Mouse Gene Spag6l (ENSMUST00000023468.5) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus sperm associated antigen 6-like (Spag6l), mRNA. (from RefSeq NM_015773)
Gencode Transcript: ENSMUST00000023468.5
Gencode Gene: ENSMUSG00000022783.11
Transcript (Including UTRs)
   Position: mm10 chr16:16,753,016-16,829,313 Size: 76,298 Total Exon Count: 11 Strand: -
Coding Region
   Position: mm10 chr16:16,753,814-16,829,219 Size: 75,406 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:16,753,016-16,829,313)mRNA (may differ from genome)Protein (507 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedSOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: SPAG6_MOUSE
DESCRIPTION: RecName: Full=Sperm-associated antigen 6; AltName: Full=Axoneme central apparatus protein; AltName: Full=Protein PF16 homolog;
FUNCTION: Important for structural integrity of the central apparatus in the sperm tail and for flagellar motility.
SUBUNIT: Interacts with SPAG16 AND SPAG17.
INTERACTION: Q5S003:Spag17; NbExp=3; IntAct=EBI-1783654, EBI-1783665;
SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton. Cell projection, cilium, flagellum. Note=Associated with microtubules. Detected on the sperm flagellum.
TISSUE SPECIFICITY: Highly expressed in testis. Not detected in prostate, ovary, spleen, thymus, small intestine, colon and peripheral blood leukocytes.
DISEASE: Note=Defects in Spag6 are a cause of hydrocephalus and of male infertility.
DISRUPTION PHENOTYPE: In null embryos the central apparatus is unstable leading to a loss, and presumably degradation of proteins to which SPAG6 normally binds, including SPAG16 AND SPAG17.
SIMILARITY: Contains 8 ARM repeats.

-  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


-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -34.3094-0.365 Picture PostScript Text
3' UTR -201.60798-0.253 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
  InterPro Domains: Graphical view of domain structure
IPR011989 - ARM-like
IPR016024 - ARM-type_fold
IPR000225 - Armadillo
IPR000357 - HEAT

Pfam Domains:
PF00514 - Armadillo/beta-catenin-like repeat
PF02985 - HEAT repeat

SCOP Domains:
48371 - ARM repeat
48431 - Lipovitellin-phosvitin complex, superhelical domain
101238 - XPC-binding domain

ModBase Predicted Comparative 3D Structure on Q9JLI7
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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGDEnsembl   
Protein SequenceProtein Sequence    
AlignmentAlignment    

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

Biological Process:
GO:0007288 sperm axoneme assembly
GO:0021591 ventricular system development
GO:0030030 cell projection organization
GO:0030317 flagellated sperm motility

Cellular Component:
GO:0005737 cytoplasm
GO:0005856 cytoskeleton
GO:0005874 microtubule
GO:0005929 cilium
GO:0015630 microtubule cytoskeleton
GO:0031514 motile cilium
GO:0042995 cell projection
GO:0097228 sperm principal piece
GO:1990716 axonemal central apparatus


-  Descriptions from all associated GenBank mRNAs
  AF173866 - Mus musculus axoneme central apparatus protein (Spag6) mRNA, complete cds.
BC090660 - Mus musculus sperm associated antigen 6, mRNA (cDNA clone MGC:116688 IMAGE:30673350), complete cds.
BC100455 - Mus musculus sperm associated antigen 6, mRNA (cDNA clone MGC:118271 IMAGE:30919921), complete cds.
AK005732 - Mus musculus adult male testis cDNA, RIKEN full-length enriched library, clone:1700007K14 product:sperm associated antigen 6, full insert sequence.
AK054199 - Mus musculus 2 days pregnant adult female oviduct cDNA, RIKEN full-length enriched library, clone:E230028C21 product:sperm associated antigen 6, full insert sequence.
AK164680 - Mus musculus 13 days embryo stomach cDNA, RIKEN full-length enriched library, clone:D530049K11 product:sperm associated antigen 6, full insert sequence.
AK053966 - Mus musculus 2 days pregnant adult female oviduct cDNA, RIKEN full-length enriched library, clone:E230008B12 product:unclassifiable, full insert sequence.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_015773, Pf16, Q8K461, Q9JLI7, Spag6, SPAG6_MOUSE, uc007yjb.1, uc007yjb.2, uc007yjb.3
UCSC ID: uc007yjb.3
RefSeq Accession: NM_015773
Protein: Q9JLI7 (aka SPAG6_MOUSE)
CCDS: CCDS27988.1

-  Gene Model Information
  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.