CCCTC-binding factor (CTCF), an 11-zinc-finger factor involved in gene regulation, utilizes different zinc fingers to bind varying DNA target sites. CTCF forms methylation-sensitive insulators that regulate X-chromosome inactivation. This gene is a paralog of CTCF and appears to be expressed primarily in the cytoplasm of spermatocytes, unlike CTCF which is expressed primarily i... See more...

Aliases for CTCFL Gene

Aliases for CTCFL Gene

  • CCCTC-Binding Factor Like 2 3 5
  • Transcriptional Repressor CTCFL 2 3 4
  • Cancer/Testis Antigen 27 2 3 4
  • Brother Of The Regulator Of Imprinted Sites 3 4
  • BORIS 3 4
  • CT27 3 4
  • CCCTC-Binding Factor (Zinc Finger Protein)-Like 2
  • Zinc Finger Protein CTCF-T 4
  • CCCTC-Binding Factor 4
  • BORIS-Like Protein 3
  • CTCF-Like Protein 4
  • CTCF Paralog 4
  • DJ579F20.2 3
  • HMGB1L1 3
  • CTCF-T 3

External Ids for CTCFL Gene

Previous GeneCards Identifiers for CTCFL Gene

  • GC20M055800
  • GC20M056710
  • GC20M056757
  • GC20M055505
  • GC20M056064
  • GC20M052853

Summaries for CTCFL Gene

Entrez Gene Summary for CTCFL Gene

  • CCCTC-binding factor (CTCF), an 11-zinc-finger factor involved in gene regulation, utilizes different zinc fingers to bind varying DNA target sites. CTCF forms methylation-sensitive insulators that regulate X-chromosome inactivation. This gene is a paralog of CTCF and appears to be expressed primarily in the cytoplasm of spermatocytes, unlike CTCF which is expressed primarily in the nucleus of somatic cells. CTCF and the protein encoded by this gene are normally expressed in a mutually exclusive pattern that correlates with resetting of methylation marks during male germ cell differentiation. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2012]

GeneCards Summary for CTCFL Gene

CTCFL (CCCTC-Binding Factor Like) is a Protein Coding gene. Diseases associated with CTCFL include Silver-Russell Syndrome and Mental Retardation, Autosomal Dominant 21. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and RNA polymerase II proximal promoter sequence-specific DNA binding. An important paralog of this gene is CTCF.

UniProtKB/Swiss-Prot Summary for CTCFL Gene

  • Testis-specific DNA binding protein responsible for insulator function, nuclear architecture and transcriptional control, which probably acts by recruiting epigenetic chromatin modifiers. Plays a key role in gene imprinting in male germline, by participating in the establishment of differential methylation at the IGF2/H19 imprinted control region (ICR). Directly binds the unmethylated H19 ICR and recruits the PRMT7 methyltransferase, leading to methylate histone H4 'Arg-3' to form H4R3sme2. This probably leads to recruit de novo DNA methyltransferases at these sites (By similarity). Seems to act as tumor suppressor. In association with DNMT1 and DNMT3B, involved in activation of BAG1 gene expression by binding to its promoter. Required for dimethylation of H3 lysine 4 (H3K4me2) of MYC and BRCA1 promoters.

Gene Wiki entry for CTCFL Gene

Additional gene information for CTCFL Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CTCFL Gene

Genomics for CTCFL Gene

GeneHancer (GH) Regulatory Elements for CTCFL Gene

Promoters and enhancers for CTCFL Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20J057522 Promoter/Enhancer 1.6 EPDnew Ensembl CraniofacialAtlas dbSUPER 500.7 +0.9 857 4.4 HNRNPK ZNF217 CTCF NRF1 ZIC2 AFF1 REST ZNF740 MYC TOE1 CTCFL HSALNG0131173 lnc-ZBP1-3
GH20J057527 Enhancer 0.7 Ensembl 500.7 -1.4 -1449 0.2 ZNF217 GATAD2B E4F1 ZNF207 NEUROD1 ZNF8 ZNF395 PKNOX1 ZNF407 DPF2 CTCFL HSALNG0131173 piR-33103-019
GH20J057408 Enhancer 1.7 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 9.9 +113.0 112951 9.8 HNRNPK PHB2 EP300 ZIC2 ZBTB11 AFF1 TARDBP RFX1 HES1 MYC RBM38 ZBP1 CTCFL ENSG00000218018 BMP7 HSALNG0131163
GH20J057495 Enhancer 1 ENCODE dbSUPER 10.8 +30.3 30252 0.2 ZNF217 CTCF REST CUX1 MYC CHD1 CTBP1 RAD21 TRIM22 TEAD1 ENSG00000218018 RBM38 MTND1P9 MTRNR2L3 RAE1 CTCFL PCK1 HMGB1P1 lnc-ZBP1-3
GH20J058179 Enhancer 1 ENCODE CraniofacialAtlas 10.2 -653.8 -653793 1 CTCF GABPA ZBTB26 REST CHD1 RAD21 GATAD2B ZKSCAN8 SMC3 SIN3A LOC105372694 PCK1 ANKRD60 CTCFL lnc-ANKRD60-1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CTCFL on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CTCFL

Top Transcription factor binding sites by QIAGEN in the CTCFL gene promoter:
  • Brachyury
  • Chx10
  • CUTL1
  • NF-1
  • Pax-4a
  • PPAR-gamma1
  • PPAR-gamma2
  • SEF-1 (1)
  • Sp1
  • USF-1

Genomic Locations for CTCFL Gene

Genomic Locations for CTCFL Gene
chr20:57,495,965-57,525,652
(GRCh38/hg38)
Size:
29,688 bases
Orientation:
Minus strand
chr20:56,071,035-56,100,708
(GRCh37/hg19)
Size:
29,674 bases
Orientation:
Minus strand

Genomic View for CTCFL Gene

Genes around CTCFL on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CTCFL Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CTCFL Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CTCFL Gene

Proteins for CTCFL Gene

  • Protein details for CTCFL Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NI51-CTCFL_HUMAN
    Recommended name:
    Transcriptional repressor CTCFL
    Protein Accession:
    Q8NI51
    Secondary Accessions:
    • A0S6W1
    • A1L4C6
    • A6XGL8
    • A6XGM2
    • A6XGM3
    • A6XGM8
    • A6XGN0
    • A6XGN1
    • A6XGN2
    • A6XGN3
    • A6XGN4
    • E7EQ27
    • E7EUE3
    • E9PBA9
    • Q5JUG4
    • Q9BZ30
    • Q9NQJ3

    Protein attributes for CTCFL Gene

    Size:
    663 amino acids
    Molecular mass:
    75747 Da
    Quaternary structure:
    • Interacts with histones, PRMT7 and SETD1A. Interacts (via N-terminus) with BAG6/BAT3.

    Alternative splice isoforms for CTCFL Gene

neXtProt entry for CTCFL Gene

Post-translational modifications for CTCFL Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Abcam antibodies for CTCFL
  • Boster Bio Antibodies for CTCFL

No data available for DME Specific Peptides for CTCFL Gene

Domains & Families for CTCFL Gene

Gene Families for CTCFL Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transcription factors

Protein Domains for CTCFL Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CTCFL Gene

GenScript: Design optimal peptide antigens:
  • BORIS-like protein (A0S6W1_HUMAN)
  • cDNA FLJ46191 fis, clone TESTI4005470, highly similar to Transcriptional repressor CTCFL (A1L4C6_HUMAN)
  • Zinc finger protein CTCF-T (CTCFL_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8NI51

UniProtKB/Swiss-Prot:

CTCFL_HUMAN :
  • Belongs to the CTCF zinc-finger protein family.
Family:
  • Belongs to the CTCF zinc-finger protein family.
genes like me logo Genes that share domains with CTCFL: view

Function for CTCFL Gene

Molecular function for CTCFL Gene

UniProtKB/Swiss-Prot Function:
Testis-specific DNA binding protein responsible for insulator function, nuclear architecture and transcriptional control, which probably acts by recruiting epigenetic chromatin modifiers. Plays a key role in gene imprinting in male germline, by participating in the establishment of differential methylation at the IGF2/H19 imprinted control region (ICR). Directly binds the unmethylated H19 ICR and recruits the PRMT7 methyltransferase, leading to methylate histone H4 'Arg-3' to form H4R3sme2. This probably leads to recruit de novo DNA methyltransferases at these sites (By similarity). Seems to act as tumor suppressor. In association with DNMT1 and DNMT3B, involved in activation of BAG1 gene expression by binding to its promoter. Required for dimethylation of H3 lysine 4 (H3K4me2) of MYC and BRCA1 promoters.

Phenotypes From GWAS Catalog for CTCFL Gene

Gene Ontology (GO) - Molecular Function for CTCFL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II proximal promoter sequence-specific DNA binding IDA 16140944
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific NAS 19274049
GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific IDA 16140944
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IDA,IEA 18413740
genes like me logo Genes that share ontologies with CTCFL: view
genes like me logo Genes that share phenotypes with CTCFL: view

Animal Models for CTCFL Gene

MGI Knock Outs for CTCFL:

Animal Model Products

CRISPR Products

Targeted motifs for CTCFL Gene
HOMER Transcription Factor Regulatory Elements motif CTCFL
  • Consensus sequence: CNNBRGCGCCCCCTGSTGGC Submotif: canonical Cell Type: K562 GEO ID: GSE32465

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology and Transcription Factor Targets for CTCFL Gene

Localization for CTCFL Gene

Subcellular locations from UniProtKB/Swiss-Prot for CTCFL Gene

Cytoplasm. Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CTCFL gene
Compartment Confidence
nucleus 5
cytosol 4
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nuclear bodies (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CTCFL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,ISS --
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IDA --
GO:0016604 nuclear body IDA --
genes like me logo Genes that share ontologies with CTCFL: view

Pathways & Interactions for CTCFL Gene

PathCards logo

SuperPathways for CTCFL Gene

No Data Available

SIGNOR curated interactions for CTCFL Gene

Activates:

Gene Ontology (GO) - Biological Process for CTCFL Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006325 chromatin organization IEA --
GO:0006349 regulation of gene expression by genetic imprinting IBA,ISS --
GO:0007049 cell cycle IEA --
GO:0010628 positive regulation of gene expression IDA 18413740
GO:0016571 histone methylation ISS --
genes like me logo Genes that share ontologies with CTCFL: view

No data available for Pathways by source for CTCFL Gene

Drugs & Compounds for CTCFL Gene

(1) Additional Compounds for CTCFL Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CTCFL: view

Transcripts for CTCFL Gene

mRNA/cDNA for CTCFL Gene

16 REFSEQ mRNAs :
34 NCBI additional mRNA sequence :
22 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CTCFL Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12a · 12b
SP1:
SP2: -
SP3:

Relevant External Links for CTCFL Gene

GeneLoc Exon Structure for
CTCFL

Expression for CTCFL Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CTCFL Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CTCFL Gene

This gene is overexpressed in Testis (x42.6).

Protein differential expression in normal tissues from HIPED for CTCFL Gene

This gene is overexpressed in Lung (14.2), Monocytes (14.1), Tlymphocyte (13.5), and CD4 Tcells (11.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CTCFL Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CTCFL

SOURCE GeneReport for Unigene cluster for CTCFL Gene:

Hs.131543

mRNA Expression by UniProt/SwissProt for CTCFL Gene:

Q8NI51-CTCFL_HUMAN
Tissue specificity: Testis specific. Specifically expressed in primary spermatocytes.
genes like me logo Genes that share expression patterns with CTCFL: view

No data available for Protein tissue co-expression partners , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for CTCFL Gene

Orthologs for CTCFL Gene

This gene was present in the common ancestor of animals.

Orthologs for CTCFL Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CTCFL 31 30
  • 98.62 (n)
OneToOne
dog
(Canis familiaris)
Mammalia CTCFL 31 30
  • 82.1 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CTCFL 30
  • 76.28 (n)
BORIS 31
  • 66 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ctcfl 17 31 30
  • 68.75 (n)
rat
(Rattus norvegicus)
Mammalia LOC100360757 30
  • 67.56 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CTCFL 31
  • 59 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CTCFL 31
  • 59 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CTCFL 31
  • 53 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii zgc:112083 31
  • 18 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta CTCF 31
  • 24 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8793 31
  • 20 (a)
OneToOne
Cin.2315 30
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.2315 30
Species where no ortholog for CTCFL was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CTCFL Gene

ENSEMBL:
Gene Tree for CTCFL (if available)
TreeFam:
Gene Tree for CTCFL (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CTCFL: view image

Paralogs for CTCFL Gene

(472) SIMAP similar genes for CTCFL Gene using alignment to 6 proteins:

  • CTCFL_HUMAN
  • A6XGN4_HUMAN
  • F5H2V8_HUMAN
  • V9GY73_HUMAN
  • V9GYX4_HUMAN
  • V9GZ46_HUMAN
genes like me logo Genes that share paralogs with CTCFL: view

Variants for CTCFL Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CTCFL Gene

SNP ID Clinical significance and condition Chr 20 pos Variation AA Info Type
rs6025606 - p.Thr177Ala
rs6070122 - p.Gln525Glu
rs6070128 - p.Glu50Gln
rs6092491 - p.Arg448His

Additional dbSNP identifiers (rs#s) for CTCFL Gene

Structural Variations from Database of Genomic Variants (DGV) for CTCFL Gene

Variant ID Type Subtype PubMed ID
dgv1256e212 CNV loss 25503493
dgv2272n106 CNV deletion 24896259
dgv7618n54 CNV loss 21841781
dgv7619n54 CNV gain+loss 21841781
dgv7620n54 CNV gain 21841781
dgv7621n54 CNV gain+loss 21841781
dgv7622n54 CNV loss 21841781
dgv7623n54 CNV loss 21841781
esv25156 CNV gain 19812545
esv2666374 CNV deletion 23128226
esv3557256 CNV deletion 23714750
esv3646212 CNV loss 21293372
esv3646213 CNV loss 21293372
nsv1055983 CNV gain 25217958
nsv1073071 CNV deletion 25765185
nsv3425 CNV insertion 18451855
nsv586312 CNV loss 21841781
nsv586313 CNV gain 21841781
nsv828758 CNV gain 20364138
nsv955140 CNV deletion 24416366

Variation tolerance for CTCFL Gene

Residual Variation Intolerance Score: 55.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.78; 58.10% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CTCFL Gene

Human Gene Mutation Database (HGMD)
CTCFL
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CTCFL

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CTCFL Gene

Disorders for CTCFL Gene

MalaCards: The human disease database

(6) MalaCards diseases for CTCFL Gene - From: DISEASES and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search CTCFL in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CTCFL

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CTCFL: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CTCFL Gene

Publications for CTCFL Gene

  1. Expression of the CTCF-paralogous cancer-testis gene, brother of the regulator of imprinted sites (BORIS), is regulated by three alternative promoters modulated by CpG methylation and by CTCF and p53 transcription factors. (PMID: 17962299) Renaud S … Lobanenkov V (Nucleic acids research 2007) 3 4 23 54
  2. The testis-specific factor CTCFL cooperates with the protein methyltransferase PRMT7 in H19 imprinting control region methylation. (PMID: 17048991) Jelinic P … Shaw P (PLoS biology 2006) 3 4 23 54
  3. The novel BORIS + CTCF gene family is uniquely involved in the epigenetics of normal biology and cancer. (PMID: 12191639) Klenova EM … Lobanenkov VV (Seminars in cancer biology 2002) 3 4 23 54
  4. BORIS, a novel male germ-line-specific protein associated with epigenetic reprogramming events, shares the same 11-zinc-finger domain with CTCF, the insulator protein involved in reading imprinting marks in the soma. (PMID: 12011441) Loukinov DI … Lobanenkov VV (Proceedings of the National Academy of Sciences of the United States of America 2002) 3 4 23 54
  5. Susceptibility for breast cancer in young patients with short rare minisatellite alleles of BORIS. (PMID: 21034534) Yoon SL … Leem SH (BMB reports 2010) 3 41 54

Products for CTCFL Gene

Sources for CTCFL Gene