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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

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