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

    Gene ID: 241066, updated on 27-Nov-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, Nov 2024]
    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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    See Carf in Genome Data Viewer
    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 (26) 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 ISS
    Inferred from Sequence or Structural Similarity
    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, 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 cellular response to calcium ion ISS
    Inferred from Sequence or Structural Similarity
    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_001285463.2 → NP_001272392.1  calcium-responsive transcription factor isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC116581, AC138597
      Conserved Domains (1) summary
      pfam15299
      Location:108 → 338
      ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

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

      See identical proteins and their annotated locations for NP_001272402.1

      Status: VALIDATED

      Source sequence(s)
      AC116581, AC138597
      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_001431923.1 → NP_001418852.1  calcium-responsive transcription factor isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC116581, AC138597

    4. NM_001431924.1 → NP_001418853.1  calcium-responsive transcription factor isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC116581, AC138597

    5. NM_001431925.1 → NP_001418854.1  calcium-responsive transcription factor isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC116581, AC138597
      UniProtKB/TrEMBL
      A8VI08

    6. NM_001431926.1 → NP_001418855.1  calcium-responsive transcription factor isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC116581, AC138597
      UniProtKB/TrEMBL
      A8VI08

    7. NM_001431927.1 → NP_001418856.1  calcium-responsive transcription factor isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC116581, AC138597

    8. NM_001431928.1 → NP_001418857.1  calcium-responsive transcription factor isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC116581, AC138597

    9. NM_139150.6 → NP_631889.1  calcium-responsive transcription factor isoform 1

      See identical proteins and their annotated locations for NP_631889.1

      Status: VALIDATED

      Source sequence(s)
      AC116581, AC138597
      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_104344.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC116581, AC138597

    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

      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

      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

      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

      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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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