Human Gene ATF7 (uc001sdz.3)
  Description: Homo sapiens activating transcription factor 7 (ATF7), transcript variant 2, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr12:53,905,843-54,020,199 Size: 114,357 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg19 chr12:53,910,921-53,994,784 Size: 83,864 Coding Exon Count: 11 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:53,905,843-54,020,199)mRNA (may differ from genome)Protein (483 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMalacardsMGI
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  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): ATF7
CDC HuGE Published Literature: ATF7
Positive Disease Associations: Body Height , height
Related Studies:
  1. Body Height
    Amidou N'Diaye et al. PLoS genetics 2011, Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry., PLoS genetics. [PubMed 21998595]
  2. height
    Okada ,et al. Hum Mol Genet 2010, A genome-wide association study in 19,633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci , Human molecular genetics 2010 . [PubMed 20189936]

-  MalaCards Disease Associations
  MalaCards Gene Search: ATF7
Diseases sorted by gene-association score: penicilliosis (2), familial atrial fibrillation (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 18.69 RPKM in Nerve - Tibial
Total median expression: 540.31 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 -59.50158-0.377 Picture PostScript Text
3' UTR -1595.825078-0.314 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
  Pfam Domains:
PF00096 - Zinc finger, C2H2 type
PF00170 - bZIP transcription factor
PF03131 - bZIP Maf transcription factor
PF07716 - Basic region leucine zipper

SCOP Domains:
57667 - C2H2 and C2HC zinc fingers

ModBase Predicted Comparative 3D Structure on P17544-6
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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Descriptions from all associated GenBank mRNAs
  AK298853 - Homo sapiens cDNA FLJ51940 complete cds, highly similar to Cyclic AMP-dependent transcription factor ATF-7.
X52943 - Human mRNA for ATF-a transcription factor.
BC136302 - Homo sapiens activating transcription factor 7, mRNA (cDNA clone MGC:167912 IMAGE:9020289), complete cds.
AK313507 - Homo sapiens cDNA, FLJ94063, highly similar to Homo sapiens activating transcription factor 7 (ATF7), mRNA.
BC042363 - Homo sapiens activating transcription factor 7, mRNA (cDNA clone IMAGE:5285571), complete cds.
BC032433 - Homo sapiens cDNA clone IMAGE:4479317, containing frame-shift errors.
BC140006 - Homo sapiens activating transcription factor 7, mRNA (cDNA clone IMAGE:8860358), complete cds.
AK054879 - Homo sapiens cDNA FLJ30317 fis, clone BRACE2003594.
DQ591685 - Homo sapiens piRNA piR-58797, complete sequence.
JD248146 - Sequence 229170 from Patent EP1572962.
JD307762 - Sequence 288786 from Patent EP1572962.
JD300345 - Sequence 281369 from Patent EP1572962.
JD359750 - Sequence 340774 from Patent EP1572962.
JD161881 - Sequence 142905 from Patent EP1572962.
JD291201 - Sequence 272225 from Patent EP1572962.
JD171690 - Sequence 152714 from Patent EP1572962.
JD553460 - Sequence 534484 from Patent EP1572962.
AK302907 - Homo sapiens cDNA FLJ55305 complete cds, highly similar to Cyclic AMP-dependent transcription factor ATF-7.
JD219248 - Sequence 200272 from Patent EP1572962.
JD093419 - Sequence 74443 from Patent EP1572962.
JD378541 - Sequence 359565 from Patent EP1572962.
AK310355 - Homo sapiens cDNA, FLJ17397.
JD125069 - Sequence 106093 from Patent EP1572962.
JD350326 - Sequence 331350 from Patent EP1572962.
JD427982 - Sequence 409006 from Patent EP1572962.
JD368565 - Sequence 349589 from Patent EP1572962.
JD078086 - Sequence 59110 from Patent EP1572962.
JD141615 - Sequence 122639 from Patent EP1572962.
JD426344 - Sequence 407368 from Patent EP1572962.
JD252371 - Sequence 233395 from Patent EP1572962.
X57197 - H.sapiens mRNA for ATFa gene.
AB463398 - Synthetic construct DNA, clone: pF1KB9735, Homo sapiens ATF7 gene for activating transcription factor 7, without stop codon, in Flexi system.
HQ257970 - Synthetic construct Homo sapiens clone IMAGE:100072279 Unknown protein gene, encodes complete protein.
KJ906066 - Synthetic construct Homo sapiens clone ccsbBroadEn_15736 ATF7 gene, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: ATFA, NM_006856, NP_006847, P17544-6, uc001sdy.3
UCSC ID: uc001sdz.3
RefSeq Accession: NM_006856
Protein: P17544-6, splice isoform of P17544 CCDS: CCDS44906.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006856.2
exon count: 12CDS single in 3' UTR: no RNA size: 6704
ORF size: 1452CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2872.00frame shift in genome: no % Coverage: 99.76
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: 4956# 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.