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
  • Calcium-Responsive Transcription Factor 3 4
  • Testis Development Protein NYD-SP24 3 4
  • ALS2CR8 3 4
  • 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. Diseases associated with CARF include Amyotrophic Lateral Sclerosis 2, Juvenile. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and proximal promoter DNA-binding transcription activator activity, RNA polymerase II-specific.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification and piRNA Summary for CARF Gene

Genomics for CARF Gene

GeneHancer (GH) Regulatory Elements for CARF Gene

Promoters and enhancers for CARF Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CARF on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CARF

Genomic Locations for CARF Gene

Genomic Locations for CARF Gene
chr2:202,912,214-202,988,263
(GRCh38/hg38)
Size:
76,050 bases
Orientation:
Plus strand
chr2:203,776,937-203,851,786
(GRCh37/hg19)
Size:
74,850 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=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAB69018.1; Type=Frameshift; 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

Antibody Products

  • Santa Cruz Biotechnology (SCBT) Antibodies for CARF

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:

Suggested Antigen Peptide Sequences for CARF Gene

GenScript: Design optimal peptide antigens:
  • Testis development protein NYD-SP24 (AL2S8_HUMAN)
  • cDNA FLJ59532, highly similar to Amyotrophic lateral sclerosis 2 chromosomalregion candidate gene 8 protein (Calcium-responsefactor) (CaRF) (Protein NYD-SP24) (B4DIA7_HUMAN)
  • cDNA FLJ60568, highly similar to Amyotrophic lateral sclerosis 2 chromosomalregion candidate gene 8 protein (Calcium-responsefactor) (CaRF) (Protein NYD-SP24) (B4DIN8_HUMAN)

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 proximal promoter sequence-specific DNA binding IEA --
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IBA 21873635
GO:0003677 DNA binding IDA,IBA 11832226
GO:0003700 DNA-binding transcription factor activity 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:
  • Carf Carf<tm1.1(KOMP)Vlcg>
  • Carf Carf<tm1.1Aew>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CARF

Clone 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
plasma membrane 1
extracellular 1
cytoskeleton 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (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:0001652 granular component IEA --
GO:0005634 nucleus IBA,ISS --
genes like me logo Genes that share ontologies with CARF: view

Pathways & Interactions for CARF Gene

PathCards logo

SuperPathways for CARF Gene

No Data Available

Gene Ontology (GO) - Biological Process for CARF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0035865 cellular response to potassium ion IBA,IDA 22174809
GO:0045944 positive regulation of transcription by RNA polymerase II IEA --
GO:0051090 regulation of DNA-binding transcription factor activity IEA --
GO:0061400 positive regulation of transcription from RNA polymerase II promoter in response to calcium ion IBA,IDA 11832226
GO:0071277 cellular response to calcium ion IDA 11832226
genes like me logo Genes that share ontologies with CARF: view

No data available for Pathways by source and SIGNOR curated interactions 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

mRNA/cDNA for CARF Gene

13 REFSEQ mRNAs :
21 NCBI additional mRNA sequence :
20 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CARF

Clone 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

Expression for CARF Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for 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

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 31 30
  • 99.45 (n)
OneToOne
dog
(Canis familiaris)
Mammalia ALS2CR8 30
  • 90.98 (n)
CARF 31
  • 87 (a)
OneToOne
cow
(Bos Taurus)
Mammalia CARF 31 30
  • 89.43 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Carf 17 31 30
  • 82.73 (n)
rat
(Rattus norvegicus)
Mammalia Carf 30
  • 81.72 (n)
oppossum
(Monodelphis domestica)
Mammalia CARF 31
  • 71 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CARF 31
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves ALS2CR8 30
  • 72.57 (n)
CARF 31
  • 66 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia carf 30
  • 62.66 (n)
zebrafish
(Danio rerio)
Actinopterygii carf 31 30
  • 57.52 (n)
OneToOne
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)
Aminode:
Evolutionary constrained regions (ECRs) for CARF: view image

Paralogs for CARF Gene

No data available for Paralogs for CARF Gene

Variants for CARF Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CARF Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
711351 Benign: not provided 202,969,913(+) A/T INTRON_VARIANT
714941 Likely Benign: not provided 202,983,584(+) C/CA FRAMESHIFT_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,THREE_PRIME_UTR_VARIANT
717827 Benign: not provided 202,983,619(+) A/G MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,THREE_PRIME_UTR_VARIANT
721243 Benign: not provided 202,982,142(+) C/T MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,INTRON_VARIANT
767842 Benign: not provided 202,974,364(+) C/T NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for CARF Gene

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)

Additional Variant Information for CARF Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for CARF Gene

MalaCards: The human disease database

(1) MalaCards diseases for CARF Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
amyotrophic lateral sclerosis 2, juvenile
  • als2
- elite association - COSMIC cancer census association via MalaCards
Search CARF in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CARF

genes like me logo Genes that share disorders with CARF: view

No data available for 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 23 54
  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 54
  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 54
  4. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier LW … Wilson RK (Nature 2005) 3 4 54
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54

Products for CARF Gene

Sources for CARF Gene