Human Gene BRAT1 (uc003smj.2)
  Description: Homo sapiens BRCA1-associated ATM activator 1 (BRAT1), mRNA.
RefSeq Summary (NM_152743): The protein encoded by this ubiquitously expressed gene interacts with the tumor suppressing BRCA1 (breast cancer 1) protein and and the ATM (ataxia telangiectasia mutated) protein. ATM is thought to be a master controller of cell cycle checkpoint signalling pathways that are required for cellular responses to DNA damage such as double-strand breaks that are induced by ionizing radiation and complexes with BRCA1 in the multi-protein complex BASC (BRAC1-associated genome surveillance complex). The protein encoded by this gene is thought to play a role in the DNA damage pathway regulated by BRCA1 and ATM. [provided by RefSeq, Mar 2012].
Transcript (Including UTRs)
   Position: hg19 chr7:2,582,148-2,595,392 Size: 13,245 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr7:2,583,166-2,594,065 Size: 10,900 Coding Exon Count: 4 

Page IndexSequence and LinksPrimersMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:2,582,148-2,595,392)mRNA (may differ from genome)Protein (286 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsGeneNetworkH-INV
HGNCLynxMalacardsMGIPubMedUniProtKB
Wikipedia

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: BRAT1
Diseases sorted by gene-association score: rigidity and multifocal seizure syndrome, lethal neonatal* (1369), epileptic encephalopathy, early infantile, 15 (3), microcephaly (1)
* = Manually curated disease association

-  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: 41.83 RPKM in Testis
Total median expression: 904.40 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 -137.80288-0.478 Picture PostScript Text
3' UTR -512.111018-0.503 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
  ModBase Predicted Comparative 3D Structure on Q6PJG6-2
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 orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  LF384065 - JP 2014500723-A/191568: Polycomb-Associated Non-Coding RNAs.
BC023561 - Homo sapiens chromosome 7 open reading frame 27, mRNA (cDNA clone IMAGE:4025532), partial cds.
BC007209 - Homo sapiens chromosome 7 open reading frame 27, mRNA (cDNA clone IMAGE:2905978), partial cds.
BC015632 - Homo sapiens chromosome 7 open reading frame 27, mRNA (cDNA clone MGC:22916 IMAGE:3839985), complete cds.
AK024461 - Homo sapiens mRNA for FLJ00053 protein, partial cds.
AK131097 - Homo sapiens mRNA for FLJ00321 protein.
AK024482 - Homo sapiens mRNA for FLJ00076 protein, partial cds.
AK131083 - Homo sapiens mRNA for FLJ00283 protein.
JD026714 - Sequence 7738 from Patent EP1572962.
JD033664 - Sequence 14688 from Patent EP1572962.
DQ587276 - Homo sapiens piRNA piR-54388, complete sequence.
JD372461 - Sequence 353485 from Patent EP1572962.
JD400848 - Sequence 381872 from Patent EP1572962.
MA619642 - JP 2018138019-A/191568: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: AK131083, BAAT1, C7orf27, Q6PJG6-2
UCSC ID: uc003smj.2
RefSeq Accession: NM_152743
Protein: Q6PJG6-2, splice isoform of Q6PJG6

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK131083.1
exon count: 5CDS single in 3' UTR: no RNA size: 5245
ORF size: 861CDS single in intron: no Alignment % ID: 99.71
txCdsPredict score: 1905.50frame shift in genome: no % Coverage: 40.10
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # 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.