UniProtKB - Q9R1D1 (CTCF_RAT)
Transcriptional repressor CTCF
Ctcf
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 an 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. Plays a role in the recruitment of CENPE to the pericentromeric/centromeric regions of the chromosome during mitosis.
By similarityRegions
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Zinc fingeri | 266 – 288 | C2H2-type 1PROSITE-ProRule annotationAdd BLAST | 23 | |
Zinc fingeri | 294 – 316 | C2H2-type 2PROSITE-ProRule annotationAdd BLAST | 23 | |
Zinc fingeri | 322 – 345 | C2H2-type 3PROSITE-ProRule annotationAdd BLAST | 24 | |
Zinc fingeri | 351 – 373 | C2H2-type 4PROSITE-ProRule annotationAdd BLAST | 23 | |
Zinc fingeri | 379 – 401 | C2H2-type 5PROSITE-ProRule annotationAdd BLAST | 23 | |
Zinc fingeri | 407 – 430 | C2H2-type 6PROSITE-ProRule annotationAdd BLAST | 24 | |
Zinc fingeri | 437 – 460 | C2H2-type 7PROSITE-ProRule annotationAdd BLAST | 24 | |
Zinc fingeri | 467 – 489 | C2H2-type 8PROSITE-ProRule annotationAdd BLAST | 23 | |
Zinc fingeri | 495 – 517 | C2H2-type 9PROSITE-ProRule annotationAdd BLAST | 23 | |
Zinc fingeri | 523 – 546 | C2H2-type 10PROSITE-ProRule annotationAdd BLAST | 24 | |
Zinc fingeri | 555 – 577 | C2H2-type 11; atypicalPROSITE-ProRule annotationAdd BLAST | 23 |
GO - Molecular functioni
- chromatin binding Source: RGD
- chromatin insulator sequence binding Source: RGD
- DNA binding Source: RGD
- DNA-binding transcription factor activity Source: RGD
- DNA-binding transcription repressor activity, RNA polymerase II-specific Source: RGD
- metal ion binding Source: UniProtKB-KW
- RNA polymerase II cis-regulatory region sequence-specific DNA binding Source: RGD
- sequence-specific DNA binding Source: RGD
- transcription cis-regulatory region binding Source: RGD
- transcription coregulator binding Source: RGD
GO - Biological processi
- chromosome segregation Source: UniProtKB-KW
- DNA methylation Source: RGD
- genetic imprinting Source: RGD
- maintenance of DNA methylation Source: RGD
- negative regulation of cell population proliferation Source: UniProtKB
- negative regulation of gene expression Source: RGD
- negative regulation of transcription, DNA-templated Source: RGD
- negative regulation of transcription by RNA polymerase II Source: RGD
- nucleosome positioning Source: RGD
- positive regulation of gene expression Source: RGD
- positive regulation of pri-miRNA transcription by RNA polymerase II Source: BHF-UCL
- positive regulation of transcription, DNA-templated Source: RGD
- protein localization to chromosome, centromeric region Source: UniProtKB
- regulation of gene expression, epigenetic Source: RGD
- regulation of gene expression by genetic imprinting Source: RGD
- regulation of histone acetylation Source: RGD
- regulation of histone methylation Source: RGD
- regulation of molecular function, epigenetic Source: RGD
- regulation of transcription, DNA-templated Source: RGD
- regulation of transcription by RNA polymerase II Source: GO_Central
Keywordsi
Molecular function | Activator, Chromatin regulator, DNA-binding, Repressor |
Biological process | Chromosome partition, Transcription, Transcription regulation |
Ligand | Metal-binding, Zinc |
Names & Taxonomyi
Protein namesi | Recommended name: Transcriptional repressor CTCFAlternative name(s): 11-zinc finger protein CCCTC-binding factor CTCFL paralog |
Gene namesi | Name:Ctcf |
Organismi | Rattus norvegicus (Rat) |
Taxonomic identifieri | 10116 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Myomorpha › Muroidea › Muridae › Murinae › Rattus |
Proteomesi |
|
Organism-specific databases
RGDi | 621344, Ctcf |
Subcellular locationi
Nucleus
- nucleoplasm By similarity
Other locations
- Chromosome By similarity
- centromere 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
Nucleus
- nucleolus Source: RGD
- nucleoplasm Source: RGD
- nucleus Source: UniProtKB
Other locations
- chromosome, centromeric region Source: UniProtKB
- condensed chromosome Source: RGD
Keywords - Cellular componenti
Centromere, Chromosome, NucleusPTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000047230 | 1 – 737 | Transcriptional repressor CTCFAdd BLAST | 737 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 1 | N-acetylmethionineBy similarity | 1 | |
Cross-linki | 18 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity | ||
Cross-linki | 74 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO)By similarity | ||
Cross-linki | 219 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity | ||
Modified residuei | 289 | PhosphothreonineBy similarity | 1 | |
Modified residuei | 317 | PhosphothreonineBy similarity | 1 | |
Modified residuei | 374 | PhosphothreonineBy similarity | 1 | |
Modified residuei | 402 | PhosphoserineBy similarity | 1 | |
Modified residuei | 609 | PhosphoserineBy similarity | 1 | |
Modified residuei | 610 | PhosphoserineBy similarity | 1 | |
Modified residuei | 612 | PhosphoserineBy similarity | 1 | |
Cross-linki | 699 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternateBy similarity | ||
Cross-linki | 699 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternateBy similarity |
Post-translational modificationi
Keywords - PTMi
Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugationProteomic databases
PaxDbi | Q9R1D1 |
PRIDEi | Q9R1D1 |
PTM databases
iPTMneti | Q9R1D1 |
PhosphoSitePlusi | Q9R1D1 |
Interactioni
Subunit structurei
Interacts with CHD8.
Interacts with LLPH.
Interacts with CENPE.
By similarityGO - Molecular functioni
- transcription coregulator binding Source: RGD
Protein-protein interaction databases
STRINGi | 10116.ENSRNOP00000023851 |
Family & Domainsi
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 180 – 211 | DisorderedSequence analysisAdd BLAST | 32 | |
Regioni | 573 – 687 | DisorderedSequence analysisAdd BLAST | 115 | |
Regioni | 699 – 727 | DisorderedSequence analysisAdd BLAST | 29 |
Compositional bias
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Compositional biasi | 613 – 633 | Acidic residuesSequence analysisAdd BLAST | 21 | |
Compositional biasi | 634 – 660 | Pro residuesSequence analysisAdd BLAST | 27 | |
Compositional biasi | 668 – 687 | Polar residuesSequence analysisAdd BLAST | 20 |
Sequence similaritiesi
Zinc finger
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Zinc fingeri | 266 – 288 | C2H2-type 1PROSITE-ProRule annotationAdd BLAST | 23 | |
Zinc fingeri | 294 – 316 | C2H2-type 2PROSITE-ProRule annotationAdd BLAST | 23 | |
Zinc fingeri | 322 – 345 | C2H2-type 3PROSITE-ProRule annotationAdd BLAST | 24 | |
Zinc fingeri | 351 – 373 | C2H2-type 4PROSITE-ProRule annotationAdd BLAST | 23 | |
Zinc fingeri | 379 – 401 | C2H2-type 5PROSITE-ProRule annotationAdd BLAST | 23 | |
Zinc fingeri | 407 – 430 | C2H2-type 6PROSITE-ProRule annotationAdd BLAST | 24 | |
Zinc fingeri | 437 – 460 | C2H2-type 7PROSITE-ProRule annotationAdd BLAST | 24 | |
Zinc fingeri | 467 – 489 | C2H2-type 8PROSITE-ProRule annotationAdd BLAST | 23 | |
Zinc fingeri | 495 – 517 | C2H2-type 9PROSITE-ProRule annotationAdd BLAST | 23 | |
Zinc fingeri | 523 – 546 | C2H2-type 10PROSITE-ProRule annotationAdd BLAST | 24 | |
Zinc fingeri | 555 – 577 | C2H2-type 11; atypicalPROSITE-ProRule annotationAdd BLAST | 23 |
Keywords - Domaini
Repeat, Zinc-fingerPhylogenomic databases
eggNOGi | KOG1721, Eukaryota |
HOGENOMi | CLU_002678_77_1_1 |
InParanoidi | Q9R1D1 |
PhylomeDBi | Q9R1D1 |
Family and domain databases
InterProi | View protein in InterPro IPR036236, Znf_C2H2_sf IPR013087, Znf_C2H2_type |
Pfami | View protein in Pfam PF00096, zf-C2H2, 6 hits |
SMARTi | View protein in SMART SM00355, ZnF_C2H2, 11 hits |
SUPFAMi | SSF57667, SSF57667, 7 hits |
PROSITEi | View protein in PROSITE PS00028, ZINC_FINGER_C2H2_1, 8 hits PS50157, ZINC_FINGER_C2H2_2, 11 hits |
(1+)i Sequence
Sequence statusi: Complete.
This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All
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
Computationally mapped potential isoform sequencesi
There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basketA0A0H2UHP0 | A0A0H2UHP0_RAT | CCCTC-binding factor, isoform CRA_a | Ctcf rCG_51518 | 738 | Annotation score: |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AF133731 mRNA Translation: AAD27869.2 |
RefSeqi | NP_114012.1, NM_031824.1 |
Genome annotation databases
GeneIDi | 83726 |
KEGGi | rno:83726 |
UCSCi | RGD:621344, rat |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AF133731 mRNA Translation: AAD27869.2 |
RefSeqi | NP_114012.1, NM_031824.1 |
3D structure databases
SMRi | Q9R1D1 |
ModBasei | Search... |
Protein-protein interaction databases
STRINGi | 10116.ENSRNOP00000023851 |
PTM databases
iPTMneti | Q9R1D1 |
PhosphoSitePlusi | Q9R1D1 |
Proteomic databases
PaxDbi | Q9R1D1 |
PRIDEi | Q9R1D1 |
Genome annotation databases
GeneIDi | 83726 |
KEGGi | rno:83726 |
UCSCi | RGD:621344, rat |
Organism-specific databases
CTDi | 10664 |
RGDi | 621344, Ctcf |
Phylogenomic databases
eggNOGi | KOG1721, Eukaryota |
HOGENOMi | CLU_002678_77_1_1 |
InParanoidi | Q9R1D1 |
PhylomeDBi | Q9R1D1 |
Miscellaneous databases
PROi | PR:Q9R1D1 |
Gene expression databases
Genevisiblei | Q9R1D1, RN |
Family and domain databases
InterProi | View protein in InterPro IPR036236, Znf_C2H2_sf IPR013087, Znf_C2H2_type |
Pfami | View protein in Pfam PF00096, zf-C2H2, 6 hits |
SMARTi | View protein in SMART SM00355, ZnF_C2H2, 11 hits |
SUPFAMi | SSF57667, SSF57667, 7 hits |
PROSITEi | View protein in PROSITE PS00028, ZINC_FINGER_C2H2_1, 8 hits PS50157, ZINC_FINGER_C2H2_2, 11 hits |
MobiDBi | Search... |
Entry informationi
Entry namei | CTCF_RAT | |
Accessioni | Q9R1D1Primary (citable) accession number: Q9R1D1 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | April 23, 2003 |
Last sequence update: | May 1, 2000 | |
Last modified: | September 29, 2021 | |
This is version 140 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
Reference proteomeDocuments
- SIMILARITY comments
Index of protein domains and families