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    CTCFL CCCTC-binding factor like [ Homo sapiens (human) ]

    Gene ID: 140690, updated on 8-Oct-2017
    Official Symbol
    CTCFLprovided by HGNC
    Official Full Name
    CCCTC-binding factor likeprovided by HGNC
    Primary source
    HGNC:HGNC:16234
    See related
    Ensembl:ENSG00000124092 MIM:607022; Vega:OTTHUMG00000032829
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CT27; BORIS; CTCF-T; HMGB1L1; dJ579F20.2
    Summary
    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]
    Orthologs
    Location:
    20q13.31
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 20 NC_000020.11 (57495965..57525652, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (56071021..56100708, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372688 Neighboring gene high mobility group box 1 pseudogene 1 Neighboring gene phosphoenolpyruvate carboxykinase 1 Neighboring gene uncharacterized LOC105372690

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    NHGRI GWAS Catalog

    Description
    Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines.
    NHGRI GWA Catalog
    Genome-wide association of lipid-lowering response to statins in combined study populations.
    NHGRI GWA Catalog
    Genome-wide association study identifies a novel locus contributing to type 2 diabetes susceptibility in Sikhs of Punjabi origin from India.
    NHGRI GWA Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    NHGRI GWA Catalog
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • MGC163358, MGC169105, MGC169106

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    RNA polymerase II core promoter proximal region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    transcription regulatory region DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    DNA methylation involved in gamete generation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cell cycle IEA
    Inferred from Electronic Annotation
    more info
     
    histone methylation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation of gene expression IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transcription from RNA polymerase II promoter IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of transcription, DNA-templated IDA
    Inferred from Direct Assay
    more info
    PubMed 
    regulation of gene expression by genetic imprinting ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    regulation of histone H3-K4 methylation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    transcription from RNA polymerase II promoter IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Preferred Names
    transcriptional repressor CTCFL
    Names
    BORIS-like protein
    brother of the regulator of imprinted sites
    cancer/testis antigen 27

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001269040.1NP_001255969.1  transcriptional repressor CTCFL isoform 1

      See identical proteins and their annotated locations for NP_001255969.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1, also known as A1) and variants 2 and 3 encode the same isoform (1).
      Source sequence(s)
      AY071919, DQ778108
      Consensus CDS
      CCDS13459.1
      UniProtKB/Swiss-Prot
      Q8NI51
      Related
      ENSP00000360239.2, OTTHUMP00000174287, ENST00000371196.6, OTTHUMT00000267821
      Conserved Domains (3) summary
      COG5048
      Location:259403
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:344364
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:385409
      zf-H2C2_2; Zinc-finger double domain
    2. NM_001269041.1NP_001255970.1  transcriptional repressor CTCFL isoform 1

      See identical proteins and their annotated locations for NP_001255970.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3, also known as C1) differs in the 5' UTR, compared to variant 1. Variants 1, 2 and 3 encode the same isoform (1).
      Source sequence(s)
      DQ778110, DQ778111
      Consensus CDS
      CCDS13459.1
      UniProtKB/Swiss-Prot
      Q8NI51
      Related
      ENSP00000476783.1, OTTHUMP00000274154, ENST00000608263.5, OTTHUMT00000472040
      Conserved Domains (3) summary
      COG5048
      Location:259403
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:344364
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:385409
      zf-H2C2_2; Zinc-finger double domain
    3. NM_001269042.1NP_001255971.1  transcriptional repressor CTCFL isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has an alternate splice site in the 3' coding region, compared to variant 1. The resulting isoform (2) lacks an internal aa in the C-terminal region, compared to isoform 1.
      Source sequence(s)
      AY071919, DQ294738, DQ778108
      UniProtKB/Swiss-Prot
      Q8NI51
      Conserved Domains (3) summary
      COG5048
      Location:259403
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:344364
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:385409
      zf-H2C2_2; Zinc-finger double domain
    4. NM_001269043.1NP_001255972.1  transcriptional repressor CTCFL isoform 3

      See identical proteins and their annotated locations for NP_001255972.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5, also known as B1) differs in the 5' and 3' UTRs and the 3' coding region, compared to variant 1. The resulting isoform (3) has a longer C-terminus, compared to isoform 1.
      Source sequence(s)
      DQ778109, DQ778111
      Consensus CDS
      CCDS58780.1
      UniProtKB/Swiss-Prot
      Q8NI51
      Related
      ENSP00000415579.2, OTTHUMP00000274173, ENST00000423479.7, OTTHUMT00000472061
      Conserved Domains (3) summary
      COG5048
      Location:259403
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:344364
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:385409
      zf-H2C2_2; Zinc-finger double domain
    5. NM_001269044.1NP_001255973.1  transcriptional repressor CTCFL isoform 4

      See identical proteins and their annotated locations for NP_001255973.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6, also known C3) differs in the 5' and 3' UTRs and the 3' coding region, compared to variant 1. The resulting isoform (4) has a longer and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      DQ778115
      Consensus CDS
      CCDS58781.1
      UniProtKB/Swiss-Prot
      Q8NI51
      Related
      ENSP00000477488.1, OTTHUMP00000274176, ENST00000608440.5, OTTHUMT00000472067
      Conserved Domains (3) summary
      COG5048
      Location:259403
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:344364
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:385409
      zf-H2C2_2; Zinc-finger double domain
    6. NM_001269045.1NP_001255974.1  transcriptional repressor CTCFL isoform 5

      See identical proteins and their annotated locations for NP_001255974.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7, also known as A5) lacks two exons and includes an alternate 3' terminal exon, compared to variant 1. The resulting isoform (5) has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AY071919, DQ778122
      Consensus CDS
      CCDS68164.1
      UniProtKB/Swiss-Prot
      Q8NI51
      UniProtKB/TrEMBL
      A6XGM9, V9GY73
      Related
      ENSP00000476458.1, OTTHUMP00000274163, ENST00000608425.5, OTTHUMT00000472049
      Conserved Domains (3) summary
      COG5048
      Location:259403
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:344364
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:385409
      zf-H2C2_2; Zinc-finger double domain
    7. NM_001269046.1NP_001255975.1  transcriptional repressor CTCFL isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8, also known as A3) has an additional segment in the 5' UTR and lacks an in-frame exon in the coding region, compared to variant 1. The resulting isoform (6) lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      AY071919, DQ778112
      Consensus CDS
      CCDS58779.1
      UniProtKB/Swiss-Prot
      Q8NI51
      Related
      ENSP00000415329.2, OTTHUMP00000274156, ENST00000429804.7, OTTHUMT00000472042
      Conserved Domains (3) summary
      COG5048
      Location:259443
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:259279
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:357378
      zf-H2C2_2; Zinc-finger double domain
    8. NM_001269047.1NP_001255976.1  transcriptional repressor CTCFL isoform 7

      See identical proteins and their annotated locations for NP_001255976.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9, also known as A6) lacks two exons and includes an alternate 3' terminal exon, compared to variant 1. The resulting isoform (7) has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      DQ778123
      Consensus CDS
      CCDS58782.1
      UniProtKB/Swiss-Prot
      Q8NI51
      Related
      ENSP00000399061.2, OTTHUMP00000274162, ENST00000422869.6, OTTHUMT00000472048
      Conserved Domains (3) summary
      COG5048
      Location:259403
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:344364
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:385409
      zf-H2C2_2; Zinc-finger double domain
    9. NM_001269048.1NP_001255977.1  transcriptional repressor CTCFL isoform 8

      See identical proteins and their annotated locations for NP_001255977.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (10, also known as C6) lacks several exons and includes an alternate 3' terminal exon, compared to variant 1. The resulting isoform (8) lacks an internal segment and has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      DQ778121
      Consensus CDS
      CCDS58778.1
      UniProtKB/Swiss-Prot
      Q8NI51
      Related
      ENSP00000409344.2, OTTHUMP00000274159, ENST00000432255.6, OTTHUMT00000472045
      Conserved Domains (3) summary
      COG5048
      Location:259413
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:259279
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:300324
      zf-H2C2_2; Zinc-finger double domain
    10. NM_001269049.1NP_001255978.1  transcriptional repressor CTCFL isoform 9

      See identical proteins and their annotated locations for NP_001255978.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (11, also kown as B3) differs in the 5' and 3' UTRs and has multiple coding region differences, compared to variant 1. The translation initiation is at a downstream in-frame AUG and the resulting isoform (9, also known as B3) has a shorter N-terminus and a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      DQ778109, DQ778125
      Consensus CDS
      CCDS68162.1
      UniProtKB/Swiss-Prot
      Q8NI51
      Related
      ENSP00000392034.3, OTTHUMP00000274178, ENST00000433949.7, OTTHUMT00000472069
      Conserved Domains (3) summary
      COG5048
      Location:54198
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:139159
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:180204
      zf-H2C2_2; Zinc-finger double domain
    11. NM_001269050.1NP_001255979.1  transcriptional repressor CTCFL isoform 10

      See identical proteins and their annotated locations for NP_001255979.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (12, also known as B4) differs in the 5' and 3' UTRs and has multiple coding region differences, compared to variant 1. The translation initiation is at a downstream in-frame AUG and the resulting isoform (10, also known as B4) has a shorter N-terminus and a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      BC060763, DQ778126
      Consensus CDS
      CCDS58777.1
      UniProtKB/Swiss-Prot
      Q8NI51
      Related
      ENSP00000439998.1, OTTHUMP00000274160, ENST00000539382.5, OTTHUMT00000472046
      Conserved Domains (3) summary
      COG5048
      Location:54198
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:139159
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:180204
      zf-H2C2_2; Zinc-finger double domain
    12. NM_001269051.1NP_001255980.1  transcriptional repressor CTCFL isoform 11

      See identical proteins and their annotated locations for NP_001255980.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (13, also known as A4) lacks multiple exons and includes an alternate 3' terminal segment, compared to variant 1. The resulting isoform (11) has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AW243377, AY071919, DQ778113
      Consensus CDS
      CCDS68163.1
      UniProtKB/Swiss-Prot
      Q8NI51
      UniProtKB/TrEMBL
      A6XGM0, V9GYX4
      Related
      ENSP00000476577.1, OTTHUMP00000274169, ENST00000481655.2, OTTHUMT00000472055
      Conserved Domains (3) summary
      COG5048
      Location:259319
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:259279
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:300324
      zf-H2C2_2; Zinc-finger double domain
    13. NM_001269052.1NP_001255981.1  transcriptional repressor CTCFL isoform 11

      See identical proteins and their annotated locations for NP_001255981.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (14, also known as C2) differs in the 5' UTR, lacks multiple exons and includes an alternate 3' terminal exon, compared to variant 1. The resulting isoform (11) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AW243377, AY071919, DQ778114
      Consensus CDS
      CCDS68163.1
      UniProtKB/Swiss-Prot
      Q8NI51
      UniProtKB/TrEMBL
      A6XGM0, V9GYX4
      Related
      ENSP00000477165.1, OTTHUMP00000274168, ENST00000608158.5, OTTHUMT00000472054
      Conserved Domains (3) summary
      COG5048
      Location:259319
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:259279
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:300324
      zf-H2C2_2; Zinc-finger double domain
    14. NM_001269054.1NP_001255983.1  transcriptional repressor CTCFL isoform 12

      See identical proteins and their annotated locations for NP_001255983.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (15, also known as B2) differs in the 5' and 3' UTRs and has multiple differences in the coding region, compared to variant 1. The resulting isoform (12) has a shorter N-terminus and a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      DQ778109, DQ778124
      Consensus CDS
      CCDS58776.1
      UniProtKB/Swiss-Prot
      Q8NI51
      Related
      ENSP00000437999.1, OTTHUMP00000274177, ENST00000502686.6, OTTHUMT00000472068
      Conserved Domains (3) summary
      COG5048
      Location:3141
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:82102
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:123147
      zf-H2C2_2; Zinc-finger double domain
    15. NM_001269055.1NP_001255984.1  transcriptional repressor CTCFL isoform 13

      See identical proteins and their annotated locations for NP_001255984.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (16, also known as B5) differs in the 5' and 3' UTRs and has multiple differences in the coding region, compared to variant 1. The resulting isoform (13) has a shorter N-terminus and a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      BC060763, DQ778127
      Consensus CDS
      CCDS68161.1
      UniProtKB/Swiss-Prot
      Q8NI51
      Related
      ENSP00000476718.1, OTTHUMP00000274161, ENST00000608903.5, OTTHUMT00000472047
      Conserved Domains (3) summary
      COG5048
      Location:3141
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:82102
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:123147
      zf-H2C2_2; Zinc-finger double domain
    16. NM_080618.3NP_542185.2  transcriptional repressor CTCFL isoform 1

      See identical proteins and their annotated locations for NP_542185.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2, also know as A2) has an additional exon in the 5' UTR, compared to variant 1. Variants 1, 2 and 3 encode the same isoform (1).
      Source sequence(s)
      AY071919, DQ778109
      Consensus CDS
      CCDS13459.1
      UniProtKB/Swiss-Prot
      Q8NI51
      Related
      ENSP00000476398.1, OTTHUMP00000274155, ENST00000609232.5, OTTHUMT00000472041
      Conserved Domains (3) summary
      COG5048
      Location:259403
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:344364
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:385409
      zf-H2C2_2; Zinc-finger double domain

    RNA

    1. NR_072975.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (17) has alternate 5' and 3' sequences and has an additional internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AY071919, DQ778118
      Related
      ENST00000426658.6, OTTHUMT00000472043

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p7 Primary Assembly

      Range
      57495965..57525652 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.1

    Genomic

    1. NC_018931.2 Alternate CHM1_1.1

      Range
      55972071..56001746 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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