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CTCFL Gene

protein-coding   GIFtS: 51

GC20M055505
CCCTC-binding factor (zinc finger protein)-like
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
BORIS 1, 2, 3, 5
CT27 1, 2, 3
CTCF-T 2
MGC163358 2
OTTHUMP00000174287 2
dJ579F20.2 1, 2
Descriptions
BORIS-like protein 2
Brother of the regulator of imprinted sites 2, 3
CCCTC-binding factor 3
CCCTC-binding factor (zinc finger protein)-like 2
CCCTC-binding factor-like protein 2
CTCF paralog 3
CTCF-like protein 3
Cancer/testis antigen 27 2, 3
Zinc finger protein CTCF-T 3
External Ids
HGNC: 162341
Entrez Gene: 1406902
UniProtKB: Q8NI513
Ensembl: ENSG000001240927
Search outside databases for aliases for CTCFL gene

Previous GC identifers: GC20M055800 GC20M056710 GC20M056757

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

EntrezGene summary for CTCFL:
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. [provided by RefSeq]

UniProtKB/Swiss-Prot: CTCFL_HUMAN, Q8NI51
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

Gene Wiki entry for CTCFL

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the CTCFL gene  

Entrez Gene cytogenetic band: 20q13.31   Ensembl cytogenetic band:  20q13.31   HGNC cytogenetic band: 20q13.31

CTCFL Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20M055505:     (about GC identifiers)

Start:
55,505,630 bp from pter
End:
55,534,041 bp from pter
Size:
28,412 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000020.9  NT_011362.9  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
About This Section

UniProtKB/Swiss-Prot: CTCFL_HUMAN, Q8NI51 (See protein sequence)
Recommended Name: Transcriptional repressor CTCFL  
Size: 663 amino acids; 75717 Da
Subunit: Interacts with histones and PRMT7
Subcellular location: Cytoplasm. Nucleus
Developmental stage: Is up-regulated in primary spermatocytes (expression overlapping with the
genome-wide erasure of methylation) to become silenced on activation of CTCF in post-meiotic
germline cells (expression corresponding to DNA remethylation)
Secondary accessions: Q5JUG4 Q9BZ30 Q9NQJ3

REFSEQ proteins: NP_542185.2  

ENSEMBL proteins: 
ENSP00000360239 ENSP00000243914 


Human Recombinant Proteins 
Browse Drug Discovery Central at Invitrogen for human recombinant proteins
Browse Purified and Recombinant Proteins at Millipore
Browse Human Recombinant Proteins at Sigma-Aldrich  
Browse R&D Systems for human recombinant proteins
Browse recombinant and purified proteins available from Enzo Life Sciences
Recombinant Proteins from Abcam (BORIS)
Human Recombinant Proteins from Abnova (CTCFL)
              OriGene Purified Recombinant Human Protein: CTCFL 

3 Gene Ontology (GO) cellular component terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0005622 intracellular IEA--
GO:0005634 nucleus IEA--
GO:0005737 cytoplasm IEA--
About this table

Antibodies for CTCFL: 
Browse Antibodies Central at Invitrogen
Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
Sigma-Aldrich Antibodies for CTCFL
Browse R&D Systems for Antibodies
Antibodies from Abcam (BORIS), each with their AbpromiseSM
Browse Abnova for Monoclonal and Polyclonal Antibodies
Novus Biologicals Antibody for CTCFL

Assays for CTCFL: 
Browse Invitrogen for biochemical assays
Browse Kits and Assays available from Millipore
Browse R&D Systems for biochemical assays
Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

3 InterPro domains/families:
 IPR015880 Znf_C2H2-like
 IPR013087 Znf_C2H2/integrase_DNA-bd
 IPR007087 Znf_C2H2


   GeneDecks  CTCFL for the domains selected above  
About GeneDecksing

Graphical View of Domain Structure for InterPro Entry Q8NI51

ProtoNet protein and cluster: Q8NI51

UniProtKB/Swiss-Prot: CTCFL_HUMAN, Q8NI51
Similarity: Belongs to the CTCF zinc-finger protein family
Similarity: Contains 11 C2H2-type zinc fingers

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (CTCFL)
Browse for Gene Knock-down Tools from Millipore
Abnova Chimera RNAi Products for Gene knock-down (CTCFL)
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_080618

              Applied Biosystems Silencer® siRNAs for CTCFL

              Sigma-Aldrich siRNA for CTCFL  
                     Sigma-Aldrich shRNA for CTCFL  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Clones:Browse Clone Ranger at Invitrogen for clones
Browse Clones for the Expression of Recombinant Proteins Available from Millipore
              OriGene GFP tagged cDNA clone in CMV expression vector: NM_080618
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_080618
                                 untagged cDNA clones in CMV expression vector (see all 3): NM_080618 

Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
              OriGene genome-wide validated SYBR primer pairs: NM_080618

UniProtKB/Swiss-Prot: CTCFL_HUMAN, Q8NI51
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

3 Gene Ontology (GO) molecular function terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0003677 DNA binding IEA--
GO:0008270 zinc ion binding IEA--
GO:0046872 metal ion binding IEA--
About this table

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section


 Gene Network CentralTM Interacting Genes and Proteins Network for  CTCFL 


2 Interacting proteins for CTCFL (ENSP000002439143) via UniProtKB, MINT, and/or STRING
InteractantInteraction Details
GeneCardExternal ID(s)
CREBZFENSP000002600583STRING (score=.779)
BRCA1ENSP000003502833STRING (score=.7)
About this table

3 Gene Ontology (GO) biological process terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0006350 transcription IEA--
GO:0006355 regulation of transcription, DNA-dependent IEA--
GO:0045786 negative regulation of cell cycle IEA--
About this table
(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse drugs & compounds from Enzo Life Sciences
Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for CTCFL

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (CTCFL)
Browse for Gene Knock-down Tools from Millipore
Abnova Chimera RNAi Products for Gene knock-down (CTCFL)
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_080618

              Sigma-Aldrich siRNA for CTCFL  
                     Sigma-Aldrich shRNA for CTCFL  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Applied Biosystems Silencer® siRNAs: 

NM_080618  

REFSEQ mRNAs for CTCFL gene: 

NM_080618.2   

Applied Biosystems TaqMan ® Gene Expression Assays: 

NM_080618  

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_080618
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_080618
                                 untagged cDNA clones in CMV expression vector (see all 3): NM_080618 

Additional cDNA sequence: 

AF336042.1 AK128070.1 AK313990.1 AY071919.1 BC060763.1 BC130486.1 DQ294738.1 DQ778108.1 
DQ778109.1 DQ778110.1 DQ778111.1 DQ778112.1 DQ778113.1 DQ778114.1 DQ778115.1 DQ778116.1 
DQ778117.1 DQ778118.1 DQ778119.1 DQ778120.1 DQ778121.2 DQ778122.1 DQ778123.1 DQ778124.1 
DQ778125.1 DQ778126.1 DQ778127.1 DQ778128.1 DQ778129.1 DQ778130.1 DQ778131.1 

5 DOTS entries:

DT.101979256  DT.99957215  DT.303300  DT.100696089  DT.97768285 

24/27 AceView cDNA sequences (see all 27 ):

AI024580 NM_080618 AY071919 BX094837 BX282332 BG527694 AL732020 BC060763 
AL844306 AI024578 AK128070 AF336042 BG687495 BU170289 AL844477 BU629814 
BG722482 AL049118 AL844304 AL844280 BQ429595 AL844410 BF209606 AW243377 

highest scoring ESTs for CTCFL:

AF336042 AI024580 AK128070 AY071919 BC060763 AI024578 AL049118 AL844280 AL844304 AL844306 

Unigene Cluster for CTCFL:

CCCTC-binding factor (zinc finger protein)-like
Hs.131543  [show with all ESTs]
Unigene Representative Sequence: DQ778119


GeneLoc Exon Structure

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

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

About this scheme

ECgene alternative splicing isoforms for CTCFL

2 Ensembl transcripts including schematic representations:
ENST00000371196  ENST00000243914  
(Experimental results according to 1GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
About This Section

CTCFL expression in normal and diseased human tissues

 Applied Biosystems TaqMan ® Gene Expression Assays for CTCFL

1 / 2 / 3

2 probe-sets matching CTCFL gene


Affymetrix
probe-set
Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

66993_at2, 3 U95-C 1 1.00 1.00 1.00 1.00 AI024580 0.80 1.00 0.91 1

1552368_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
About this table
Data from (Publications) and GNF BioGPS
    About these images
About these images

CGAP SAGE TAG: AGCCCCTGTG

SOURCE GeneReport for Unigene cluster: Hs.131543

UniProtKB/Swiss-Prot: CTCFL_HUMAN, Q8NI51
Tissue specificity: Testis specific. Specifically expressed in primary spermatocytes

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section


Orthologs for CTCFL gene from 4 species
Organism Gene Locus Description Human
Similarity
NCBI accessions
dog
(Canis familiaris)
CTCFL1   -- CCCTC-binding factor (zinc finger protein)-like 81.67(n)
76.79(a)
477271  XM_534463.2  XP_534463.2 
chimpanzee
(Pan troglodytes)
CTCFL1   -- CCCTC-binding factor (zinc finger protein)-like 98.64(n)
97.74(a)
458360  XM_514743.2  XP_514743.2 
mouse
(Mus musculus)
Ctcfl1, 5 25
CCCTC-binding factor (zinc finger protein)-like1, 5 68.64(n)1
60.9(a)1
6647991  NM_001081387.11  NP_001074856.11 
 AL8375095  AL9285995  (see all 9)
sea squirt
(Ciona intestinalis)
Cin.23152   -- Ciona intestinalis cDNA, clonecitb042m20, full insert more 69.97(n)  AK116486.1 
About this table        Species with no ortholog for CTCFL

ENSEMBL Gene Tree for CTCFL
(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section

Paralogs for CTCFL gene
CTCF2  HINFP2  ZFP642  

(According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section


10/219 NCBI SNPs in CTCFL are shown (see all 219 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 75)
ABGenomic DataTranscription DataAllele Frequencies
SNP IDValidChr 20 posSequenceRecsAA
Chg
TypeMoreRecsAllele
freq
PopTotal
sample
More
------------
rs60701281,2
A,C,F,H55532520(+) ACGCTC/GGGCCT 1 E/Q mis1 ese38Minor allele frequency- G:0.29EU EA WA 832
rs60256061,2
A,C,F,H55532139(+) TCCAGC/TAGTTT 1 T/A mis1 ese38Minor allele frequency- T:0.21EU EA WA 836
rs81226341,2
C,F,H55506388(+) TCTAGT/CATTTC 1 -- ut31 ese37Minor allele frequency- C:0.03EU EA WA NA 562
rs60701221,2
C,F,H55517169(+) CTTCTG/CTCGGA 1 E/Q mis1 ese38Minor allele frequency- C:0.01EU EA WA 836
rs60924911,2
C,F,H55521202(+) AGTTGC/TGCATA 1 R/H mis1 ese34Minor allele frequency- T:0.01EU EA WA 406
rs72730991,2
F,H55533848(+) AGGAGG/AGGAGG 1 -- ng31 trp34Minor allele frequency- A:0.07EU EA WA 418
rs116995561,2
C,H55506620(+) GACTAT/CTTTGA 1 -- ut314Minor allele frequency- C:0.00EU EA WA 420
rs60255921,2
H55505451(+) ggtcaG/Aatact 1 -- ng514Minor allele frequency- A:0.00EU EA WA 420
rs21492851,2
H55506318(+) CAAAAA/TTCTAA 1 -- ut31 ese34Minor allele frequency- T:0.00EU EA WA 416
rs60701201,2
H55506699(+) TTTGAG/AGTGTT 1 -- ut31 ese34Minor allele frequency- A:0.00EU EA WA 420
About this table

HapMap Linkage Disequilibrium images for CTCFL (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

OMIM: 607022

4 Novoseek disease relationships for CTCFL gene

Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
testicular cancer 51.07 1 17363524 (1)
cancer 21.49 17 12191639 (3), 18095639 (2), 17363524 (2), 17962299 (2) (see all 6)
cancer lung 15.13 9 16140944 (5), 17260018 (3)
tumors 0.00 6 17062669 (2), 18095639 (1)
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(Possibly Related Articles in Doctor's Guide)
About This Section

  --

(in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
About This Section

10/23 PubMed articles for CTCFL gene (see all 23 ):
(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)
(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
About This Section

Entrez Gene: 140690 HGNC: 16234 AceView: CTCFL Ensembl:ENSG00000124092 euGenes: HUgn140690
ECgene: CTCFL H-InvDB: CTCFL
(According to HUGE)
About This Section

  --
(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

  --
(Available from WIS Yeda, Salk, Tufts)
About This Section

  --
(Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
About This Section



Products for CTCFL:
 TaqMan ® Gene Expression Assays
 TaqMan ® Genotyping Assays
  Free SNP selection tool



  Invitrogen iPath Pathways  Invitrogen BLOCK-iT™ RNAi
  Invitrogen Antibodies  Invitrogen Assays
  Invitrogen Clones  Invitrogen Q-PCR Products
  Invitrogen Human Recombinant Kinases  Invitrogen Custom Antibody and Peptide Service
  Invitrogen Proteins / Assays / Screening Services  Search Invitrogen catalog for CTCFL-related products

 Millipore Custom Antibody & Bulk Services
 Millipore Preclinical / Clinical Development Services
 Millipore Immunoassay Services
 Millipore Target Screening & Profiling Services


 Predesigned and custom siRNAs for CTCFL Antibodies for CTCFL
 Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
 Lentivirus-delivered shRNAs for CTCFL Browse small molecules at Sigma-Aldrich
 "Your Favorite Gene" Pathwaysfeedback


  
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 Recombinant Proteins (CTCFL)
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 Recombinant Proteins
(BORIS)
 Antibodies (BORIS)
 Tagged/untagged cDNA clones
 Validated SYBR primer pairs
 Purified proteins from HEK293T cells
 Western blot validated antibodies
 shRNA in GFP-retroviral vector
 Search Tocris compounds for CTCFL




 Search www.enzolifesicences.com for proteins, assays, substrates, inhibitors & antibodies
 Antibodies for CTCFL

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