Human Gene SPATA48 (uc011kcj.2)
  Description: Homo sapiens chromosome 7 open reading frame 72 (SPATA48), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr7:50,135,682-50,198,852 Size: 63,171 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr7:50,135,682-50,198,765 Size: 63,084 Coding Exon Count: 9 

Page IndexSequence and LinksPrimersGene AllelesRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Model InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:50,135,682-50,198,852)mRNA (may differ from genome)Protein (438 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsLynxMGI
neXtProtPubMedTreefamUniProtKBBioGrid 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


+  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: 3.58 RPKM in Testis
Total median expression: 4.28 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
3' UTR -43.7387-0.503 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
  Pfam Domains:
PF15073 - Domain of unknown function (DUF4540)

ModBase Predicted Comparative 3D Structure on A4D263
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
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003674 molecular_function

Biological Process:
GO:0008150 biological_process

Cellular Component:
GO:0005575 cellular_component


-  Descriptions from all associated GenBank mRNAs
  JD308590 - Sequence 289614 from Patent EP1572962.
JD303290 - Sequence 284314 from Patent EP1572962.
JD095883 - Sequence 76907 from Patent EP1572962.
JD412049 - Sequence 393073 from Patent EP1572962.
JD462525 - Sequence 443549 from Patent EP1572962.
JD476986 - Sequence 458010 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A4D263, A6NDX9, C7orf72, CG072_HUMAN, NM_001161834, NP_001155306
UCSC ID: uc011kcj.2
RefSeq Accession: NM_001161834
Protein: A4D263 (aka CG072_HUMAN)
CCDS: CCDS47585.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001161834.2
exon count: 9CDS single in 3' UTR: no RNA size: 1405
ORF size: 1317CDS single in intron: no Alignment % ID: 99.93
txCdsPredict score: 2834.00frame shift in genome: no % Coverage: 99.93
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.