Human Gene CTCF (ENST00000264010.10) from GENCODE V44
Description: Homo sapiens CCCTC-binding factor (CTCF), transcript variant 1, mRNA. (from RefSeq NM_006565) RefSeq Summary (NM_006565): This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. Depending upon the context of the site, the protein can bind a histone acetyltransferase (HAT)-containing complex and function as a transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as a transcriptional repressor. If the protein is bound to a transcriptional insulator element, it can block communication between enhancers and upstream promoters, thereby regulating imprinted expression. Mutations in this gene have been associated with invasive breast cancers, prostate cancers, and Wilms' tumors. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]. Gencode Transcript: ENST00000264010.10 Gencode Gene: ENSG00000102974.16 Transcript (Including UTRs) Position: hg38 chr16:67,562,526-67,639,177 Size: 76,652 Total Exon Count: 12 Strand: + Coding Region Position: hg38 chr16:67,610,833-67,637,872 Size: 27,040 Coding Exon Count: 10
ID:CTCF_HUMAN DESCRIPTION: RecName: Full=Transcriptional repressor CTCF; AltName: Full=11-zinc finger protein; AltName: Full=CCCTC-binding factor; AltName: Full=CTCFL paralog; FUNCTION: 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. SUBUNIT: Interacts with CHD8. SUBCELLULAR LOCATION: Nucleus, nucleoplasm. Chromosome. Chromosome, centromere. 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. TISSUE SPECIFICITY: Ubiquitous. Absent in primary spermatocytes. DOMAIN: The 11 zinc fingers are highly conserved among vertebrates, exhibiting almost identical amino acid sequences. Different subsets or combination of individual zinc fingers gives the ability to CTCF to recognize multiple DNA target sites. PTM: Sumoylated on Lys-74 and Lys-689; sumoylation of CTCF contributes to the repressive function of CTCF on the MYC P2 promoter (By similarity). MISCELLANEOUS: More than 13'00 CTCF-binding sites in potential insulators were identified in the human genome. SIMILARITY: Belongs to the CTCF zinc-finger protein family. SIMILARITY: Contains 11 C2H2-type zinc fingers.
The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.
ModBase Predicted Comparative 3D Structure on P49711
Front
Top
Side
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.
Orthologous Genes in Other Species
Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
Gene Ontology (GO) Annotations with Structured Vocabulary
Molecular Function: GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding GO:0003676 nucleic acid binding GO:0003677 DNA binding GO:0003700 transcription factor activity, sequence-specific DNA binding GO:0003714 transcription corepressor activity GO:0005515 protein binding GO:0008270 zinc ion binding GO:0043035 chromatin insulator sequence binding GO:0043565 sequence-specific DNA binding GO:0044212 transcription regulatory region DNA binding GO:0046872 metal ion binding
Biological Process: GO:0000122 negative regulation of transcription from RNA polymerase II promoter GO:0006325 chromatin organization GO:0006351 transcription, DNA-templated GO:0006355 regulation of transcription, DNA-templated GO:0007059 chromosome segregation GO:0008285 negative regulation of cell proliferation GO:0010628 positive regulation of gene expression GO:0016584 nucleosome positioning GO:0040029 regulation of gene expression, epigenetic GO:0040030 regulation of molecular function, epigenetic GO:0045892 negative regulation of transcription, DNA-templated GO:0045893 positive regulation of transcription, DNA-templated GO:0070602 regulation of centromeric sister chromatid cohesion GO:0071459 protein localization to chromosome, centromeric region
AK314804 - Homo sapiens cDNA, FLJ95678. U25435 - Human transcriptional repressor (CTCF) mRNA, complete cds. BC014267 - Homo sapiens CCCTC-binding factor (zinc finger protein), mRNA (cDNA clone MGC:10345 IMAGE:3840827), complete cds. AB209793 - Homo sapiens mRNA for CCCTC-binding factor (zinc finger protein) variant protein. AB385545 - Synthetic construct DNA, clone: pF1KB5285, Homo sapiens CTCF gene for transcriptional repressor CTCF, complete cds, without stop codon, in Flexi system. BT009915 - Homo sapiens CCCTC-binding factor (zinc finger protein) mRNA, complete cds. DQ895834 - Synthetic construct Homo sapiens clone IMAGE:100010294; FLH188107.01L; RZPDo839G07149D CCCTC-binding factor (zinc finger protein) (CTCF) gene, encodes complete protein. EU176369 - Synthetic construct Homo sapiens clone IMAGE:100006473; FLH188111.01X; RZPDo839G07150D CCCTC-binding factor (zinc finger protein) (CTCF) gene, encodes complete protein. KJ893105 - Synthetic construct Homo sapiens clone ccsbBroadEn_02499 CTCF gene, encodes complete protein. AK093395 - Homo sapiens cDNA FLJ36076 fis, clone TESTI2019760, highly similar to TRANSCRIPTIONAL REPRESSOR CTCF. AX748098 - Sequence 1623 from Patent EP1308459. JD369691 - Sequence 350715 from Patent EP1572962. CU676951 - Synthetic construct Homo sapiens gateway clone IMAGE:100020450 5' read CTCF mRNA. JD405374 - Sequence 386398 from Patent EP1572962. JD549984 - Sequence 531008 from Patent EP1572962. JD328896 - Sequence 309920 from Patent EP1572962. JD516772 - Sequence 497796 from Patent EP1572962. JD494488 - Sequence 475512 from Patent EP1572962. JD167412 - Sequence 148436 from Patent EP1572962. JD167196 - Sequence 148220 from Patent EP1572962. JD563881 - Sequence 544905 from Patent EP1572962. JD080811 - Sequence 61835 from Patent EP1572962. JD261801 - Sequence 242825 from Patent EP1572962. JD280186 - Sequence 261210 from Patent EP1572962.
Biochemical and Signaling Pathways
BioCarta from NCI Cancer Genome Anatomy Project h_ctcfPathway - CTCF: First Multivalent Nuclear Factor
Reactome (by CSHL, EBI, and GO)
Protein P49711 (Reactome details) participates in the following event(s):
R-HSA-5617472 Activation of anterior HOX genes in hindbrain development during early embryogenesis R-HSA-5619507 Activation of HOX genes during differentiation R-HSA-1266738 Developmental Biology
US Server
