Carf calcium responsive transcription factor [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Carfprovided by RGD
Official Full Name: calcium responsive transcription factorprovided by RGD
Primary source: RGD:1306822
See related: EnsemblRapid:ENSRNOG00000017491 AllianceGenome:RGD:1306822
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Als2cr8
Summary: Enables DNA binding activity and DNA-binding transcription activator activity, RNA polymerase II-specific. Involved in cellular response to calcium ion. Located in nucleus. Orthologous to human CARF (calcium responsive transcription factor). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Kidney (RPKM 50.4), Brain (RPKM 47.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 9q32

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	9	NC_086027.1 (68996419..69046480)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	9	NC_051344.1 (61502368..61552433)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	9	NC_005108.4 (66878526..66928658)

Chromosome 9 - NC_086027.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology 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
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cellular response to calcium ion	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to calcium ion	IEA Inferred from Electronic Annotation more info
involved_in cellular response to calcium ion	ISO Inferred from Sequence Orthology more info
involved_in cellular response to calcium ion	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology 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
located_in granular component	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology 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

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)

NM_001106915.1 → NP_001100385.1 calcium-responsive transcription factor

See identical proteins and their annotated locations for NP_001100385.1

Status: PROVISIONAL

Source sequence(s)

CH473965

UniProtKB/Swiss-Prot

D4A7U2

Related

ENSRNOP00000023536.4, ENSRNOT00000023536.8

Conserved Domains (1) summary

pfam15299
Location:119 → 349

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086027.1 Reference GRCr8

Range

68996419..69046480

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039083318.2 → XP_038939246.1 calcium-responsive transcription factor isoform X2

Conserved Domains (1) summary

pfam15299
Location:316 → 543

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
XM_006244971.4 → XP_006245033.2 calcium-responsive transcription factor isoform X1

Related

ENSRNOP00000100921.1, ENSRNOT00000126635.1

Conserved Domains (1) summary

pfam15299
Location:316 → 543

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
XM_039083319.2 → XP_038939247.1 calcium-responsive transcription factor isoform X3

UniProtKB/TrEMBL

A0A0G2K3E6

Related

ENSRNOP00000072606.1, ENSRNOT00000087194.3

Conserved Domains (1) summary

pfam15299
Location:203 → 430

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
XM_006244974.5 → XP_006245036.1 calcium-responsive transcription factor isoform X5

Conserved Domains (1) summary

pfam15299
Location:231 → 461

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
XM_039083321.2 → XP_038939249.1 calcium-responsive transcription factor isoform X4

Conserved Domains (1) summary

pfam15299
Location:1 → 197

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
XM_039083320.2 → XP_038939248.1 calcium-responsive transcription factor isoform X4

Conserved Domains (1) summary

pfam15299
Location:1 → 197

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
XM_017596367.3 → XP_017451856.1 calcium-responsive transcription factor isoform X4

Conserved Domains (1) summary

pfam15299
Location:1 → 197

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8