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

Gene ID: 140690, updated on 23-Nov-2021

Summary

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
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]
Expression
Restricted expression toward testis (RPKM 3.5) See more
Orthologs
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Genomic context

See CTCFL in Genome Data Viewer
Location:
20q13.31
Exon count:
16
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 20 NC_000020.11 (57495965..57525652, complement)
105.20201022 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 Sharpr-MPRA regulatory region 5175 Neighboring gene high mobility group box 1 pseudogene 1 Neighboring gene phosphoenolpyruvate carboxykinase 1 Neighboring gene uncharacterized LOC105372690

Genomic regions, transcripts, and products

Expression

  • 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Discovery of genetic biomarkers contributing to variation in drug response of cytidine analogues using human lymphoblastoid cell lines.
GeneReviews: Not available
Genome-wide association of lipid-lowering response to statins in combined study populations.
GeneReviews: Not available
Genome-wide association study identifies a novel locus contributing to type 2 diabetes susceptibility in Sikhs of Punjabi origin from India.
GeneReviews: Not available
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC163358, MGC169105, MGC169106

Gene Ontology Provided by GOA

Component Evidence Code Pubs
is_active_in chromosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 
located_in nuclear body IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
transcriptional repressor CTCFL
Names
BORIS-like protein
brother of the regulator of imprinted sites
cancer/testis antigen 27

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_001269040.2NP_001255969.1  transcriptional repressor CTCFL isoform 1

    See identical proteins and their annotated locations for NP_001255969.1

    Status: REVIEWED

    Source sequence(s)
    AL035541, AL160176
    Consensus CDS
    CCDS13459.1
    UniProtKB/Swiss-Prot
    Q8NI51
    Related
    ENSP00000360239.2, ENST00000371196.6
    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]
    cd20908
    Location:392432
    SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins
  2. NM_001269041.2NP_001255970.1  transcriptional repressor CTCFL isoform 1

    See identical proteins and their annotated locations for NP_001255970.1

    Status: REVIEWED

    Source sequence(s)
    AL035541, AL160176
    Consensus CDS
    CCDS13459.1
    UniProtKB/Swiss-Prot
    Q8NI51
    Related
    ENSP00000476783.1, ENST00000608263.5
    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]
    cd20908
    Location:392432
    SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins
  3. NM_001269042.2NP_001255971.1  transcriptional repressor CTCFL isoform 2

    Status: REVIEWED

    Source sequence(s)
    AL035541, AL160176
    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]
    cd20908
    Location:392432
    SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins
  4. NM_001269043.2NP_001255972.1  transcriptional repressor CTCFL isoform 3

    See identical proteins and their annotated locations for NP_001255972.1

    Status: REVIEWED

    Source sequence(s)
    AL035541, AL160176
    Consensus CDS
    CCDS58780.1
    UniProtKB/Swiss-Prot
    Q8NI51
    Related
    ENSP00000415579.2, ENST00000423479.7
    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_001269044.3NP_001255973.1  transcriptional repressor CTCFL isoform 4

    See identical proteins and their annotated locations for NP_001255973.1

    Status: REVIEWED

    Source sequence(s)
    AL035541, AL160176
    Consensus CDS
    CCDS58781.1
    UniProtKB/Swiss-Prot
    Q8NI51
    Related
    ENSP00000477488.1, ENST00000608440.5
    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]
    cd20908
    Location:392432
    SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins
  6. NM_001269045.2NP_001255974.1  transcriptional repressor CTCFL isoform 5

    See identical proteins and their annotated locations for NP_001255974.1

    Status: REVIEWED

    Source sequence(s)
    AL035541, AL160176
    Consensus CDS
    CCDS68164.1
    UniProtKB/Swiss-Prot
    Q8NI51
    UniProtKB/TrEMBL
    A6XGM9, V9GY73
    Related
    ENSP00000476458.1, ENST00000608425.5
    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_001269046.2NP_001255975.1  transcriptional repressor CTCFL isoform 6

    Status: REVIEWED

    Source sequence(s)
    AL035541, AL160176
    Consensus CDS
    CCDS58779.1
    UniProtKB/Swiss-Prot
    Q8NI51
    Related
    ENSP00000415329.2, ENST00000429804.7
    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_001269047.2NP_001255976.1  transcriptional repressor CTCFL isoform 7

    See identical proteins and their annotated locations for NP_001255976.1

    Status: REVIEWED

    Source sequence(s)
    AL035541, AL160176
    Consensus CDS
    CCDS58782.1
    UniProtKB/Swiss-Prot
    Q8NI51
    Related
    ENSP00000399061.2, ENST00000422869.6
    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_001269048.3NP_001255977.1  transcriptional repressor CTCFL isoform 8

    See identical proteins and their annotated locations for NP_001255977.1

    Status: REVIEWED

    Source sequence(s)
    AL035541, AL160176
    Consensus CDS
    CCDS58778.1
    UniProtKB/Swiss-Prot
    Q8NI51
    Related
    ENSP00000409344.2, ENST00000432255.6
    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_001269049.2NP_001255978.1  transcriptional repressor CTCFL isoform 9

    See identical proteins and their annotated locations for NP_001255978.1

    Status: REVIEWED

    Source sequence(s)
    AL035541, AL160176
    Consensus CDS
    CCDS68162.1
    UniProtKB/Swiss-Prot
    Q8NI51
    Related
    ENSP00000392034.3, ENST00000433949.7
    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_001269050.3NP_001255979.1  transcriptional repressor CTCFL isoform 10

    See identical proteins and their annotated locations for NP_001255979.1

    Status: REVIEWED

    Source sequence(s)
    AL035541, AL160176
    Consensus CDS
    CCDS58777.1
    UniProtKB/Swiss-Prot
    Q8NI51
    Related
    ENSP00000439998.1, ENST00000539382.5
    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_001269051.2NP_001255980.1  transcriptional repressor CTCFL isoform 11

    See identical proteins and their annotated locations for NP_001255980.1

    Status: REVIEWED

    Source sequence(s)
    AL035541, AL160176
    Consensus CDS
    CCDS68163.1
    UniProtKB/Swiss-Prot
    Q8NI51
    UniProtKB/TrEMBL
    A6XGM0, V9GYX4
    Related
    ENSP00000476577.1, ENST00000481655.2
    Conserved Domains (2) summary
    sd00017
    Location:259279
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:271296
    zf-H2C2_2; Zinc-finger double domain
  13. NM_001269052.3NP_001255981.1  transcriptional repressor CTCFL isoform 11

    See identical proteins and their annotated locations for NP_001255981.1

    Status: REVIEWED

    Source sequence(s)
    AL035541, AL160176
    Consensus CDS
    CCDS68163.1
    UniProtKB/Swiss-Prot
    Q8NI51
    UniProtKB/TrEMBL
    A6XGM0, V9GYX4
    Related
    ENSP00000477165.1, ENST00000608158.5
    Conserved Domains (2) summary
    sd00017
    Location:259279
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:271296
    zf-H2C2_2; Zinc-finger double domain
  14. NM_001269054.2NP_001255983.1  transcriptional repressor CTCFL isoform 12

    See identical proteins and their annotated locations for NP_001255983.1

    Status: REVIEWED

    Source sequence(s)
    AL035541, AL160176
    Consensus CDS
    CCDS58776.1
    UniProtKB/Swiss-Prot
    Q8NI51
    Related
    ENSP00000437999.1, ENST00000502686.6
    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_001269055.3NP_001255984.1  transcriptional repressor CTCFL isoform 13

    See identical proteins and their annotated locations for NP_001255984.1

    Status: REVIEWED

    Source sequence(s)
    AL035541, AL160176
    Consensus CDS
    CCDS68161.1
    UniProtKB/Swiss-Prot
    Q8NI51
    Related
    ENSP00000476718.1, ENST00000608903.5
    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_001386993.1NP_001373922.1  transcriptional repressor CTCFL isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL035541, AL160176
    Related
    ENSP00000243914.3, ENST00000243914.8
    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]
    cd20908
    Location:392432
    SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins
  17. NM_001386994.1NP_001373923.1  transcriptional repressor CTCFL isoform 2

    Status: REVIEWED

    Source sequence(s)
    AL035541, AL160176
    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]
    cd20908
    Location:392432
    SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins
  18. NM_001386995.1NP_001373924.1  transcriptional repressor CTCFL isoform 2

    Status: REVIEWED

    Source sequence(s)
    AL035541, AL160176
    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]
    cd20908
    Location:392432
    SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins
  19. NM_001386996.1NP_001373925.1  transcriptional repressor CTCFL isoform 11

    Status: REVIEWED

    Source sequence(s)
    AL035541, AL160176
    Conserved Domains (2) summary
    sd00017
    Location:259279
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:271296
    zf-H2C2_2; Zinc-finger double domain
  20. NM_001386997.1NP_001373926.1  transcriptional repressor CTCFL isoform 14

    Status: REVIEWED

    Source sequence(s)
    AL035541, AL160176
    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]
    pfam13909
    Location:436460
    zf-H2C2_5; C2H2-type zinc-finger domain
  21. NM_080618.4NP_542185.2  transcriptional repressor CTCFL isoform 1

    See identical proteins and their annotated locations for NP_542185.2

    Status: REVIEWED

    Source sequence(s)
    AL035541, AL160176
    Consensus CDS
    CCDS13459.1
    UniProtKB/Swiss-Prot
    Q8NI51
    Related
    ENSP00000476398.1, ENST00000609232.5
    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]
    cd20908
    Location:392432
    SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins

RNA

  1. NR_072975.3 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL035541, AL160176
    Related
    ENST00000426658.6
  2. NR_170377.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL035541, AL160176
    Related
    ENST00000422109.6

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p13 Primary Assembly

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