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Protein

Transcriptional repressor CTCF

Gene

Ctcf

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

Chromatin binding factor that binds to DNA sequence specific sites. Involved in transcriptional regulation by binding to chromatin insulators and preventing interaction between promoter and nearby enhancers and silencers. Acts as transcriptional repressor binding to promoters of vertebrate MYC gene and BAG1 gene. Also binds to the PLK and PIM1 promoters. Acts as a transcriptional activator of APP. Regulates APOA1/C3/A4/A5 gene cluster and controls MHC class II gene expression. Plays an essential role in oocyte and preimplantation embryo development by activating or repressing transcription. Seems to act as tumor suppressor. Plays a critical role in the epigenetic regulation. Participates in the allele-specific gene expression at the imprinted IGF2/H19 gene locus. On the maternal allele, binding within the H19 imprinting control region (ICR) mediates maternally inherited higher-order chromatin conformation to restrict enhancer access to IGF2. Plays a critical role in gene silencing over considerable distances in the genome. Preferentially interacts with unmethylated DNA, preventing spreading of CpG methylation and maintaining methylation-free zones. Inversely, binding to target sites is prevented by CpG methylation. Plays a important role in chromatin remodeling. Can dimerize when it is bound to different DNA sequences, mediating long-range chromatin looping. Mediates interchromosomal association between IGF2/H19 and WSB1/NF1 and may direct distant DNA segments to a common transcription factory. Causes local loss of histone acetylation and gain of histone methylation in the beta-globin locus, without affecting transcription. When bound to chromatin, it provides an anchor point for nucleosomes positioning. Seems to be essential for homologous X-chromosome pairing. May participate with Tsix in establishing a regulatable epigenetic switch for X chromosome inactivation. May play a role in preventing the propagation of stable methylation at the escape genes from X-inactivation. Involved in sister chromatid cohesion. Associates with both centromeres and chromosomal arms during metaphase and required for cohesin localization to CTCF sites. Regulates asynchronous replication of IGF2/H19 (By similarity).By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri266 – 28823C2H2-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri294 – 31623C2H2-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri322 – 34524C2H2-type 3PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri351 – 37323C2H2-type 4PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri379 – 40123C2H2-type 5PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri407 – 43024C2H2-type 6PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri437 – 46024C2H2-type 7PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri467 – 48923C2H2-type 8PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri495 – 51723C2H2-type 9PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri523 – 54624C2H2-type 10PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri555 – 57723C2H2-type 11; atypicalPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • DNA binding Source: RGD
  • metal ion binding Source: UniProtKB-KW
  • transcription factor activity, sequence-specific DNA binding Source: RGD

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Activator, Chromatin regulator, Repressor

Keywords - Biological processi

Chromosome partition, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Transcriptional repressor CTCF
Alternative name(s):
11-zinc finger protein
CCCTC-binding factor
CTCFL paralog
Gene namesi
Name:Ctcf
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi621344. Ctcf.

Subcellular locationi

  • Nucleusnucleoplasm By similarity
  • Chromosome By similarity
  • Chromosomecentromere By similarity

  • Note: May translocate to the nucleolus upon cell differentiation. Associates with both centromeres and chromosomal arms during metaphase. Associates with the H19 ICR in mitotic chromosomes. May be preferentially excluded from heterochromatin during interphase (By similarity).By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Centromere, Chromosome, Nucleus

Pathology & Biotechi

Keywords - Diseasei

Tumor suppressor

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 737737Transcriptional repressor CTCFPRO_0000047230Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionineBy similarity
Cross-linki74 – 74Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)By similarity
Modified residuei289 – 2891PhosphothreonineBy similarity
Modified residuei317 – 3171PhosphothreonineBy similarity
Modified residuei374 – 3741PhosphothreonineBy similarity
Modified residuei402 – 4021PhosphoserineBy similarity
Modified residuei609 – 6091PhosphoserineBy similarity
Modified residuei610 – 6101PhosphoserineBy similarity
Modified residuei612 – 6121PhosphoserineBy similarity
Cross-linki699 – 699Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternateBy similarity
Cross-linki699 – 699Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateBy similarity

Post-translational modificationi

Sumoylated on Lys-74 and Lys-699; sumoylation of CTCF contributes to the repressive function of CTCF on the MYC P2 promoter.By similarity

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiQ9R1D1.
PRIDEiQ9R1D1.

PTM databases

iPTMnetiQ9R1D1.
PhosphoSiteiQ9R1D1.

Expressioni

Gene expression databases

BgeeiENSRNOG00000017674.
GenevisibleiQ9R1D1. RN.

Interactioni

Subunit structurei

Interacts with CHD8.By similarity

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000023851.

Structurei

3D structure databases

ProteinModelPortaliQ9R1D1.
SMRiQ9R1D1. Positions 399-462, 515-591.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi634 – 67744Pro-richAdd
BLAST

Sequence similaritiesi

Belongs to the CTCF zinc-finger protein family.Curated
Contains 11 C2H2-type zinc fingers.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri266 – 28823C2H2-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri294 – 31623C2H2-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri322 – 34524C2H2-type 3PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri351 – 37323C2H2-type 4PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri379 – 40123C2H2-type 5PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri407 – 43024C2H2-type 6PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri437 – 46024C2H2-type 7PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri467 – 48923C2H2-type 8PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri495 – 51723C2H2-type 9PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri523 – 54624C2H2-type 10PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri555 – 57723C2H2-type 11; atypicalPROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1721. Eukaryota.
COG5048. LUCA.
HOGENOMiHOG000276534.
HOVERGENiHBG000350.
InParanoidiQ9R1D1.
OrthoDBiEOG091G06B4.
PhylomeDBiQ9R1D1.

Family and domain databases

Gene3Di3.30.160.60. 9 hits.
InterProiIPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
SMARTiSM00355. ZnF_C2H2. 11 hits.
[Graphical view]
PROSITEiPS00028. ZINC_FINGER_C2H2_1. 8 hits.
PS50157. ZINC_FINGER_C2H2_2. 11 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9R1D1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEGEAVEAIV EESETFIKGK ERKTYQRRRE GGQEEDACHL PQNQTDGGEV
60 70 80 90 100
VQDVNSSVQM VMMEQLDPTL LQMKTEVMEG TVAPEAEAAV DDTQIITLQV
110 120 130 140 150
VNMEEQPINI GELQLVQVPV PVTVPVATTS VEELQGAYEN EVSKEGLAES
160 170 180 190 200
EPMICHTLPL PEGFQVVKVG ANGEVETLEQ GELPPQEDPS WQKDPDYQPP
210 220 230 240 250
AKKTKKTKKS KLRYTEEGKD VDVSVYDFEE EQQEGLLSEV NAEKVVGNMK
260 270 280 290 300
PPKPTKIKKK GVKKTFQCEL CSYTCPRRSN LDRHMKSHTD ERPHKCHLCG
310 320 330 340 350
RAFRTVTLLR NHLNTHTGTR PHKCPDCDMA FVTSGELVRH RRYKHTHEKP
360 370 380 390 400
FKCSMCDYAS VEVSKLKRHI RSHTGERPFQ CSLCSYASRD TYKLKRHMRT
410 420 430 440 450
HSGEKPYECY ICHARFTQSG TMKMHILQKH TENVAKFHCP HCDTVIARKS
460 470 480 490 500
DLGVHLRKQH SYIEQGKKCR YCDAVFHERY ALIQHQKSHK NEKRFKCDQC
510 520 530 540 550
DYACRQERHM IMHKRTHTGE KPYACSHCDK TFRQKQLLDM HFKRYHDPNF
560 570 580 590 600
VPAAFVCSKC GKTFTRRNTM ARHADNCAGP DGVEGENGGE TKKSKRGRKR
610 620 630 640 650
KMRSKKEDSS DSENAEPDLD DNEEEEEPAV EIEPEPEPQP QPQPQPQPQP
660 670 680 690 700
VAPAPPPAKK RRGRPPGRTN QPKQNQPTAI IQVEDQNTGA IENIIVEVKK
710 720 730
EPDAEPAEGE EEEAQAAPAD APNGDLTPEM ILSMMDR
Length:737
Mass (Da):83,880
Last modified:May 1, 2000 - v1
Checksum:iB89A7AA7252DA7CE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF133731 mRNA. Translation: AAD27869.2.
RefSeqiNP_114012.1. NM_031824.1.
UniGeneiRn.18612.

Genome annotation databases

GeneIDi83726.
KEGGirno:83726.
UCSCiRGD:621344. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF133731 mRNA. Translation: AAD27869.2.
RefSeqiNP_114012.1. NM_031824.1.
UniGeneiRn.18612.

3D structure databases

ProteinModelPortaliQ9R1D1.
SMRiQ9R1D1. Positions 399-462, 515-591.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000023851.

PTM databases

iPTMnetiQ9R1D1.
PhosphoSiteiQ9R1D1.

Proteomic databases

PaxDbiQ9R1D1.
PRIDEiQ9R1D1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi83726.
KEGGirno:83726.
UCSCiRGD:621344. rat.

Organism-specific databases

CTDi10664.
RGDi621344. Ctcf.

Phylogenomic databases

eggNOGiKOG1721. Eukaryota.
COG5048. LUCA.
HOGENOMiHOG000276534.
HOVERGENiHBG000350.
InParanoidiQ9R1D1.
OrthoDBiEOG091G06B4.
PhylomeDBiQ9R1D1.

Miscellaneous databases

PROiQ9R1D1.

Gene expression databases

BgeeiENSRNOG00000017674.
GenevisibleiQ9R1D1. RN.

Family and domain databases

Gene3Di3.30.160.60. 9 hits.
InterProiIPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
SMARTiSM00355. ZnF_C2H2. 11 hits.
[Graphical view]
PROSITEiPS00028. ZINC_FINGER_C2H2_1. 8 hits.
PS50157. ZINC_FINGER_C2H2_2. 11 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiCTCF_RAT
AccessioniPrimary (citable) accession number: Q9R1D1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 23, 2003
Last sequence update: May 1, 2000
Last modified: September 7, 2016
This is version 109 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

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 one 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.