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carf calcium responsive transcription factor [ Danio rerio (zebrafish) ]

Gene ID: 555728, updated on 17-Sep-2024

Summary

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Official Symbol
carfprovided by ZNC
Official Full Name
calcium responsive transcription factorprovided by ZNC
Primary source
ZFIN:ZDB-GENE-070912-172
See related
Ensembl:ENSDARG00000019950 AllianceGenome:ZFIN:ZDB-GENE-070912-172
Gene type
protein coding
RefSeq status
MODEL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
als2cr8; si:ch211-195c14.1
Summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of transcription from RNA polymerase II promoter in response to calcium ion. Predicted to be active in nucleus. Orthologous to human CARF (calcium responsive transcription factor). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
human mouse all
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Genomic context

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See carf in Genome Data Viewer
Location:
chromosome: 9
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 9 NC_007120.7 (13229593..13251327)
105 previous assembly GRCz10 (GCF_000002035.5) 9 NC_007120.6 (13258368..13280124)

Chromosome 9 - NC_007120.7Genomic Context describing neighboring genes Neighboring gene bone morphogenetic protein receptor, type II b (serine/threonine kinase) Neighboring gene uncharacterized LOC103911618 Neighboring gene family with sequence similarity 117 member Bb Neighboring gene KIAA2012 ortholog Neighboring gene frizzled class receptor 7a

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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Related articles in PubMed

  1. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
  2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
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
  
Process Evidence Code Pubs
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
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

NCBI Reference Sequences (RefSeq)

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RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007120.7 Reference GRCz11 Primary Assembly

    Range
    13229593..13251327
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_021478846.2 → XP_021334521.1  calcium-responsive transcription factor isoform X1

    UniProtKB/TrEMBL
    A0A8M9QJZ6
    Conserved Domains (2) summary
    pfam15299
    Location:234 → 485
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
    cl27427
    Location:552 → 653
    AccB; Biotin carboxyl carrier protein [Coenzyme transport and metabolism, Lipid transport and metabolism]

  2. XM_021478848.2 → XP_021334523.1  calcium-responsive transcription factor isoform X2

    UniProtKB/TrEMBL
    A0A8M9PSK7
    Conserved Domains (2) summary
    pfam15299
    Location:230 → 481
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
    cl27427
    Location:548 → 649
    AccB; Biotin carboxyl carrier protein [Coenzyme transport and metabolism, Lipid transport and metabolism]

  3. XM_021478845.2 → XP_021334520.1  calcium-responsive transcription factor isoform X1

    UniProtKB/TrEMBL
    A0A8M9QJZ6
    Conserved Domains (2) summary
    pfam15299
    Location:234 → 485
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
    cl27427
    Location:552 → 653
    AccB; Biotin carboxyl carrier protein [Coenzyme transport and metabolism, Lipid transport and metabolism]

  4. XM_068223558.1 → XP_068079659.1  calcium-responsive transcription factor isoform X3

    Related
    ENSDARP00000118967.2, ENSDART00000141705.4

  5. XM_021478847.2 → XP_021334522.1  calcium-responsive transcription factor isoform X2

    UniProtKB/TrEMBL
    A0A8M9PSK7
    Conserved Domains (2) summary
    pfam15299
    Location:230 → 481
    ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
    cl27427
    Location:548 → 649
    AccB; Biotin carboxyl carrier protein [Coenzyme transport and metabolism, Lipid transport and metabolism]

  6. XM_068223560.1 → XP_068079661.1  calcium-responsive transcription factor isoform X5

  7. XM_068223559.1 → XP_068079660.1  calcium-responsive transcription factor isoform X4

    Related
    ENSDARP00000153281.1, ENSDART00000179850.1

RNA

  1. XR_011016793.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version

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