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0  structures 136  species 0  interactions 339  sequences 30  architectures

Family: ALS2CR8 (PF15299)

Summary: Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "ALS2CR8". More...

ALS2CR8 Edit Wikipedia article

CARF
Identifiers
AliasesCARF, ALS2CR8, NYD-SP24, calcium responsive transcription factor
External IDsOMIM: 607586 MGI: 2182269 HomoloGene: 11689 GeneCards: CARF
Gene location (Human)
Chromosome 2 (human)
Chr.Chromosome 2 (human)[1]
Chromosome 2 (human)
Genomic location for CARF
Genomic location for CARF
Band2q33.2Start202,912,214 bp[1]
End202,988,263 bp[1]
RNA expression pattern
PBB GE ALS2CR8 219834 at fs.png
More reference expression data
Orthologs
SpeciesHumanMouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_001285463
NM_001285473
NM_139150

RefSeq (protein)

NP_001272392
NP_001272402
NP_631889

Location (UCSC)Chr 2: 202.91 – 202.99 MbChr 1: 60.1 – 60.15 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8 protein also known as calcium-response factor (CaRF) is a protein that in humans is encoded by the ALS2CR8 gene.[5][6]

Knocking out the Carf (Als2cr8) gene in mice results in learning associated deficits. Furthermore, Carf has been shown to function as a transcription factor that regulates the expression of BDNF.[7]

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000138380 - Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000026017 - Ensembl, May 2017
  3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ^ Hadano S, Hand CK, Osuga H, Yanagisawa Y, Otomo A, Devon RS, Miyamoto N, Showguchi-Miyata J, Okada Y, Singaraja R, Figlewicz DA, Kwiatkowski T, Hosler BA, Sagie T, Skaug J, Nasir J, Brown RH Jr, Scherer SW, Rouleau GA, Hayden MR, Ikeda JE (Oct 2001). "A gene encoding a putative GTPase regulator is mutated in familial amyotrophic lateral sclerosis 2". Nat Genet. 29 (2): 166–73. doi:10.1038/ng1001-166. PMID 11586298.
  6. ^ "Entrez Gene: ALS2CR8 amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 8".
  7. ^ Tao X, West AE, Chen WG, Corfas G, Greenberg ME (January 2002). "A calcium-responsive transcription factor, CaRF, that regulates neuronal activity-dependent expression of BDNF". Neuron. 33 (3): 383–95. doi:10.1016/S0896-6273(01)00561-X. PMID 11832226.

External links

Further reading


This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8 Provide feedback

This domain is found in amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8 protein [1].

Literature references

  1. Tao X, West AE, Chen WG, Corfas G, Greenberg ME;, Neuron. 2002;33:383-395.: A calcium-responsive transcription factor, CaRF, that regulates neuronal activity-dependent expression of BDNF. PUBMED:11832226 EPMC:11832226


This tab holds annotation information from the InterPro database.

InterPro entry IPR029309

This entry represents calcium-responsive transcription factor (CaRF, also known as amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8 protein) [PUBMED:11832226]. CaRF acts as a transcriptional activator that mediates the calcium- and neuron-selective induction of BDNF exon III transcription. It binds to the consensus calcium-response element CaRE1 5'-CTATTTCGAG-3' sequence [PUBMED:11832226].

Gene Ontology

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Domain organisation

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Alignments

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(19)
Full
(339)
Representative proteomes UniProt
(488)
NCBI
(1355)
Meta
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RP15
(147)
RP35
(204)
RP55
(272)
RP75
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Key: ✓ available, x not generated, not available.

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  Seed
(19)
Full
(339)
Representative proteomes UniProt
(488)
NCBI
(1355)
Meta
(0)
RP15
(147)
RP35
(204)
RP55
(272)
RP75
(342)
Alignment:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(19)
Full
(339)
Representative proteomes UniProt
(488)
NCBI
(1355)
Meta
(0)
RP15
(147)
RP35
(204)
RP55
(272)
RP75
(342)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped Download   Download   Download   Download   Download   Download   Download   Download    

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Jackhmmer:Q8N187
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Eberhardt R , Coggill P , Hetherington K
Number in seed: 19
Number in full: 339
Average length of the domain: 202.40 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 33.74 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 28.9 28.9
Trusted cut-off 30.5 29.1
Noise cut-off 28.2 28.6
Model length: 218
Family (HMM) version: 7
Download: download the raw HMM for this family

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