Carf calcium response factor [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Carfprovided by MGI
Official Full Name: calcium response factorprovided by MGI
Primary source: MGI:MGI:2182269
See related: Ensembl:ENSMUSG00000026017 AllianceGenome:MGI:2182269
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Als2cr8; ECBRC-FC1; ECBRC-FC2
Summary: Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II. Acts upstream of or within regulation of DNA-binding transcription factor activity. Located in granular component. Is expressed in several structures, including central nervous system; eye; genitourinary system; gut; and skeletal muscle tissue. Orthologous to human CARF (calcium responsive transcription factor). [provided by Alliance of Genome Resources, Jan 2025]
Expression: Broad expression in testis adult (RPKM 2.5), CNS E18 (RPKM 1.9) and 25 other tissues See more
Orthologs: human all
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Genomic context

Location:: 1 C2; 1 30.45 cM

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	1	NC_000067.7 (60137380..60193112)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	1	NC_000067.6 (60098221..60153953)

Chromosome 1 - NC_000067.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

This report that loss of CaRF leads to enhanced NMDAR-dependent induction of both Bdnf IV and the activity-regulated gene Arc, and we investigate potential mechanisms as well as biological consequences of this change in transcriptional regulation.
Title: The transcription factor calcium-response factor limits NMDA receptor-dependent transcription in the developing brain.
Carf(+/-) and Carf(-/-) mice were impaired in their ability to acquire timed response thresholds relative to Carf(+/+) mice.
Title: Acquisition of response thresholds for timed performance is regulated by a calcium-responsive transcription factor, CaRF.
These data strongly support the characterization of CaRF as a unique transcription factor and provide the first insight into the program of CaRF-regulated transcription in neurons.
Title: Genome-wide identification of calcium-response factor (CaRF) binding sites predicts a role in regulation of neuronal signaling pathways.
the data of this study reveal novel roles for CaRF in the organization and/or function of neural circuits that underlie essential aspects of learning and memory.
Title: Reduced cortical BDNF expression and aberrant memory in Carf knock-out mice.
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.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (2)
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA binding	ISS Inferred from Sequence or Structural Similarity 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	IMP Inferred from Mutant Phenotype more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
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	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of DNA-binding transcription factor activity	IGI Inferred from Genetic Interaction more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
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 chromosomal region candidate gene 8 protein homolog; calcium-response factor CaRF

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_001285463.2 → NP_001272392.1 calcium-responsive transcription factor isoform 2

Status: VALIDATED

Source sequence(s)

AC116581, AC138597

Conserved Domains (1) summary

pfam15299
Location:108 → 338

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
NM_001285473.2 → NP_001272402.1 calcium-responsive transcription factor isoform 3

Status: VALIDATED

Source sequence(s)

AC116581, AC138597

Consensus CDS

CCDS78592.1

UniProtKB/TrEMBL

A8VI08

Related

ENSMUSP00000027171.6, ENSMUST00000027171.12

Conserved Domains (1) summary

pfam15299
Location:192 → 419

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
NM_001431923.1 → NP_001418852.1 calcium-responsive transcription factor isoform 4

Status: VALIDATED

Source sequence(s)

AC116581, AC138597
NM_001431924.1 → NP_001418853.1 calcium-responsive transcription factor isoform 4

Status: VALIDATED

Source sequence(s)

AC116581, AC138597
NM_001431925.1 → NP_001418854.1 calcium-responsive transcription factor isoform 3

Status: VALIDATED

Source sequence(s)

AC116581, AC138597

UniProtKB/TrEMBL

A8VI08
NM_001431926.1 → NP_001418855.1 calcium-responsive transcription factor isoform 3

Status: VALIDATED

Source sequence(s)

AC116581, AC138597

UniProtKB/TrEMBL

A8VI08
NM_001431927.1 → NP_001418856.1 calcium-responsive transcription factor isoform 5

Status: VALIDATED

Source sequence(s)

AC116581, AC138597
NM_001431928.1 → NP_001418857.1 calcium-responsive transcription factor isoform 6

Status: VALIDATED

Source sequence(s)

AC116581, AC138597
NM_139150.6 → NP_631889.1 calcium-responsive transcription factor isoform 1

Status: VALIDATED

Source sequence(s)

AC116581, AC138597

Consensus CDS

CCDS14989.1

UniProtKB/Swiss-Prot

B2RRZ9, Q8VHI4

Related

ENSMUSP00000141169.2, ENSMUST00000187978.7

Conserved Domains (1) summary

pfam15299
Location:227 → 454

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

RNA

NR_104344.2 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC116581, AC138597

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000067.7 Reference GRCm39 C57BL/6J

Range

60137380..60193112

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030254084.1 → XP_030109944.1 calcium-responsive transcription factor isoform X1

UniProtKB/Swiss-Prot

B2RRZ9, Q8VHI4

Conserved Domains (1) summary

pfam15299
Location:227 → 454

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
XM_006495975.2 → XP_006496038.1 calcium-responsive transcription factor isoform X3

Conserved Domains (1) summary

pfam15299
Location:192 → 419

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
XM_036164953.1 → XP_036020846.1 calcium-responsive transcription factor isoform X2

Conserved Domains (1) summary

pfam15299
Location:198 → 425

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
XM_036164965.1 → XP_036020858.1 calcium-responsive transcription factor isoform X5

Conserved Domains (1) summary

pfam15299
Location:166 → 393

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
XM_036164962.1 → XP_036020855.1 calcium-responsive transcription factor isoform X4

Conserved Domains (1) summary

pfam15299
Location:227 → 406

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
XM_017320602.1 → XP_017176091.1 calcium-responsive transcription factor isoform X3

Conserved Domains (1) summary

pfam15299
Location:192 → 419

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
XM_030254087.1 → XP_030109947.1 calcium-responsive transcription factor isoform X2

Conserved Domains (1) summary

pfam15299
Location:198 → 425

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
XM_036164967.1 → XP_036020860.1 calcium-responsive transcription factor isoform X6

Conserved Domains (1) summary

pfam15299
Location:11 → 128

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
XM_006495977.2 → XP_006496040.1 calcium-responsive transcription factor isoform X5

Conserved Domains (1) summary

pfam15299
Location:166 → 393

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
XM_036164947.1 → XP_036020840.1 calcium-responsive transcription factor isoform X1

UniProtKB/Swiss-Prot

B2RRZ9, Q8VHI4

Conserved Domains (1) summary

pfam15299
Location:227 → 454

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
XM_006495974.2 → XP_006496037.1 calcium-responsive transcription factor isoform X3

Conserved Domains (1) summary

pfam15299
Location:192 → 419

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
XM_017320598.3 → XP_017176087.1 calcium-responsive transcription factor isoform X2

Conserved Domains (1) summary

pfam15299
Location:198 → 425

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
XM_036164963.1 → XP_036020856.1 calcium-responsive transcription factor isoform X5

Conserved Domains (1) summary

pfam15299
Location:166 → 393

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
XM_011238510.1 → XP_011236812.1 calcium-responsive transcription factor isoform X1

UniProtKB/Swiss-Prot

B2RRZ9, Q8VHI4

Conserved Domains (1) summary

pfam15299
Location:227 → 454

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
XM_036164961.1 → XP_036020854.1 calcium-responsive transcription factor isoform X4

Conserved Domains (1) summary

pfam15299
Location:227 → 406

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
XM_036164954.1 → XP_036020847.1 calcium-responsive transcription factor isoform X3

UniProtKB/TrEMBL

A8VI08

Conserved Domains (1) summary

pfam15299
Location:192 → 419

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
XM_036164949.1 → XP_036020842.1 calcium-responsive transcription factor isoform X2

Conserved Domains (1) summary

pfam15299
Location:198 → 425

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8
XM_036164966.1 → XP_036020859.1 calcium-responsive transcription factor isoform X5

Conserved Domains (1) summary

pfam15299
Location:166 → 393

ALS2CR8; Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8