pfam15299
    Location:192 → 419
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  3. NM_139150.5 → NP_631889.1  calcium-responsive transcription factor isoform 1

    See identical proteins and their annotated locations for NP_631889.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC138597, AF454947, AK044738, BF456537
    Consensus CDS
    CCDS14989.1
    UniProtKB/Swiss-Prot
    B2RRZ9, Q8VHI4
    Related
    ENSMUSP00000141169.2, ENSMUST00000187978.7
    Conserved Domains (1) summary
    pfam15299
    Location:227 → 454
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

RNA

  1. NR_104344.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) has multiple differences compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC138597, AF454947, BF456537, EU170503

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_000067.7 Reference GRCm39 C57BL/6J

    Range
    60137380..60193112
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030254084.1 → XP_030109944.1  calcium-responsive transcription factor isoform X1

    UniProtKB/Swiss-Prot
    B2RRZ9, Q8VHI4
    Conserved Domains (1) summary
    pfam15299
    Location:227 → 454
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  2. XM_006495975.2 → XP_006496038.1  calcium-responsive transcription factor isoform X3

    See identical proteins and their annotated locations for XP_006496038.1

    UniProtKB/TrEMBL
    A8VI08
    Conserved Domains (1) summary
    pfam15299
    Location:192 → 419
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  3. XM_036164953.1 → XP_036020846.1  calcium-responsive transcription factor isoform X2

    Conserved Domains (1) summary
    pfam15299
    Location:198 → 425
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  4. XM_036164965.1 → XP_036020858.1  calcium-responsive transcription factor isoform X5

    Conserved Domains (1) summary
    pfam15299
    Location:166 → 393
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  5. XM_036164962.1 → XP_036020855.1  calcium-responsive transcription factor isoform X4

    Conserved Domains (1) summary
    pfam15299
    Location:227 → 406
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  6. XM_017320602.1 → XP_017176091.1  calcium-responsive transcription factor isoform X3

    UniProtKB/TrEMBL
    A8VI08
    Conserved Domains (1) summary
    pfam15299
    Location:192 → 419
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  7. XM_030254087.1 → XP_030109947.1  calcium-responsive transcription factor isoform X2

    Conserved Domains (1) summary
    pfam15299
    Location:198 → 425
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  8. XM_036164967.1 → XP_036020860.1  calcium-responsive transcription factor isoform X6

    Conserved Domains (1) summary
    pfam15299
    Location:11 → 128
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  9. XM_006495977.2 → XP_006496040.1  calcium-responsive transcription factor isoform X5

    See identical proteins and their annotated locations for XP_006496040.1

    Conserved Domains (1) summary
    pfam15299
    Location:166 → 393
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  10. XM_036164947.1 → XP_036020840.1  calcium-responsive transcription factor isoform X1

    UniProtKB/Swiss-Prot
    B2RRZ9, Q8VHI4
    Conserved Domains (1) summary
    pfam15299
    Location:227 → 454
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  11. XM_006495974.2 → XP_006496037.1  calcium-responsive transcription factor isoform X3

    See identical proteins and their annotated locations for XP_006496037.1

    UniProtKB/TrEMBL
    A8VI08
    Conserved Domains (1) summary
    pfam15299
    Location:192 → 419
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  12. XM_017320598.3 → XP_017176087.1  calcium-responsive transcription factor isoform X2

    Conserved Domains (1) summary
    pfam15299
    Location:198 → 425
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  13. XM_036164963.1 → XP_036020856.1  calcium-responsive transcription factor isoform X5

    Conserved Domains (1) summary
    pfam15299
    Location:166 → 393
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  14. XM_011238510.1 → XP_011236812.1  calcium-responsive transcription factor isoform X1

    See identical proteins and their annotated locations for XP_011236812.1

    UniProtKB/Swiss-Prot
    B2RRZ9, Q8VHI4
    Conserved Domains (1) summary
    pfam15299
    Location:227 → 454
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  15. XM_036164961.1 → XP_036020854.1  calcium-responsive transcription factor isoform X4

    Conserved Domains (1) summary
    pfam15299
    Location:227 → 406
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  16. XM_036164954.1 → XP_036020847.1  calcium-responsive transcription factor isoform X3

    UniProtKB/TrEMBL
    A8VI08
    Conserved Domains (1) summary
    pfam15299
    Location:192 → 419
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  17. XM_036164949.1 → XP_036020842.1  calcium-responsive transcription factor isoform X2

    Conserved Domains (1) summary
    pfam15299
    Location:198 → 425
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

  18. XM_036164966.1 → XP_036020859.1  calcium-responsive transcription factor isoform X5

    Conserved Domains (1) summary
    pfam15299
    Location:166 → 393
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

RNA

  1. XR_001784597.3 RNA Sequence

  2. XR_004942477.1 RNA Sequence

  3. XR_004942486.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8VHI4.1 GenPept UniProtKB/Swiss-Prot:Q8VHI4

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