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TRERF1 Gene

protein-coding   GIFtS: 51

GC06M042303
transcriptional regulating factor 1
(Previous name: breast cancer anti-estrogen resistance 2 )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: BCAR2)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases
BCAR2 2, 3
FLJ21198 2
HSA277276 1, 2
OTTHUMP00000016399 2
RAPA 1, 2, 3
RP1-139D8.5 2
TREP132 3
TReP-132 1, 2
dJ139D8.5 1, 2
rapa-1 2
rapa-2 2
Descriptions
Breast cancer anti-estrogen resistance 2 1, 2, 3
Transcriptional-regulating protein 132 3
Zinc finger protein rapa 3
Zinc finger transcription factor TReP-132 3
transcriptional regulating factor 1 2
transcriptional regulating protein 132 2
External Ids
HGNC: 182731
Entrez Gene: 558092
UniProtKB: Q96PN73
Ensembl: ENSG000001244967
Search outside databases for aliases for TRERF1 gene

Previous GC identifer: GC06M042242

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

EntrezGene summary for TRERF1:
This gene encodes a zinc-finger transcriptional regulating protein which interacts with CBP/p300 to
regulate the human gene CYP11A1. [provided by RefSeq]

UniProtKB/Swiss-Prot: TREF1_HUMAN, Q96PN7
Function: Activates transcription of CYP11A1. Interaction with CREBBP and EP300 results in a
synergistic transcriptional activation of CYP11A1

Gene Wiki entry for TRERF1

(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 TRERF1 gene  

Entrez Gene cytogenetic band: 6p21.1-p12.1   Ensembl cytogenetic band:  6p21.1   HGNC cytogenetic band: 6p21.1-p12.1

TRERF1 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 6         GeneLoc Exon Structure

GeneLoc location for GC06M042303:     (about GC identifiers)

Start:
42,300,647 bp from pter
End:
42,527,767 bp from pter
Size:
227,121 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000006.10  NT_007592.14  
(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: TREF1_HUMAN, Q96PN7 (See protein sequence)
Recommended Name: Transcriptional-regulating factor 1  
Size: 1200 amino acids; 132256 Da
Subunit: Interacts with CREBBP and EP300
Subcellular location: Nucleus
Secondary accessions: Q05GC6 Q7Z6T2 Q7Z6T3 Q9NQ72 Q9NQ73 Q9NUN9
Alternative splicing: 5 isoforms:  Q96PN7-1   Q96PN7-2   Q96PN7-3   Q96PN7-4   Q96PN7-5   

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_277037.1  

    ENSEMBL proteins: 
    ENSP00000346285 ENSP00000362008 ENSP00000362005 ENSP00000362013 ENSP00000339438 


    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 (TReP132)
    Browse Abnova for Human Recombinant Proteins
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622 intracellular IEA--
    GO:0005634 nucleus IDA11349124
    About this table

    Antibodies for TRERF1: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Browse Antibodies at Sigma-Aldrich
    Browse R&D Systems for Antibodies
    Antibodies from Abcam (TReP132), each with their AbpromiseSM
    Browse Abnova for Monoclonal and Polyclonal Antibodies
    Novus Biologicals Antibodies for TRERF1

    Assays for TRERF1: 
    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

    5/6 InterPro domains/families (see all 6 ):
     IPR000949 ELM2
     IPR015880 Znf_C2H2-like
     IPR017884 SANT_eukarya
     IPR001005 SANT_DNA-bd
     IPR014778 Myb_DNA-bd


       GeneDecks  TRERF1 for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q96PN7

    ProtoNet protein and cluster: Q96PN7

    UniProtKB/Swiss-Prot: TREF1_HUMAN, Q96PN7
    Similarity: Contains 3 C2H2-type zinc fingers
    Similarity: Contains 1 ELM2 domain
    Similarity: Contains 1 SANT domain

    (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 (TRERF1)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (TRERF1)
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 3): NM_033501

                  Applied Biosystems Silencer® siRNAs for TRERF1

                  Sigma-Aldrich siRNA for TRERF1  
                         Sigma-Aldrich shRNA for TRERF1  
                         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_033502
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_033502
                                     untagged cDNA clones in CMV expression vector (see all 2): NM_018415 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_033502

    UniProtKB/Swiss-Prot: TREF1_HUMAN, Q96PN7
    Function: Activates transcription of CYP11A1. Interaction with CREBBP and EP300 results in a
    synergistic transcriptional activation of CYP11A1

    5/7 Gene Ontology (GO) molecular function terms (links to tree view) (see all 7 ):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003700 transcription factor activity IDA11349124
    GO:0008134 transcription factor binding IPI11349124
    GO:0008270 zinc ion binding IEA--
    GO:0008301 DNA bending activity NAS11349124
    GO:0016455 RNA polymerase II transcription mediator activity NAS11349124
    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  TRERF1 


    5/10 Interacting proteins for TRERF1 (ENSP000003620133) via UniProtKB, MINT, and/or STRING (see all 10 )
    InteractantInteraction Details
    GeneCardExternal ID(s)
    NR5A1ENSP000003626903STRING (score=.992)
    CD86ENSP000003320493STRING (score=.914)
    LILRB4ENSP000002704523STRING (score=.879)
    LILRB2ENSP000003199603STRING (score=.871)
    LILRB1ENSP000003159973STRING (score=.86)
    About this table

    5/7 Gene Ontology (GO) biological process terms (links to tree view) (see all 7 ):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006350 transcription IEA--
    GO:0006694 steroid biosynthetic process NAS11349124
    GO:0006707 cholesterol catabolic process NAS11349124
    GO:0007275 multicellular organismal development NAS11349124
    GO:0042592 homeostatic process NAS11349124
    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 TRERF1
    1 Novoseek chemical compound relationship for TRERF1 gene
    Compound   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    steroid 49.06 1 12556907 (1)
    About this table


    (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 (TRERF1)
    Browse for Gene Knock-down Tools from Millipore
    Abnova Chimera RNAi Products for Gene knock-down (TRERF1)
                   OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 3): NM_033501

                  Sigma-Aldrich siRNA for TRERF1  
                         Sigma-Aldrich shRNA for TRERF1  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_033502  

    REFSEQ mRNAs for TRERF1 gene: 

    NM_033502.2   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_033502  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_033502
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_033502
                                     untagged cDNA clones in CMV expression vector (see all 2): NM_018415 

    Additional cDNA sequence: 

    AF111801.1 AF297872.1 AJ277275.1 AJ277276.1 AK002096.1 AK127493.1 AK308473.1 AM404182.1 
    AM404183.1 AM404259.1 

    10 DOTS entries:

    DT.102823818  DT.100757479  DT.306866  DT.95274464  DT.100707313  DT.102823817  DT.121343431  DT.427964 
    DT.97837632  DT.99970910 

    24/96 AceView cDNA sequences (see all 96 ):

    AW518695 BM701209 AW117866 BX489946 BX952047 BE645262 AA878783 AK127493 
    BM784836 NM_033502 BX508943 AF297872 BF724270 BU859373 BQ775152 AI299636 
    NM_033501 BM770293 AA811416 AA926899 AW006022 CD705237 BX504990 BX489945 

    highest scoring ESTs for TRERF1:

    AW006022 AF297872 AA252764 AA252826 AA493429 AA804960 AA878783 AI056311 AI299636 AI375580 

    Unigene Cluster for TRERF1:

    Transcriptional regulating factor 1
    Hs.485392  [show with all ESTs]
    Unigene Representative Sequence: AM404182


    GeneLoc Exon Structure

    5/7 Alternative Splicing Database (ASD) splice patterns (SP) for TRERF1 (see all 7 )

    ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b · 12c · 12d ^ 13a · 13b
    SP1:                                                                                                                        
    SP2:                    -                                                                                                   
    SP3:                                                                                                                        
    SP4:                                                                                      -                 -               
    SP5:                                                                                                                        

    About this scheme

    ECgene alternative splicing isoforms for TRERF1

    5 Ensembl transcripts including schematic representations:
    ENST00000354325  ENST00000372917  ENST00000372914  ENST00000372922  ENST00000340840  
    (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

    TRERF1 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for TRERF1

    1 / 2 / 3

    8 probe-sets matching TRERF1 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
    73752_at2, 3 U95-E 1 1.00 1.00 0.89 0.95 AI375580 0.60 1.00 0.82 1
    51773_at2, 3 U95-B 1 0.94 1.00 0.72 1.06 AW006022 0.80 1.00 0.91 1

    233324_at2, 3 U133-B 1 1.00 1.00 -- -- AK002096 0.60 1.00 0.82 1

    229016_s_at2, 3 U133-B 1 1.00 1.00 -- -- AJ277276 0.60 0.75 0.68 1

    238520_at2, 3 U133-B 1 1.00 1.00 -- -- BF724270 0.40 1.00 0.76 1

    233324_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    229016_s_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    238520_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    GeneDecks  TRERF1 for binary patterns associated with the probe-sets selected above  
    About GeneDecksing
    About this table    
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: --

    SOURCE GeneReport for Unigene cluster: Hs.485392

    UniProtKB/Swiss-Prot: TREF1_HUMAN, Q96PN7
    Tissue specificity: Highest expression was seen in thymus, testis and adrenal cortex, expressed
    also in the adrenal medulla, thyroid, and stomach. Highly expressed in steroidogenic JEG-3 and
    MCF-7 cells, low expression was seen in non-steroidogenic HepG2 and HK293 cells

    (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 TRERF1 gene from 5 species
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    TRERF11   -- transcriptional regulating factor 1 90.92(n)
    92.79(a)
    608906  XM_859860.1  XP_864953.1 
    chimpanzee
    (Pan troglodytes)
    TRERF11   -- transcriptional regulating factor 1 97.94(n)
    97.66(a)
    462695  XM_518475.2  XP_518475.2 
    cow
    (Bos taurus)
    TRERF11   -- transcriptional regulating factor 1 90.2(n)
    91.15(a)
    504797  XM_865759.2  XP_870852.1 
    mouse
    (Mus musculus)
    Trerf11, 5 175
    transcriptional regulating factor 11, 5 88.39(n)1
    90.93(a)1
    2248291  NM_172622.11  NP_766210.11 
     AI4292945  AK0351765  (see all 17)
    chicken
    (Gallus gallus)
    TRERF11   -- transcriptional regulating factor 1 69.51(n)
    69.42(a)
    421386  XM_419445.2  XP_419445.2 
    About this table        Species with no ortholog for TRERF1

    ENSEMBL Gene Tree for TRERF1
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for TRERF1 gene
    ZNF5412  C14orf432  

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


    10/1319 NCBI SNPs in TRERF1 are shown (see all 1319 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 408)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 6 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs22952751,2
    A,C,F,H42332524(-) TGTGCT/AGTTCC 1 S/C mis1 ese318Minor allele frequency- A:0.08EA NA EU WA 2964
    rs119706791,2
    C,F,H42438791(+) CAGCCA/GGGGCC 1 -- ut514Minor allele frequency- G:0.10EU EA WA 420
    rs126612551,2
    A,C,H42529761(+) GGAAAG/AGCTTC 1 -- ng314Minor allele frequency- A:0.00EU EA WA 416
    rs117517651,2
    C,F,H42304105(+) ATCATC/TCAAGA 1 D/N mis14Minor allele frequency- T:0.01EU EA WA 420
    rs168954811,2
    F,H42345441(+) GTGAAC/TGTGGC 1 -- ut51 ese37Minor allele frequency- T:0.06NA EU EA WA 562
    rs359783181,2
    C,F42311931(+) CACAGT/GTGGGC 1 T/N mis15Minor allele frequency- G:0.01NA EU EA WA 488
    rs351622771,2
    C,F42344016(+) TCCTGT/CGTCAG 1 A/T mis15Minor allele frequency- C:0.02NA EU EA WA 492
    rs177042221,2
    C,F,H42341496(+) GCTCTC/TCCATC 1 G/G syn18Minor allele frequency- T:0.04NA EU EA WA 638
    rs22952741,2
    C,F,H42340453(-) TCCCAC/TGGGGG 1 H/H syn1 ese39Minor allele frequency- T:0.15EA NA EU WA 1904
    rs77446941,2
    A,F,H42304190(+) TCCACA/GTCCTT 1 D/D syn1 ese34Minor allele frequency- G:0.04EU EA WA 418
    About this table

    HapMap Linkage Disequilibrium images for TRERF1 (up to first 250kb)

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

    OMIM: 610322

    Human Gene Mutation Database: TRERF1

    (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

    10/17 PubMed articles for TRERF1 gene (see all 17 ):
    (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: 55809 HGNC: 18273 AceView: TRERF1 Ensembl:ENSG00000124496 euGenes: HUgn55809
    ECgene: TRERF1 H-InvDB: TRERF1
    (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 TRERF1:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



      Invitrogen iPath Pathways  Invitrogen BLOCK-iT™ RNAi
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      Invitrogen Proteins / Assays / Screening Services  Search Invitrogen catalog for TRERF1-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 TRERF1 Browse antibodies at Sigma-Aldrich
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for TRERF1 Browse small molecules at Sigma-Aldrich
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