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

Gene ID: 79800, updated on 13-Mar-2020

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
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
Expression
Broad expression in testis (RPKM 5.9), thyroid (RPKM 3.4) and 24 other tissues See more
Orthologs

Genomic context

See CARF in Genome Data Viewer
Location:
2q33.2
Exon count:
24
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (202912218..202988263)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (203776978..203851060)

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 neurobeachin like 1 Neighboring gene ribosomal protein L7 pseudogene 14

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

Function Evidence Code Pubs
DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription activator activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
granular component IEA
Inferred from Electronic Annotation
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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)

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
    UniProtKB/TrEMBL
    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_001282911.2NP_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
    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
    UniProtKB/TrEMBL
    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
    UniProtKB/TrEMBL
    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
    UniProtKB/TrEMBL
    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 Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    202912218..202988263
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017004963.2XP_016860452.1  calcium-responsive transcription factor isoform X3

    UniProtKB/TrEMBL
    B4DIA7
    Conserved Domains (1) summary
    pfam15299
    Location:165395
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
  2. XM_005246859.3XP_005246916.1  calcium-responsive transcription factor isoform X1

    See identical proteins and their annotated locations for XP_005246916.1

    UniProtKB/Swiss-Prot
    Q8N187
    UniProtKB/TrEMBL
    A0A024R427
    Conserved Domains (1) summary
    pfam15299
    Location:253483
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
  3. XM_011511867.2XP_011510169.1  calcium-responsive transcription factor isoform X1

    See identical proteins and their annotated locations for XP_011510169.1

    UniProtKB/Swiss-Prot
    Q8N187
    UniProtKB/TrEMBL
    A0A024R427
    Conserved Domains (1) summary
    pfam15299
    Location:253483
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
  4. XM_011511868.3XP_011510170.1  calcium-responsive transcription factor isoform X5

    Conserved Domains (1) summary
    pfam15299
    Location:253483
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
  5. XM_006712760.3XP_006712823.1  calcium-responsive transcription factor isoform X8

    Conserved Domains (1) summary
    pfam15299
    Location:253366
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
  6. XM_005246858.3XP_005246915.1  calcium-responsive transcription factor isoform X1

    See identical proteins and their annotated locations for XP_005246915.1

    UniProtKB/Swiss-Prot
    Q8N187
    UniProtKB/TrEMBL
    A0A024R427
    Conserved Domains (1) summary
    pfam15299
    Location:253483
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
  7. XM_024453151.1XP_024308919.1  calcium-responsive transcription factor isoform X9

    Conserved Domains (1) summary
    pfam15299
    Location:1139
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
  8. XM_024453150.1XP_024308918.1  calcium-responsive transcription factor isoform X7

    Conserved Domains (1) summary
    pfam15299
    Location:1200
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
  9. XM_017004962.1XP_016860451.1  calcium-responsive transcription factor isoform X2

    Conserved Domains (1) summary
    pfam15299
    Location:223453
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
  10. XM_017004964.1XP_016860453.1  calcium-responsive transcription factor isoform X4

    UniProtKB/TrEMBL
    C9JI92
  11. XM_017004966.1XP_016860455.1  calcium-responsive transcription factor isoform X6

    Conserved Domains (1) summary
    pfam15299
    Location:151381
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
  12. XM_017004965.2XP_016860454.1  calcium-responsive transcription factor isoform X4

    UniProtKB/TrEMBL
    C9JI92
    Related
    ENSP00000416160.1, ENST00000414439.5
  13. XM_011511869.3XP_011510171.1  calcium-responsive transcription factor isoform X7

    See identical proteins and their annotated locations for XP_011510171.1

    Conserved Domains (1) summary
    pfam15299
    Location:1200
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

RNA

  1. XR_001738948.1 RNA Sequence

    Related
    ENST00000422368.5
  2. XR_001738946.2 RNA Sequence

  3. XR_001738947.2 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.
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