Human Gene TFCP2 (uc001rxw.3)
  Description: Homo sapiens transcription factor CP2 (TFCP2), transcript variant 1, mRNA.
RefSeq Summary (NM_005653): This gene encodes a transcription factor that binds the alpha-globin promoter and activates transcription of the alpha-globin gene. The encoded protein regulates erythroid gene expression, plays a role in the transcriptional switch of globin gene promoters, and it activates many other cellular and viral gene promoters. The gene product interacts with certain inflammatory response factors, and polymorphisms of this gene may be involved in the pathogenesis of Alzheimer's disease. [provided by RefSeq, Mar 2010].
Transcript (Including UTRs)
   Position: hg19 chr12:51,487,539-51,566,926 Size: 79,388 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg19 chr12:51,489,024-51,566,205 Size: 77,182 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:51,487,539-51,566,926)mRNA (may differ from genome)Protein (502 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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MGIneXtProtOMIMPubMedTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TFCP2_HUMAN
DESCRIPTION: RecName: Full=Alpha-globin transcription factor CP2; AltName: Full=SAA3 enhancer factor; AltName: Full=Transcription factor LSF;
FUNCTION: Binds a variety of cellular and viral promoters including fibrinogen, alpha-globin, SV40 and HIV-1 promoters. Activation of the alpha-globin promoter in erythroid cells is via synergistic interaction with UBP1 (By similarity). Functions as part of the SSP (stage selector protein) complex. Facilitates the interaction of the gamma-globin genes with enhancer elements contained in the locus control region in fetal erythroid cells. Interacts by binding to the stage selector element (SSE) in the proximal gamma-globin promoter.
SUBUNIT: Binds to DNA as a dimer, isoform 3 does not bind to DNA or affect the binding of isoform 1 to DNA. Interacts with UBP1 and PIAS1, and is probably part of a complex containing TFCP2, UBP1 and PIAS1 (By similarity). Component of the SSP (stage selector protein) complex, which appears to be a heteromer of TFCP2 and 2 copies of NFE4.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Ubiquitous. Expressed in brain, ovary, kidney, thymus, spleen, liver, adrenal, heart and lung (at protein level).
DEVELOPMENTAL STAGE: Expressed in fetal erythroid tissue.
MISCELLANEOUS: In PubMed:8114710 authors noted that a 10-fold molar excess of isoform 3 over isoform 1 inhibited DNA-binding.
SIMILARITY: Belongs to the grh/CP2 family. CP2 subfamily.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TFCP2
CDC HuGE Published Literature: TFCP2
Positive Disease Associations: Alzheimer's Disease , Alzheimer's disease depressive disorder, major , Cholesterol, LDL
Related Studies:
  1. Alzheimer's Disease
    Taylor, A. E. et al. 2001, Genetic association of an LBP-1c/CP2/LSF gene polymorphism with late onset Alzheimer's disease., Journal of medical genetics. 2001 Apr;38(4):232-3. [PubMed 11283204]
    Our data support LBP-1c/CP2/LSF as a candidate gene/risk factor for AD and provide justification for future studies to investigate the role of this gene in Alzheimer's disease.
  2. Alzheimer's disease
    Bertram, L. et al. 2005, Further evidence for LBP-1c/CP2/LSF association in Alzheimer's disease families, J Med Genet 2005 42(11) 857-62. [PubMed 16272261]
    This is the first study to examine LBP-1c/CP2/LSF in AD families, and the fifth to independently show significant association. While our results support a role of this gene in AD pathogenesis, the direction of the effect remains uncertain, possibly indicating linkage disequilibrium with another variant nearby.
  3. Alzheimer's disease depressive disorder, major
    Schahab, S. et al. 2006, Association of Polymorphism in the Transcription Factor LBP-1c/CP2/LSF Gene with Alzheimer's Disease and Major Depression, Dement Geriatr Cogn Disord 2006 22(1) 95-98. [PubMed 16710089]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: TFCP2
Diseases sorted by gene-association score: body dysmorphic disorder (11), deafness, autosomal dominant 28 (7), spastic hemiplegia (5), alzheimer disease (3)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 14.46 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 478.98 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -300.40721-0.417 Picture PostScript Text
3' UTR -412.961485-0.278 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR007604 - CP2
IPR013761 - SAM/pointed

Pfam Domains:
PF04516 - CP2 transcription factor

SCOP Domains:
47769 - SAM/Pointed domain

ModBase Predicted Comparative 3D Structure on Q12800
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
      
      
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0000987 core promoter proximal region sequence-specific DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0008022 protein C-terminus binding
GO:0008134 transcription factor binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0042789 mRNA transcription from RNA polymerase II promoter
GO:0045944 positive regulation of transcription from RNA polymerase II promoter

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005829 cytosol
GO:0032991 macromolecular complex


-  Descriptions from all associated GenBank mRNAs
  M84810 - Human alpha-globin transcription factor CP2 mRNA sequence.
AK291264 - Homo sapiens cDNA FLJ77484 complete cds, highly similar to Homo sapiens transcription factor CP2 (TFCP2), mRNA.
BC003634 - Homo sapiens transcription factor CP2, mRNA (cDNA clone MGC:3901 IMAGE:3529119), complete cds.
U03494 - Human transcription factor LSF mRNA, complete cds.
U03495 - Human transcription factor LSF-ID mRNA, complete cds.
KJ892267 - Synthetic construct Homo sapiens clone ccsbBroadEn_01661 TFCP2 gene, encodes complete protein.
AB464305 - Synthetic construct DNA, clone: pF1KB8381, Homo sapiens TFCP2 gene for transcription factor CP2, without stop codon, in Flexi system.
AK308087 - Homo sapiens cDNA, FLJ98035.
CU678544 - Synthetic construct Homo sapiens gateway clone IMAGE:100020273 5' read TFCP2 mRNA.
JD449266 - Sequence 430290 from Patent EP1572962.
JD340528 - Sequence 321552 from Patent EP1572962.
JD540808 - Sequence 521832 from Patent EP1572962.
JD174268 - Sequence 155292 from Patent EP1572962.
JD358751 - Sequence 339775 from Patent EP1572962.
JD230356 - Sequence 211380 from Patent EP1572962.
JD144080 - Sequence 125104 from Patent EP1572962.
JD473255 - Sequence 454279 from Patent EP1572962.
JD426148 - Sequence 407172 from Patent EP1572962.
JD474631 - Sequence 455655 from Patent EP1572962.
JD382543 - Sequence 363567 from Patent EP1572962.
JD435564 - Sequence 416588 from Patent EP1572962.
JD164147 - Sequence 145171 from Patent EP1572962.
JD360107 - Sequence 341131 from Patent EP1572962.
JD227031 - Sequence 208055 from Patent EP1572962.
JD460687 - Sequence 441711 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K5E9, LSF, NM_005653, NP_005644, Q12800, Q12801, Q9UD75, Q9UD77, SEF, TFCP2_HUMAN
UCSC ID: uc001rxw.3
RefSeq Accession: NM_005653
Protein: Q12800 (aka TFCP2_HUMAN)
CCDS: CCDS8808.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_005653.4
exon count: 15CDS single in 3' UTR: no RNA size: 3715
ORF size: 1509CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3020.50frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.