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Aliases for CARF Gene

Aliases for CARF Gene

  • Calcium Responsive Transcription Factor 2 3 5
  • Calcium-Response Factor 2 3 4
  • Amyotrophic Lateral Sclerosis 2 Chromosomal Region Candidate Gene 8 Protein 3 4
  • Amyotrophic Lateral Sclerosis 2 (Juvenile) Chromosome Region, Candidate 8 2 3
  • Testis Development Protein NYD-SP24 3 4
  • ALS2CR8 3 4
  • Calcium-Responsive Transcription Factor 3
  • NYD-SP24 3
  • CaRF 4

External Ids for CARF Gene

Previous HGNC Symbols for CARF Gene

  • ALS2CR8

Previous GeneCards Identifiers for CARF Gene

  • GC04P185045
  • GC04P184950
  • GC04P185061
  • GC04P184740
  • GC04P184602
  • GC02P203777

Summaries for CARF Gene

GeneCards Summary for CARF Gene

CARF (Calcium Responsive Transcription Factor) is a Protein Coding gene. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding.

UniProtKB/Swiss-Prot for CARF Gene

  • Acts as a transcriptional activator that mediates the calcium- and neuron-selective induction of BDNF exon III transcription. Binds to the consensus calcium-response element CaRE1 5-CTATTTCGAG-3 sequence.

Gene Wiki entry for CARF Gene

Additional gene information for CARF Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CARF Gene

Genomics for CARF Gene

Regulatory Elements for CARF Gene

Enhancers for CARF Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02H202965 1.4 FANTOM5 Ensembl ENCODE 23.6 +53.5 53529 1 HDAC1 TBP PKNOX1 ATF1 ARNT SIN3A BATF CHAMP1 ATF7 RUNX3 NBEAL1 CARF NOP58 WDR12 FZD7 RAPH1 ICA1L GC02M202945 GC02P202987
GH02H203237 1.1 ENCODE 19.6 +327.1 327057 3 HDGF PKNOX1 ARID4B SIN3A FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF207 NOP58 CARF ICA1L CYP20A1 GC02M203237 PIR57218
GH02H202030 1.9 FANTOM5 Ensembl ENCODE dbSUPER 11 -877.0 -877021 9 ATF1 ZNF133 SIN3A ZNF2 YY1 ETS1 GLIS2 ZNF143 ZNF207 FOS NOP58 FZD7 CDK15 KIAA2012 CARF LOC100420110 LOC729224 RNU6-440P FAM117B TMEM237
GH02H202655 1 Ensembl dbSUPER 15.7 -256.2 -256214 0 ZNF211 ZSCAN4 ZNF266 BATF ZNF366 EED PRDM10 RUNX3 IKZF2 MTA2 NOP58 CARF FAM117B CDK15 GC02P202671
GH02H202015 0.8 ENCODE 14.3 -897.2 -897151 1 TAL1 ZNF140 KLF17 ZIC2 TCF12 HIC1 ZFHX2 ZNF366 ZBTB48 PATZ1 NOP58 CARF KIAA2012 RNU6-440P ENSG00000272966 CDK15 LOC729224 ICA1L GC02P202013 ENSG00000273209
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CARF on UCSC Golden Path with GeneCards custom track

Genomic Location for CARF Gene

Chromosome:
2
Start:
202,912,214 bp from pter
End:
202,987,857 bp from pter
Size:
75,644 bases
Orientation:
Plus strand

Genomic View for CARF Gene

Genes around CARF on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CARF Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CARF Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CARF Gene

Proteins for CARF Gene

  • Protein details for CARF Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N187-CARTF_HUMAN
    Recommended name:
    Calcium-responsive transcription factor
    Protein Accession:
    Q8N187
    Secondary Accessions:
    • B4E1W7
    • G3V1K7
    • Q8ND29
    • Q8WXC0
    • Q96J78
    • Q96Q38
    • Q96Q39
    • Q9H712

    Protein attributes for CARF Gene

    Size:
    725 amino acids
    Molecular mass:
    80698 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAB15088.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB69018.1; Type=Frameshift; Positions=715; Evidence={ECO:0000305};

    Alternative splice isoforms for CARF Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CARF Gene

Post-translational modifications for CARF Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CARF Gene

Domains & Families for CARF Gene

Gene Families for CARF Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for CARF Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

Q8N187

UniProtKB/Swiss-Prot:

CARTF_HUMAN :
  • The N-terminus is necessary for DNA-binding. The C-terminus is necessary for transcriptional activation (PubMed:11832226).
Domain:
  • The N-terminus is necessary for DNA-binding. The C-terminus is necessary for transcriptional activation (PubMed:11832226).
genes like me logo Genes that share domains with CARF: view

Function for CARF Gene

Molecular function for CARF Gene

UniProtKB/Swiss-Prot Function:
Acts as a transcriptional activator that mediates the calcium- and neuron-selective induction of BDNF exon III transcription. Binds to the consensus calcium-response element CaRE1 5-CTATTTCGAG-3 sequence.

Phenotypes From GWAS Catalog for CARF Gene

Gene Ontology (GO) - Molecular Function for CARF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding IEA --
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding IEA --
GO:0003677 DNA binding IDA,IEA 11832226
GO:0003700 transcription factor activity, sequence-specific DNA binding IDA 11832226
genes like me logo Genes that share ontologies with CARF: view
genes like me logo Genes that share phenotypes with CARF: view

Animal Models for CARF Gene

MGI Knock Outs for CARF:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CARF Gene

Localization for CARF Gene

Subcellular locations from UniProtKB/Swiss-Prot for CARF Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CARF gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Intermediate filaments (2)
  • Nucleoli fibrillar center (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CARF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS --
GO:0005654 nucleoplasm IEA --
GO:0005730 nucleolus IEA --
genes like me logo Genes that share ontologies with CARF: view

Pathways & Interactions for CARF Gene

No Data Available

Interacting Proteins for CARF Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000316224%0d%0a9606.ENSP00000394932%0d%0a
Selected Interacting proteins: Q8N187-CARTF_HUMAN ENSP00000316224 for CARF Gene via IID STRING

SIGNOR curated interactions for CARF Gene

Activates:
Inactivates:
Is inactivated by:

Gene Ontology (GO) - Biological Process for CARF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription from RNA polymerase II promoter IEA --
GO:0035865 cellular response to potassium ion IDA 22174809
GO:0045944 positive regulation of transcription from RNA polymerase II promoter IEA --
genes like me logo Genes that share ontologies with CARF: view

No data available for Pathways by source for CARF Gene

Drugs & Compounds for CARF Gene

(1) Drugs for CARF Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with CARF: view

Transcripts for CARF Gene

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for CARF Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b · 7c ^ 8 ^ 9a · 9b · 9c ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^
SP1: - - - - - - -
SP2: - - -
SP3: - - - - - - - -
SP4: - - - -
SP5: - - - - - - - - -
SP6: - - - - - -
SP7: - - - -
SP8: - - - - - - -
SP9: - - - -
SP10: - - - - -
SP11: - - - - - - -
SP12: - - - - -
SP13: - -

ExUns: 17 ^ 18 ^ 19 ^ 20
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:

Relevant External Links for CARF Gene

GeneLoc Exon Structure for
CARF
ECgene alternative splicing isoforms for
CARF

Expression for CARF Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CARF Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CARF Gene



Protein tissue co-expression partners for CARF Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CARF Gene:

CARF

Evidence on tissue expression from TISSUES for CARF Gene

  • Intestine(4.2)
  • Lymph node(4.2)
  • Nervous system(4)
genes like me logo Genes that share expression patterns with CARF: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CARF Gene

Orthologs for CARF Gene

This gene was present in the common ancestor of chordates.

Orthologs for CARF Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ALS2CR8 33 34
  • 99.45 (n)
dog
(Canis familiaris)
Mammalia ALS2CR8 33
  • 90.98 (n)
CARF 34
  • 87 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CARF 33 34
  • 89.43 (n)
mouse
(Mus musculus)
Mammalia Carf 33 16 34
  • 82.73 (n)
rat
(Rattus norvegicus)
Mammalia Carf 33
  • 81.72 (n)
oppossum
(Monodelphis domestica)
Mammalia CARF 34
  • 71 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CARF 34
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves ALS2CR8 33
  • 72.57 (n)
CARF 34
  • 66 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia carf 33
  • 62.66 (n)
zebrafish
(Danio rerio)
Actinopterygii carf 33 34
  • 57.52 (n)
Species where no ortholog for CARF was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CARF Gene

ENSEMBL:
Gene Tree for CARF (if available)
TreeFam:
Gene Tree for CARF (if available)

Paralogs for CARF Gene

No data available for Paralogs for CARF Gene

Variants for CARF Gene

Sequence variations from dbSNP and Humsavar for CARF Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs1000080800 -- 202,935,164(+) TGTAT(A/T)TATTT intron-variant
rs1000177427 -- 202,949,074(+) CTTAC(A/G)CCTGT intron-variant
rs1000188138 -- 202,965,251(+) GATTA(A/T)ATGCA intron-variant
rs1000194436 -- 202,987,791(+) GGAGG(A/G)ATTTT utr-variant-3-prime
rs1000198006 -- 202,964,823(+) GGTGT(A/T)TACTA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CARF Gene

Variant ID Type Subtype PubMed ID
esv3594003 CNV gain 21293372
nsv1001799 CNV gain 25217958
nsv214438 CNV deletion 16902084
nsv961552 CNV duplication 23825009

Variation tolerance for CARF Gene

Residual Variation Intolerance Score: 27.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.34; 63.16% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CARF Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CARF

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CARF Gene

Disorders for CARF Gene

Relevant External Links for CARF

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CARF

No disorders were found for CARF Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CARF Gene

Publications for CARF Gene

  1. A calcium-responsive transcription factor, CaRF, that regulates neuronal activity-dependent expression of BDNF. (PMID: 11832226) Tao X … Greenberg ME (Neuron 2002) 2 3 4 22 60
  2. A gene encoding a putative GTPase regulator is mutated in familial amyotrophic lateral sclerosis 2. (PMID: 11586298) Hadano S … Ikeda JE (Nature genetics 2001) 2 3 4 60
  3. Regulation of brain-derived neurotrophic factor exon IV transcription through calcium responsive elements in cortical neurons. (PMID: 22174809) Zheng F … Wang H (PloS one 2011) 3 4 60
  4. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier LW … Wilson RK (Nature 2005) 3 4 60
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60

Products for CARF Gene

Sources for CARF Gene

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