Human Gene SPECC1 (ENST00000395527.9_6) from GENCODE V47lift37
  Description: sperm antigen with calponin homology and coiled-coil domains 1, transcript variant 6 (from RefSeq NM_001243439.2)
Gencode Transcript: ENST00000395527.9_6
Gencode Gene: ENSG00000128487.19_16
Transcript (Including UTRs)
   Position: hg19 chr17:19,912,672-20,222,339 Size: 309,668 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr17:19,999,965-20,217,378 Size: 217,414 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:19,912,672-20,222,339)mRNA (may differ from genome)Protein (1068 aa)
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WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CYTSB_HUMAN
DESCRIPTION: RecName: Full=Cytospin-B; AltName: Full=Nuclear structure protein 5; Short=NSP5; AltName: Full=Sperm antigen HCMOGT-1; AltName: Full=Sperm antigen with calponin homology and coiled-coil domains 1;
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Highly expressed in testis. Barely detectable in other tissues. Also highly expressed in some cancer cell lines.
DISEASE: Note=A chromosomal aberration involving CYTSB may be a cause of juvenile myelomonocytic leukemia. Translocation t(5;17)(q33;p11.2) with PDGFRB.
SIMILARITY: Belongs to the cytospin-A family.
SIMILARITY: Contains 1 CH (calponin-homology) domain.
SEQUENCE CAUTION: Sequence=AAH33618.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=BAB16440.1; Type=Frameshift; Positions=8;
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/HCMOGT1ID174.html";

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: SPECC1
Diseases sorted by gene-association score: juvenile myelomonocytic leukemia (11)

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

+  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: 7.89 RPKM in Testis
Total median expression: 156.09 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -32.7087-0.376 Picture PostScript Text
3' UTR -1822.404961-0.367 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
IPR001715 - CH-domain

Pfam Domains:
PF00307 - Calponin homology (CH) domain
PF11971 - CAMSAP CH domain

SCOP Domains:
47576 - Calponin-homology domain, CH-domain
58104 - Methyl-accepting chemotaxis protein (MCP) signaling domain

ModBase Predicted Comparative 3D Structure on Q5M775
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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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0005634 nucleus
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  AK094274 - Homo sapiens cDNA FLJ36955 fis, clone BRACE2005858, highly similar to Homo sapiens HCMOGT-1 mRNA for sperm antigen.
AK295093 - Homo sapiens cDNA FLJ50011 complete cds, highly similar to Homo sapiens spectrin domain with coiled-coils 1 (SPECC1), transcript variant, mRNA.
AK314341 - Homo sapiens cDNA, FLJ95102.
AY816328 - Homo sapiens structure protein NSP5b3a mRNA, complete cds.
AY816329 - Homo sapiens structure protein NSP5b3b mRNA, complete cds.
AB041533 - Homo sapiens HCMOGT-1 mRNA for sperm antigen, complete cds.
AK301318 - Homo sapiens cDNA FLJ50032 complete cds, highly similar to Homo sapiens spectrin domain with coiled-coils 1 (SPECC1), transcript variant, mRNA.
AK304186 - Homo sapiens cDNA FLJ53275 complete cds, highly similar to Homo sapiens spectrin domain with coiled-coils 1 (SPECC1), transcript variant, mRNA.
AY816327 - Homo sapiens structure protein NSP5a3b mRNA, complete cds.
BC021123 - Homo sapiens cytospin B, mRNA (cDNA clone MGC:31992 IMAGE:3614358), complete cds.
AK295811 - Homo sapiens cDNA FLJ54411 complete cds, highly similar to Homo sapiens spectrin domain with coiled-coils 1 (SPECC1), transcript variant, mRNA.
AK298601 - Homo sapiens cDNA FLJ54420 complete cds, highly similar to Homo sapiens spectrin domain with coiled-coils 1 (SPECC1), transcript variant, mRNA.
JD336034 - Sequence 317058 from Patent EP1572962.
JD329498 - Sequence 310522 from Patent EP1572962.
JD230855 - Sequence 211879 from Patent EP1572962.
AY816326 - Homo sapiens structure protein NSP5a3a mRNA, complete cds.
BC050058 - Homo sapiens cytospin B, mRNA (cDNA clone MGC:51241 IMAGE:5277450), complete cds.
BC033618 - Homo sapiens cytospin B, mRNA (cDNA clone IMAGE:4508298), partial cds.
DQ580155 - Homo sapiens piRNA piR-48267, complete sequence.
E06871 - cDNA encoding human sperm membrane antigen peptide.
DQ584729 - Homo sapiens piRNA piR-51841, complete sequence.
JD334369 - Sequence 315393 from Patent EP1572962.
JD545149 - Sequence 526173 from Patent EP1572962.
JD225286 - Sequence 206310 from Patent EP1572962.
JD417333 - Sequence 398357 from Patent EP1572962.
JD185458 - Sequence 166482 from Patent EP1572962.
DQ576770 - Homo sapiens piRNA piR-44882, complete sequence.

-  Other Names for This Gene
  Alternate Gene Symbols: B4DHH0, B7WNS8, CYTSB, CYTSB_HUMAN, ENST00000395527.1, ENST00000395527.2, ENST00000395527.3, ENST00000395527.4, ENST00000395527.5, ENST00000395527.6, ENST00000395527.7, ENST00000395527.8, NM_001243439, NSP5, Q5IBP1, Q5IBP2, Q5IBP3, Q5IBP4, Q5M772, Q5M773, Q5M774, Q5M775, Q86XT8, Q8N4U4, Q8WU84, Q9HCQ3, uc318xma.1, uc318xma.2
UCSC ID: ENST00000395527.9_6
RefSeq Accession: NM_001243439.2
Protein: Q5M775 (aka CYTSB_HUMAN)

-  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.