Human Gene SPAG1 (uc003yji.2)
  Description: Homo sapiens sperm associated antigen 1 (SPAG1), transcript variant 1, mRNA.
RefSeq Summary (NM_003114): The correlation of anti-sperm antibodies with cases of unexplained infertility implicates a role for these antibodies in blocking fertilization. Improved diagnosis and treatment of immunologic infertility, as well as identification of proteins for targeted contraception, are dependent on the identification and characterization of relevant sperm antigens. The protein expressed by this gene is recognized by anti-sperm agglutinating antibodies from an infertile woman. Furthermore, immunization of female rats with the recombinant human protein reduced fertility. This protein localizes to the plasma membrane of germ cells in the testis and to the post-acrosomal plasma membrane of mature spermatozoa. Recombinant polypeptide binds GTP and exhibits GTPase activity. Thus, this protein may regulate GTP signal transduction pathways involved in spermatogenesis and fertilization. Two transcript variants of this gene encode the same protein. [provided by RefSeq, Jul 2008]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments.
Transcript (Including UTRs)
   Position: hg19 chr8:101,170,563-101,254,132 Size: 83,570 Total Exon Count: 19 Strand: +
Coding Region
   Position: hg19 chr8:101,174,509-101,253,250 Size: 78,742 Coding Exon Count: 18 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:101,170,563-101,254,132)mRNA (may differ from genome)Protein (926 aa)
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WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SPAG1_HUMAN
DESCRIPTION: RecName: Full=Sperm-associated antigen 1; AltName: Full=HSD-3.8; AltName: Full=Infertility-related sperm protein Spag-1;
FUNCTION: Plays a role in fertilization. Binds GTP and has GTPase activity.
SUBCELLULAR LOCATION: Cytoplasm.
TISSUE SPECIFICITY: Detected in sperm and testis, in particular in pachytene primary spermatocytes.
MISCELLANEOUS: Antibodies against SPAG1 interfere with fertilization (By similarity).
SIMILARITY: Contains 9 TPR repeats.
SEQUENCE CAUTION: Sequence=AAH55091.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence;

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SPAG1
CDC HuGE Published Literature: SPAG1
Positive Disease Associations: Leukocyte Count
Related Studies:
  1. Leukocyte Count
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: SPAG1
Diseases sorted by gene-association score: ciliary dyskinesia, primary, 28* (919), primary ciliary dyskinesia 28: spag1-related primary ciliary dyskinesia* (500), epilepsy, nocturnal frontal lobe, 5* (283), kcnt1-related nocturnal frontal lobe epilepsy, autosomal dominant* (283), ciliary dyskinesia, primary, 1, with or without situs inversus* (126), kartagener syndrome* (105), carbuncle (16), theileriasis (12), infertility (11), myofascial pain syndrome (7), primary ciliary dyskinesia (4)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 7.43 RPKM in Testis
Total median expression: 99.28 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
5' UTR -136.00284-0.479 Picture PostScript Text
3' UTR -158.76882-0.180 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
IPR023114 - Elongated_TPR_rpt_dom
IPR025986 - RPAP3-like_C
IPR001440 - TPR-1
IPR013026 - TPR-contain_dom
IPR011990 - TPR-like_helical
IPR019734 - TPR_repeat

Pfam Domains:
PF00515 - Tetratricopeptide repeat
PF07719 - Tetratricopeptide repeat
PF13181 - Tetratricopeptide repeat
PF13877 - Potential Monad-binding region of RPAP3

SCOP Domains:
81901 - HCP-like
48439 - Protein prenylyltransferase
48452 - TPR-like

ModBase Predicted Comparative 3D Structure on Q07617
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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 orthologGenome BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
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 RGDEnsemblFlyBase  
 Protein SequenceProtein SequenceProtein Sequence  
 AlignmentAlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0005525 GTP binding
GO:0016787 hydrolase activity

Biological Process:
GO:0007338 single fertilization
GO:0070286 axonemal dynein complex assembly

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AK057482 - Homo sapiens cDNA FLJ32920 fis, clone TESTI2006866, highly similar to Sperm-associated antigen 1.
BC055091 - Homo sapiens sperm associated antigen 1, mRNA (cDNA clone IMAGE:6614099), partial cds.
GQ472210 - Homo sapiens epididymis secretory protein Li 268 (HEL-S-268) mRNA, partial cds.
AF311312 - Homo sapiens infertility-related sperm protein mRNA, complete cds.
JD453464 - Sequence 434488 from Patent EP1572962.
JD549397 - Sequence 530421 from Patent EP1572962.
JD555365 - Sequence 536389 from Patent EP1572962.
JD217909 - Sequence 198933 from Patent EP1572962.
JD340536 - Sequence 321560 from Patent EP1572962.
JD280424 - Sequence 261448 from Patent EP1572962.
JD134864 - Sequence 115888 from Patent EP1572962.
JD567124 - Sequence 548148 from Patent EP1572962.
JD350074 - Sequence 331098 from Patent EP1572962.
JD562044 - Sequence 543068 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NP70, NM_003114, NP_757367, Q07617, Q7Z5G1, SPAG1_HUMAN
UCSC ID: uc003yji.2
RefSeq Accession: NM_003114
Protein: Q07617 (aka SPAG1_HUMAN)
CCDS: CCDS34930.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SPAG1:
pcd (Primary Ciliary Dyskinesia)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_003114.4
exon count: 19CDS single in 3' UTR: no RNA size: 3958
ORF size: 2781CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5649.50frame shift in genome: no % Coverage: 99.72
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.