Human Gene SPACA9 (ENST00000350499.6) from GENCODE V44
  Description: Homo sapiens sperm acrosome associated 9 (SPACA9), transcript variant 3, mRNA. (from RefSeq NM_018956)
Gencode Transcript: ENST00000350499.6
Gencode Gene: ENSG00000165698.16
Transcript (Including UTRs)
   Position: hg38 chr9:132,878,898-132,890,201 Size: 11,304 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg38 chr9:132,883,948-132,889,968 Size: 6,021 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Methods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:132,878,898-132,890,201)mRNA (may differ from genome)Protein (168 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGencodeGeneCardsHPRD
LynxMGIneXtProtOMIMPubMedUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CI009_HUMAN
DESCRIPTION: RecName: Full=Uncharacterized protein C9orf9;

-  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


-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 55.89 RPKM in Testis
Total median expression: 294.77 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 -57.90154-0.376 Picture PostScript Text
3' UTR -74.40233-0.319 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 Q96E40
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0048306 calcium-dependent protein binding

Cellular Component:
GO:0001669 acrosomal vesicle
GO:0005737 cytoplasm
GO:0005881 cytoplasmic microtubule
GO:0031410 cytoplasmic vesicle


-  Descriptions from all associated GenBank mRNAs
  BC012940 - Homo sapiens chromosome 9 open reading frame 9, mRNA (cDNA clone MGC:21178 IMAGE:4478288), complete cds.
AK075259 - Homo sapiens cDNA FLJ90778 fis, clone THYRO1001128.
AJ011375 - Homo sapiens mRNA for hypothetical protein (C9orf9 gene).
CR457210 - Homo sapiens full open reading frame cDNA clone RZPDo834H088D for gene C9orf9, chromosome 9 open reading frame 9; complete cds, incl. stopcodon.
JF432604 - Synthetic construct Homo sapiens clone IMAGE:100073841 chromosome 9 open reading frame 9 (C9orf9) gene, encodes complete protein.
KJ902198 - Synthetic construct Homo sapiens clone ccsbBroadEn_11592 C9orf9 gene, encodes complete protein.
DQ600025 - Homo sapiens piRNA piR-38091, complete sequence.
AK130389 - Homo sapiens cDNA FLJ26879 fis, clone PRS09162.

-  Other Names for This Gene
  Alternate Gene Symbols: C9orf9, CI009_HUMAN, ENST00000350499.1, ENST00000350499.2, ENST00000350499.3, ENST00000350499.4, ENST00000350499.5, NM_018956, Q96E40, Q9UGQ0, uc004cby.1, uc004cby.2
UCSC ID: ENST00000350499.6
RefSeq Accession: NM_018956
Protein: Q96E40 (aka CI009_HUMAN)
CCDS: CCDS6955.1

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