Human Gene SPATS1 (ENST00000323108.12) from GENCODE V44
  Description: Event=Alternative splicing; Named isoforms=2; Name=1; IsoId=Q496A3-1; Sequence=Displayed; Name=2; IsoId=Q496A3-2; Sequence=VSP_028787; Note=No experimental confirmation available. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay; (from UniProt Q496A3)
Gencode Transcript: ENST00000323108.12
Gencode Gene: ENSG00000249481.7
Transcript (Including UTRs)
   Position: hg38 chr6:44,342,660-44,377,166 Size: 34,507 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg38 chr6:44,343,096-44,377,063 Size: 33,968 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr6:44,342,660-44,377,166)mRNA (may differ from genome)Protein (300 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Spermatogenesis-associated serine-rich protein 1;

-  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

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 5.54 RPKM in Testis
Total median expression: 5.59 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 -32.70101-0.324 Picture PostScript Text
3' UTR -16.60103-0.161 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 Q496A3
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Descriptions from all associated GenBank mRNAs
  AK126641 - Homo sapiens cDNA FLJ44683 fis, clone BRACE3010702.
AK058171 - Homo sapiens cDNA FLJ25442 fis, clone TST08489.
BC100956 - Homo sapiens spermatogenesis associated, serine-rich 1, mRNA (cDNA clone MGC:119210 IMAGE:40004668), complete cds.
BC100957 - Homo sapiens spermatogenesis associated, serine-rich 1, mRNA (cDNA clone MGC:119211 IMAGE:40004669), complete cds.
BC100958 - Homo sapiens spermatogenesis associated, serine-rich 1, mRNA (cDNA clone MGC:119212 IMAGE:40004672), complete cds.
BC100959 - Homo sapiens spermatogenesis associated, serine-rich 1, mRNA (cDNA clone MGC:119213 IMAGE:40004675), complete cds.
BC110065 - Homo sapiens spermatogenesis associated, serine-rich 1, mRNA (cDNA clone MGC:133020 IMAGE:40004676), complete cds.
BC111414 - Homo sapiens spermatogenesis associated, serine-rich 1, mRNA (cDNA clone MGC:133021 IMAGE:40004677), complete cds.
JD277717 - Sequence 258741 from Patent EP1572962.
KJ900477 - Synthetic construct Homo sapiens clone ccsbBroadEn_09871 SPATS1 gene, encodes complete protein.
JD428121 - Sequence 409145 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: AK058171, ENST00000323108.1, ENST00000323108.10, ENST00000323108.11, ENST00000323108.2, ENST00000323108.3, ENST00000323108.4, ENST00000323108.5, ENST00000323108.6, ENST00000323108.7, ENST00000323108.8, ENST00000323108.9, Q496A2, Q496A3, Q496A5, Q96LJ0, SPAS1_HUMAN, uc021yzz.1, uc021yzz.2
UCSC ID: ENST00000323108.12
RefSeq Accession: NM_145026
Protein: Q496A3 (aka SPAS1_HUMAN)
CCDS: CCDS4911.1

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