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

Gene ID: 79800, updated on 12-Aug-2022

Summary

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 factor activity. Involved in cellular response to potassium ion and positive regulation of transcription from RNA polymerase II promoter in response to calcium ion. Predicted to be located in granular component. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis (RPKM 5.9), thyroid (RPKM 3.4) and 24 other tissues See more
Orthologs
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Genomic context

See CARF in Genome Data Viewer
Location:
2q33.2
Exon count:
20
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (202912275..202988263)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (203393728..203469790)
105.20220307 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 WD repeat domain 12 Neighboring gene keratin 8 pseudogene 52 Neighboring gene chromosome 18 open reading frame 32 pseudogene Neighboring gene Sharpr-MPRA regulatory region 6032 Neighboring gene neurobeachin like 1

Genomic regions, transcripts, and products

Expression

  • Project title: 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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ12675, FLJ21579, DKFZp667N246

Gene Ontology Provided by GOA

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
PubMed 
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

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_001104586.4NP_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
    Q8N187, Q9H712
    UniProtKB/TrEMBL
    A0A024R405, A0A024R427
    Related
    ENSP00000384006.2, ENST00000402905.7
    Conserved Domains (1) summary
    pfam15299
    Location:253483
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
  2. NM_001282910.3NP_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/Swiss-Prot
    Q8N187
    Related
    ENSP00000396221.1, ENST00000428585.5
    Conserved Domains (1) summary
    pfam15299
    Location:177407
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
  3. NM_001282911.3NP_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/Swiss-Prot
    Q8N187
    Related
    ENSP00000316224.9, ENST00000320443.12
    Conserved Domains (1) summary
    pfam15299
    Location:177407
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
  4. NM_001282912.3NP_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
    Related
    ENSP00000416160.1, ENST00000414439.5
    Conserved Domains (1) summary
    pfam15299
    Location:165395
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
  5. NM_001322427.3NP_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
    Q8N187, Q9H712
    UniProtKB/TrEMBL
    A0A024R405, A0A024R427
    Conserved Domains (1) summary
    pfam15299
    Location:253483
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
  6. NM_001322428.3NP_001309357.1  calcium-responsive transcription factor isoform 1

    Status: VALIDATED

    Source sequence(s)
    AB053309, AC010900, AK316432, AY032876
    Consensus CDS
    CCDS42801.1
    UniProtKB/Swiss-Prot
    Q8N187, Q9H712
    UniProtKB/TrEMBL
    A0A024R405, A0A024R427
    Conserved Domains (1) summary
    pfam15299
    Location:253483
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
  7. NM_001322429.3NP_001309358.1  calcium-responsive transcription factor isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC010900, AK295499, AL834188, AY032876
    Conserved Domains (1) summary
    pfam15299
    Location:241471
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
  8. NM_001352676.2NP_001339605.1  calcium-responsive transcription factor isoform 6

    Status: VALIDATED

    Source sequence(s)
    AC010900
    Conserved Domains (1) summary
    pfam15299
    Location:67297
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
  9. NM_001352677.2NP_001339606.1  calcium-responsive transcription factor isoform 7

    Status: VALIDATED

    Source sequence(s)
    AC010900
    Conserved Domains (1) summary
    pfam15299
    Location:151381
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
  10. NM_001352678.2NP_001339607.1  calcium-responsive transcription factor isoform 8

    Status: VALIDATED

    Source sequence(s)
    AC010900
    Conserved Domains (1) summary
    pfam15299
    Location:1139
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
  11. NM_001352679.2NP_001339608.1  calcium-responsive transcription factor isoform 8

    Status: VALIDATED

    Source sequence(s)
    AC010900
    Conserved Domains (1) summary
    pfam15299
    Location:1139
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
  12. NM_024744.17NP_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
    Q8N187, Q9H712
    UniProtKB/TrEMBL
    A0A024R405, A0A024R427
    Related
    ENSP00000414644.1, ENST00000438828.4
    Conserved Domains (1) summary
    pfam15299
    Location:253483
    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: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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_047445855.1XP_047301811.1  calcium-responsive transcription factor isoform X1

    Related
    ENSP00000392274.1, ENST00000422368.5
  2. XM_047445856.1XP_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)

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.