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    CARF calcium responsive transcription factor [ Homo sapiens (human) ]

    Gene ID: 79800, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CARFprovided by HGNC
    Official Full Name
    calcium responsive transcription factorprovided by HGNC
    Primary source
    HGNC:HGNC:14435
    See related
    Ensembl:ENSG00000138380 MIM:607586; AllianceGenome:HGNC:14435
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ALS2CR8; NYD-SP24
    Summary
    Enables DNA binding activity and DNA-binding transcription activator activity, RNA polymerase II-specific. Involved in cellular response to calcium ion. Predicted to be located in granular component. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in testis (RPKM 5.9), thyroid (RPKM 3.4) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CARF in Genome Data Viewer
    Location:
    2q33.2
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (202912275..202988263)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (203393728..203469790)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (203776998..203852986)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene islet cell autoantigen 1 like Neighboring gene keratin 8 pseudogene 15 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12249 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12250 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17005 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17006 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17007 Neighboring gene WD repeat domain 12 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:203790595-203791095 Neighboring gene keratin 8 pseudogene 52 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17008 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:203853358-203853583 Neighboring gene chromosome 18 open reading frame 32 pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:203879278-203879831 Neighboring gene Sharpr-MPRA regulatory region 6032 Neighboring gene neurobeachin like 1 Neighboring gene ribosomal protein L7 pseudogene 14

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Inhibition of MicroRNA-302c on Stemness of Colon Cancer Stem Cells via the CARF/Wnt/β-Catenin Axis. Zhang Y, et al. Dig Dis Sci, 2021 Jun. PMID 32617772
    2. Molecular Insights Into Withaferin-A-Induced Senescence: Bioinformatics and Experimental Evidence to the Role of NFκB and CARF. Bhargava P, et al. J Gerontol A Biol Sci Med Sci, 2019 Jan 16. PMID 29718136
    3. Tumor suppressor activity of miR-451: Identification of CARF as a new target. Li L, et al. Sci Rep, 2018 Jan 10. PMID 29321561, Free PMC Article
    4. 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
    5. A calcium-responsive transcription factor, CaRF, that regulates neuronal activity-dependent expression of BDNF. Tao X, et al. Neuron, 2002 Jan 31. PMID 11832226

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Inhibition of MicroRNA-302c on Stemness of Colon Cancer Stem Cells via the CARF/Wnt/beta-Catenin Axis.
      Title: Inhibition of MicroRNA-302c on Stemness of Colon Cancer Stem Cells via the CARF/Wnt/β-Catenin Axis.
    2. Wi-A caused upregulation of CARF (collaborator of ARF) demonstrating an activation of DNA damage oxidative stress response in both cancer and normal cells. In line with this, upregulation of p21WAF1, p16INK4A, and hypophosphorylated pRB and induction of senescence were observed demonstrating that Wi-A-induced senescence is mediated by multiple pathways in which CARF-mediated DNA damage and oxidative stress play a major ro
      Title: Molecular Insights Into Withaferin-A-Induced Senescence: Bioinformatics and Experimental Evidence to the Role of NFκB and CARF.
    3. Data demonstrate that CARF is a new target of miR-451 that mediates its tumor suppressor function in normal and stressed biological states.
      Title: Tumor suppressor activity of miR-451: Identification of CARF as a new target.
    4. 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

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ12675, FLJ21579, DKFZp667N246

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cellular response to calcium ion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    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
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    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
    testis development protein NYD-SP24

    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_001104586.4 → NP_001098056.1  calcium-responsive transcription factor isoform 1

      See identical proteins and their annotated locations for NP_001098056.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1). Variants 1, 2, 6 and 7 encode the same isoform (1).
      Source sequence(s)
      AC010900, AF454946, BC021999
      Consensus CDS
      CCDS42801.1
      UniProtKB/Swiss-Prot
      B4E1W7, G3V1K7, Q8N187, Q8ND29, Q8WXC0, Q96J78, Q96Q38, Q96Q39, Q9H712
      UniProtKB/TrEMBL
      B7ZAW7
      Related
      ENSP00000384006.2, ENST00000402905.7
      Conserved Domains (1) summary
      pfam15299
      Location:253 → 483
      ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

    2. NM_001282910.3 → NP_001269839.1  calcium-responsive transcription factor isoform 2

      See identical proteins and their annotated locations for NP_001269839.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon in the coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1. Variants 3 and 4 encode the same isoform (2).
      Source sequence(s)
      AC010900, BC021999
      Consensus CDS
      CCDS63091.1
      UniProtKB/TrEMBL
      B7ZAW7
      Related
      ENSP00000396221.1, ENST00000428585.5
      Conserved Domains (1) summary
      pfam15299
      Location:177 → 407
      ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

    3. NM_001282911.3 → NP_001269840.1  calcium-responsive transcription factor isoform 2

      See identical proteins and their annotated locations for NP_001269840.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) has an additional exon in the 5' UTR and lacks an in-frame exon in the coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1. Variants 3 and 4 encode the same isoform (2).
      Source sequence(s)
      AC010900, AF454946, AK316432, BC021999
      Consensus CDS
      CCDS63091.1
      UniProtKB/TrEMBL
      B7ZAW7
      Related
      ENSP00000316224.9, ENST00000320443.12
      Conserved Domains (1) summary
      pfam15299
      Location:177 → 407
      ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

    4. NM_001282912.3 → NP_001269841.1  calcium-responsive transcription factor isoform 3

      See identical proteins and their annotated locations for NP_001269841.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks two consecutive internal exons, which results in an alternate upstream start codon, compared to variant 1. The resulting isoform (3) is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AC010900, AF454946, AK295499, BC021999
      UniProtKB/TrEMBL
      B4DIA7, B7ZAW7
      Related
      ENSP00000416160.1, ENST00000414439.5
      Conserved Domains (1) summary
      pfam15299
      Location:165 → 395
      ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

    5. NM_001322427.3 → NP_001309356.1  calcium-responsive transcription factor isoform 1

      Status: VALIDATED

      Source sequence(s)
      AB053309, AB053310, AC010900, AY032876, BC021999
      Consensus CDS
      CCDS42801.1
      UniProtKB/Swiss-Prot
      B4E1W7, G3V1K7, Q8N187, Q8ND29, Q8WXC0, Q96J78, Q96Q38, Q96Q39, Q9H712
      UniProtKB/TrEMBL
      B7ZAW7
      Conserved Domains (1) summary
      pfam15299
      Location:253 → 483
      ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

    6. NM_001322428.3 → NP_001309357.1  calcium-responsive transcription factor isoform 1

      Status: VALIDATED

      Source sequence(s)
      AB053309, AC010900, AK316432, AY032876
      Consensus CDS
      CCDS42801.1
      UniProtKB/Swiss-Prot
      B4E1W7, G3V1K7, Q8N187, Q8ND29, Q8WXC0, Q96J78, Q96Q38, Q96Q39, Q9H712
      UniProtKB/TrEMBL
      B7ZAW7
      Conserved Domains (1) summary
      pfam15299
      Location:253 → 483
      ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

    7. NM_001322429.3 → NP_001309358.1  calcium-responsive transcription factor isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC010900, AK295499, AL834188, AY032876
      UniProtKB/TrEMBL
      B7ZAW7
      Conserved Domains (1) summary
      pfam15299
      Location:241 → 471
      ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

    8. NM_001352676.2 → NP_001339605.1  calcium-responsive transcription factor isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC010900
      UniProtKB/TrEMBL
      B7ZAW7
      Conserved Domains (1) summary
      pfam15299
      Location:67 → 297
      ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

    9. NM_001352677.2 → NP_001339606.1  calcium-responsive transcription factor isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC010900
      Conserved Domains (1) summary
      pfam15299
      Location:151 → 381
      ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

    10. NM_001352678.2 → NP_001339607.1  calcium-responsive transcription factor isoform 8

      Status: VALIDATED

      Source sequence(s)
      AC010900
      Conserved Domains (1) summary
      pfam15299
      Location:1 → 139
      ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

    11. NM_001352679.2 → NP_001339608.1  calcium-responsive transcription factor isoform 8

      Status: VALIDATED

      Source sequence(s)
      AC010900
      Conserved Domains (1) summary
      pfam15299
      Location:1 → 139
      ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

    12. NM_024744.17 → NP_079020.13  calcium-responsive transcription factor isoform 1

      See identical proteins and their annotated locations for NP_079020.13

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has an alternate splice site and an additional exon in the 5' UTR, compared to variant 1. Variants 1, 2, 6 and 7 encode the same isoform (1).
      Source sequence(s)
      AB053309, AC010900, BC021999, DA405623
      Consensus CDS
      CCDS42801.1
      UniProtKB/Swiss-Prot
      B4E1W7, G3V1K7, Q8N187, Q8ND29, Q8WXC0, Q96J78, Q96Q38, Q96Q39, Q9H712
      UniProtKB/TrEMBL
      B7ZAW7
      Related
      ENSP00000414644.1, ENST00000438828.4
      Conserved Domains (1) summary
      pfam15299
      Location:253 → 483
      ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

    RNA

    1. NR_136330.3 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC010900, AL834188, AY032876

    2. NR_136331.3 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AB053309, AC010900, AK299366, AY032876, BC021999

    3. NR_148033.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC010900

    4. NR_148034.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC010900

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      202912275..202988263
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047445855.1 → XP_047301811.1  calcium-responsive transcription factor isoform X1

      Related
      ENSP00000392274.1, ENST00000422368.5

    2. XM_047445856.1 → XP_047301812.1  calcium-responsive transcription factor isoform X2

    RNA

    1. XR_007081622.1 RNA Sequence

    2. XR_007081643.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      203393728..203469790
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054343966.1 → XP_054199941.1  calcium-responsive transcription factor isoform X3

      UniProtKB/Swiss-Prot
      B4E1W7, G3V1K7, Q8N187, Q8ND29, Q8WXC0, Q96J78, Q96Q38, Q96Q39, Q9H712

    2. XM_054343965.1 → XP_054199940.1  calcium-responsive transcription factor isoform X3

      UniProtKB/Swiss-Prot
      B4E1W7, G3V1K7, Q8N187, Q8ND29, Q8WXC0, Q96J78, Q96Q38, Q96Q39, Q9H712

    3. XM_054343977.1 → XP_054199952.1  calcium-responsive transcription factor isoform X9

    4. XM_054343973.1 → XP_054199948.1  calcium-responsive transcription factor isoform X6

    5. XM_054343967.1 → XP_054199942.1  calcium-responsive transcription factor isoform X3

      UniProtKB/Swiss-Prot
      B4E1W7, G3V1K7, Q8N187, Q8ND29, Q8WXC0, Q96J78, Q96Q38, Q96Q39, Q9H712

    6. XM_054343963.1 → XP_054199938.1  calcium-responsive transcription factor isoform X3

      UniProtKB/Swiss-Prot
      B4E1W7, G3V1K7, Q8N187, Q8ND29, Q8WXC0, Q96J78, Q96Q38, Q96Q39, Q9H712

    7. XM_054343969.1 → XP_054199944.1  calcium-responsive transcription factor isoform X3

      UniProtKB/Swiss-Prot
      B4E1W7, G3V1K7, Q8N187, Q8ND29, Q8WXC0, Q96J78, Q96Q38, Q96Q39, Q9H712

    8. XM_054343964.1 → XP_054199939.1  calcium-responsive transcription factor isoform X3

      UniProtKB/Swiss-Prot
      B4E1W7, G3V1K7, Q8N187, Q8ND29, Q8WXC0, Q96J78, Q96Q38, Q96Q39, Q9H712

    9. XM_054343971.1 → XP_054199946.1  calcium-responsive transcription factor isoform X4

    10. XM_054343978.1 → XP_054199953.1  calcium-responsive transcription factor isoform X10

    11. XM_054343974.1 → XP_054199949.1  calcium-responsive transcription factor isoform X7

      UniProtKB/TrEMBL
      B4DIA7

    12. XM_054343968.1 → XP_054199943.1  calcium-responsive transcription factor isoform X3

      UniProtKB/Swiss-Prot
      B4E1W7, G3V1K7, Q8N187, Q8ND29, Q8WXC0, Q96J78, Q96Q38, Q96Q39, Q9H712

    13. XM_054343970.1 → XP_054199945.1  calcium-responsive transcription factor isoform X4

    14. XM_054343980.1 → XP_054199955.1  calcium-responsive transcription factor isoform X1

    15. XM_054343983.1 → XP_054199958.1  calcium-responsive transcription factor isoform X2

    16. XM_054343962.1 → XP_054199937.1  calcium-responsive transcription factor isoform X3

      UniProtKB/Swiss-Prot
      B4E1W7, G3V1K7, Q8N187, Q8ND29, Q8WXC0, Q96J78, Q96Q38, Q96Q39, Q9H712

    17. XM_054343972.1 → XP_054199947.1  calcium-responsive transcription factor isoform X5

    18. XM_054343975.1 → XP_054199950.1  calcium-responsive transcription factor isoform X8

      UniProtKB/TrEMBL
      C9JI92

    19. XM_054343979.1 → XP_054199954.1  calcium-responsive transcription factor isoform X11

    20. XM_054343976.1 → XP_054199951.1  calcium-responsive transcription factor isoform X8

      UniProtKB/TrEMBL
      C9JI92

    21. XM_054343982.1 → XP_054199957.1  calcium-responsive transcription factor isoform X12

    22. XM_054343981.1 → XP_054199956.1  calcium-responsive transcription factor isoform X12

    RNA

    1. XR_008486520.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001322430.1: Suppressed sequence

      Description
      NM_001322430.1: This RefSeq was removed because currently there is support for the transcript but not for the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N187.2 GenPept UniProtKB/Swiss-Prot:Q8N187

    Gene LinkOut

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

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