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Protein

Calcium-responsive transcription factor

Gene

CARF

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.2 Publications

GO - Molecular functioni

GO - Biological processi

  • cellular response to calcium ion Source: UniProtKB
  • cellular response to potassium ion Source: UniProtKB
  • positive regulation of transcription from RNA polymerase II promoter in response to calcium ion Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Activator

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Calcium-responsive transcription factor
Alternative name(s):
Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8 protein
Calcium-response factor
Short name:
CaRF
Testis development protein NYD-SP24
Gene namesi
Name:CARF
Synonyms:ALS2CR8
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 2

Organism-specific databases

HGNCiHGNC:14435. CARF.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA24748.

Polymorphism and mutation databases

BioMutaiCARF.
DMDMi85540610.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 725725Calcium-responsive transcription factorPRO_0000076172Add
BLAST

Proteomic databases

PaxDbiQ8N187.
PRIDEiQ8N187.

PTM databases

PhosphoSiteiQ8N187.

Expressioni

Gene expression databases

BgeeiQ8N187.
CleanExiHS_ALS2CR8.
ExpressionAtlasiQ8N187. baseline and differential.
GenevisibleiQ8N187. HS.

Organism-specific databases

HPAiHPA034557.

Interactioni

Protein-protein interaction databases

BioGridi122897. 3 interactions.
IntActiQ8N187. 3 interactions.
MINTiMINT-1472416.
STRINGi9606.ENSP00000316224.

Structurei

3D structure databases

ProteinModelPortaliQ8N187.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domaini

The N-terminus is necessary for DNA-binding. The C-terminus is necessary for transcriptional activation (PubMed:11832226).1 Publication

Phylogenomic databases

eggNOGiNOG45356.
GeneTreeiENSGT00390000013916.
HOGENOMiHOG000033888.
HOVERGENiHBG080829.
InParanoidiQ8N187.
OMAiAVMNNNS.
OrthoDBiEOG761BTC.
PhylomeDBiQ8N187.
TreeFamiTF333279.

Family and domain databases

InterProiIPR029309. CaRF.
[Graphical view]
PfamiPF15299. ALS2CR8. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8N187-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MEQSNDSLRV NHNDGEESKT SAQVFEHLIC MDSRDSSFGQ NDSPTVLPIT
60 70 80 90 100
TREANNSLIS QNIPGPLTQT QTLSAEQFHL VDQNGQAIQY ELQSLGESNA
110 120 130 140 150
QMMIVASPTE NGQVLRVIPP TQTGMAQVII PQGQLVDVNS PRDVPEEKPS
160 170 180 190 200
NRNLPTVRVD TLADNTSNYI LHPQTSFPLP KKSVTGMLEE PLLGPLQPLS
210 220 230 240 250
SNTPIWACRL RSCEKIGDSY RGYCVSETEL ESVLTFHKQQ TQSVWGTRQS
260 270 280 290 300
PSPAKPATRL MWKSQYVPYD GIPFVNAGSR AVVMECQYGP RRKGFQLKKV
310 320 330 340 350
SEQESRSCQL YKATCPARIY IKKVQKFPEY RVPTDPKIDK KIIRMEQEKA
360 370 380 390 400
FNMLKKNLVD AGGVLRWYVQ LPTQQAHQYH ELETPCLTLS PSPFPVSSLE
410 420 430 440 450
EEETAVRDEN CALPSRLHPQ VAHKIQELVS QGIEQVYAVR KQLRKFVERE
460 470 480 490 500
LFKPDEVPER HNLSFFPTVN DIKNHIHEVQ KSLRNGDTVY NSEIIPATLQ
510 520 530 540 550
WTTDSGNILK ETMTVTFAEG NSPGESITTK VETNQTRGSL SPEPTHLLSS
560 570 580 590 600
LSSFQPKIFT QLQGLQLQPR YTSPDESPAV VSVNNQPSSS PSGLLDTIGS
610 620 630 640 650
AVMNNNSLLL GQSHSLQRDT CLTQNNSTAS TMGNLPEPDQ NLVAMDELVE
660 670 680 690 700
VGDVEDTGNL EGTVHRILLG DVQTIPIQII DNHSALIEEN PESTISVSQV
710 720
KQEPKEPALS MEAKKTVDYK KLSAT
Length:725
Mass (Da):80,698
Last modified:January 10, 2006 - v2
Checksum:i871D8874DF8D1384
GO
Isoform 2 (identifier: Q8N187-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-102: Missing.
     279-309: SRAVVMECQYGPRRKGFQLKKVSEQESRSCQ → TFLKNYFKRFSSSHSPLSKCDFPKVITFLFW
     310-725: Missing.

Note: No experimental confirmation available.
Show »
Length:207
Mass (Da):23,212
Checksum:iB63FE62A853BF86E
GO
Isoform 3 (identifier: Q8N187-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     27-102: Missing.

Show »
Length:649
Mass (Da):72,385
Checksum:iA9DE9008C08D9DB8
GO

Sequence cautioni

The sequence BAB15088.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAB69018.1 differs from that shown. Reason: Frameshift at position 715. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti238 – 2381K → E in AAK66819 (Ref. 2) Curated
Sequence conflicti238 – 2381K → E in BAB15088 (PubMed:14702039).Curated
Sequence conflicti286 – 2861C → R in BAG64929 (PubMed:14702039).Curated
Sequence conflicti300 – 3012VS → SQ in BAB15088 (PubMed:14702039).Curated
Sequence conflicti465 – 4651F → L in AAH33777 (PubMed:15489334).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 102102Missing in isoform 2. 1 PublicationVSP_016785Add
BLAST
Alternative sequencei27 – 10276Missing in isoform 3. 1 PublicationVSP_055713Add
BLAST
Alternative sequencei279 – 30931SRAVV…SRSCQ → TFLKNYFKRFSSSHSPLSKC DFPKVITFLFW in isoform 2. 1 PublicationVSP_016786Add
BLAST
Alternative sequencei310 – 725416Missing in isoform 2. 1 PublicationVSP_016787Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB053309 mRNA. Translation: BAB69018.1. Frameshift.
AB053310 mRNA. Translation: BAB69019.1.
AY032876 mRNA. Translation: AAK66819.2.
AF454946 mRNA. Translation: AAL62330.1.
AK025232 mRNA. Translation: BAB15088.1. Different initiation.
AK304014 mRNA. Translation: BAG64929.1.
AC010900 Genomic DNA. Translation: AAY24288.1.
CH471063 Genomic DNA. Translation: EAW70320.1.
BC033777 mRNA. Translation: AAH33777.1.
AL834188 mRNA. Translation: CAD38882.2.
CCDSiCCDS42801.1. [Q8N187-1]
CCDS63091.1. [Q8N187-3]
RefSeqiNP_001098056.1. NM_001104586.2. [Q8N187-1]
NP_001269839.1. NM_001282910.1. [Q8N187-3]
NP_001269840.1. NM_001282911.1. [Q8N187-3]
NP_001269841.1. NM_001282912.1.
NP_079020.13. NM_024744.15. [Q8N187-1]
XP_005246915.1. XM_005246858.2. [Q8N187-1]
XP_005246916.1. XM_005246859.2. [Q8N187-1]
XP_006712820.1. XM_006712757.2. [Q8N187-1]
UniGeneiHs.444982.

Genome annotation databases

EnsembliENST00000320443; ENSP00000316224; ENSG00000138380. [Q8N187-3]
ENST00000402905; ENSP00000384006; ENSG00000138380. [Q8N187-1]
ENST00000428585; ENSP00000396221; ENSG00000138380. [Q8N187-3]
ENST00000434998; ENSP00000415948; ENSG00000138380. [Q8N187-2]
ENST00000438828; ENSP00000414644; ENSG00000138380. [Q8N187-1]
GeneIDi79800.
KEGGihsa:79800.
UCSCiuc002uzn.3. human. [Q8N187-2]
uc002uzo.2. human. [Q8N187-1]
uc010zia.1. human.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB053309 mRNA. Translation: BAB69018.1. Frameshift.
AB053310 mRNA. Translation: BAB69019.1.
AY032876 mRNA. Translation: AAK66819.2.
AF454946 mRNA. Translation: AAL62330.1.
AK025232 mRNA. Translation: BAB15088.1. Different initiation.
AK304014 mRNA. Translation: BAG64929.1.
AC010900 Genomic DNA. Translation: AAY24288.1.
CH471063 Genomic DNA. Translation: EAW70320.1.
BC033777 mRNA. Translation: AAH33777.1.
AL834188 mRNA. Translation: CAD38882.2.
CCDSiCCDS42801.1. [Q8N187-1]
CCDS63091.1. [Q8N187-3]
RefSeqiNP_001098056.1. NM_001104586.2. [Q8N187-1]
NP_001269839.1. NM_001282910.1. [Q8N187-3]
NP_001269840.1. NM_001282911.1. [Q8N187-3]
NP_001269841.1. NM_001282912.1.
NP_079020.13. NM_024744.15. [Q8N187-1]
XP_005246915.1. XM_005246858.2. [Q8N187-1]
XP_005246916.1. XM_005246859.2. [Q8N187-1]
XP_006712820.1. XM_006712757.2. [Q8N187-1]
UniGeneiHs.444982.

3D structure databases

ProteinModelPortaliQ8N187.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi122897. 3 interactions.
IntActiQ8N187. 3 interactions.
MINTiMINT-1472416.
STRINGi9606.ENSP00000316224.

PTM databases

PhosphoSiteiQ8N187.

Polymorphism and mutation databases

BioMutaiCARF.
DMDMi85540610.

Proteomic databases

PaxDbiQ8N187.
PRIDEiQ8N187.

Protocols and materials databases

DNASUi79800.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000320443; ENSP00000316224; ENSG00000138380. [Q8N187-3]
ENST00000402905; ENSP00000384006; ENSG00000138380. [Q8N187-1]
ENST00000428585; ENSP00000396221; ENSG00000138380. [Q8N187-3]
ENST00000434998; ENSP00000415948; ENSG00000138380. [Q8N187-2]
ENST00000438828; ENSP00000414644; ENSG00000138380. [Q8N187-1]
GeneIDi79800.
KEGGihsa:79800.
UCSCiuc002uzn.3. human. [Q8N187-2]
uc002uzo.2. human. [Q8N187-1]
uc010zia.1. human.

Organism-specific databases

CTDi79800.
GeneCardsiGC02P203777.
HGNCiHGNC:14435. CARF.
HPAiHPA034557.
MIMi607586. gene.
neXtProtiNX_Q8N187.
PharmGKBiPA24748.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG45356.
GeneTreeiENSGT00390000013916.
HOGENOMiHOG000033888.
HOVERGENiHBG080829.
InParanoidiQ8N187.
OMAiAVMNNNS.
OrthoDBiEOG761BTC.
PhylomeDBiQ8N187.
TreeFamiTF333279.

Miscellaneous databases

GeneWikiiALS2CR8.
GenomeRNAii79800.
NextBioi35477142.
PROiQ8N187.
SOURCEiSearch...

Gene expression databases

BgeeiQ8N187.
CleanExiHS_ALS2CR8.
ExpressionAtlasiQ8N187. baseline and differential.
GenevisibleiQ8N187. HS.

Family and domain databases

InterProiIPR029309. CaRF.
[Graphical view]
PfamiPF15299. ALS2CR8. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2).
  2. "NYD-SP24: cloning a novel gene related to testis development from human testis."
    Sha J.H.
    Submitted (AUG-2001) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
    Tissue: Testis.
  3. "A calcium-responsive transcription factor, CaRF, that regulates neuronal activity-dependent expression of BDNF."
    Tao X., West A.E., Chen W.G., Corfas G., Greenberg M.E.
    Neuron 33:383-395(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, DNA-BINDING.
  4. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 29-301 (ISOFORM 1).
    Tissue: Colon and Trachea.
  5. "Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
    Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H.
    , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
    Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  7. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Testis.
  8. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-278 (ISOFORM 1).
    Tissue: Lymph node.
  9. "Regulation of brain-derived neurotrophic factor exon IV transcription through calcium responsive elements in cortical neurons."
    Zheng F., Zhou X., Luo Y., Xiao H., Wayman G., Wang H.
    PLoS ONE 6:E28441-E28441(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiCARTF_HUMAN
AccessioniPrimary (citable) accession number: Q8N187
Secondary accession number(s): B4E1W7
, G3V1K7, Q8ND29, Q8WXC0, Q96J78, Q96Q38, Q96Q39, Q9H712
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 10, 2006
Last sequence update: January 10, 2006
Last modified: June 24, 2015
This is version 96 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 2
    Human chromosome 2: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.