Human Gene SYCP3 (ENST00000392924.2_7) from GENCODE V47lift37
  Description: synaptonemal complex protein 3, transcript variant 2 (from RefSeq NM_153694.5)
Gencode Transcript: ENST00000392924.2_7
Gencode Gene: ENSG00000139351.15_10
Transcript (Including UTRs)
   Position: hg19 chr12:102,122,426-102,133,240 Size: 10,815 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr12:102,122,705-102,131,713 Size: 9,009 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:102,122,426-102,133,240)mRNA (may differ from genome)Protein (236 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SYCP3_HUMAN
DESCRIPTION: RecName: Full=Synaptonemal complex protein 3; Short=SCP-3;
FUNCTION: Component of the transverse filaments of synaptonemal complexes (SCS), formed between homologous chromosomes during meiotic prophase. Has an essential meiotic function in spermatogenesis. May be important for testis development.
SUBUNIT: Interacts with SYCP2 (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity). Note=In tripartite segments of synaptonemal complexes, irrespective of whether these are synapsed or unsynapsed (By similarity).
TISSUE SPECIFICITY: Testis-specific.
DISEASE: Defects in SYCP3 are the cause of spermatogenic failure type 4 (SPGF4) [MIM:270960]. An infertility disorder characterized by azoospermia, a condition of having no sperm present in the ejaculate. Testicular histology shows arrest of spermatogenesis at the pachytene stage of primary spermatocytes.
SIMILARITY: Belongs to the XLR/SYCP3 family.

-  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: SYCP3
Diseases sorted by gene-association score: spermatogenic failure 4* (1019), sycp3-related pregnancy loss, susceptibility to* (100), azoospermia (22), gemistocytic astrocytoma (7), mannosidosis, beta (6), male reproductive system disease (1)
* = 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: 82.30 RPKM in Testis
Total median expression: 90.48 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 -43.00129-0.333 Picture PostScript Text
3' UTR -42.20279-0.151 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
IPR006888 - Cor1/Xlr/Xmr

Pfam Domains:
PF04803 - Cor1/Xlr/Xmr conserved region

ModBase Predicted Comparative 3D Structure on Q8IZU3
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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    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding

Biological Process:
GO:0007049 cell cycle
GO:0007141 male meiosis I
GO:0035093 spermatogenesis, exchange of chromosomal proteins
GO:0051301 cell division
GO:0051321 meiotic cell cycle

Cellular Component:
GO:0000775 chromosome, centromeric region
GO:0000795 synaptonemal complex
GO:0000800 lateral element
GO:0005634 nucleus
GO:0005694 chromosome


-  Descriptions from all associated GenBank mRNAs
  AF517774 - Homo sapiens putative SCP3 protein mRNA, complete cds.
AK125930 - Homo sapiens cDNA FLJ43942 fis, clone TESTI4014276, moderately similar to Rattus norvegicus Synaptonemal complex protein 3 (Sycp3).
BC062662 - Homo sapiens synaptonemal complex protein 3, mRNA (cDNA clone MGC:71888 IMAGE:6616222), complete cds.
AF492003 - Homo sapiens synaptonemal complex protein 3 (SYCP3) mRNA, complete cds.
KJ893752 - Synthetic construct Homo sapiens clone ccsbBroadEn_03146 SYCP3 gene, encodes complete protein.
AB590807 - Synthetic construct DNA, clone: pFN21AE1727, Homo sapiens SYCP3 gene for synaptonemal complex protein 3, without stop codon, in Flexi system.
LF380673 - JP 2014500723-A/188176: Polycomb-Associated Non-Coding RNAs.
LF380674 - JP 2014500723-A/188177: Polycomb-Associated Non-Coding RNAs.
LF380668 - JP 2014500723-A/188171: Polycomb-Associated Non-Coding RNAs.
LF380676 - JP 2014500723-A/188179: Polycomb-Associated Non-Coding RNAs.
LF380666 - JP 2014500723-A/188169: Polycomb-Associated Non-Coding RNAs.
LF380382 - JP 2014500723-A/187885: Polycomb-Associated Non-Coding RNAs.
JD223890 - Sequence 204914 from Patent EP1572962.
JD471283 - Sequence 452307 from Patent EP1572962.
MA616250 - JP 2018138019-A/188176: Polycomb-Associated Non-Coding RNAs.
MA616251 - JP 2018138019-A/188177: Polycomb-Associated Non-Coding RNAs.
MA616245 - JP 2018138019-A/188171: Polycomb-Associated Non-Coding RNAs.
MA616253 - JP 2018138019-A/188179: Polycomb-Associated Non-Coding RNAs.
MA616243 - JP 2018138019-A/188169: Polycomb-Associated Non-Coding RNAs.
MA615959 - JP 2018138019-A/187885: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q8IZU3 (Reactome details) participates in the following event(s):

R-HSA-912467 BRCA1 is recruited to unsynapsed regions
R-HSA-912470 ATR phosphorylates Histone H2A.X at unsynapsed regions
R-HSA-912450 ATR Kinase is recruited to unsynapsed regions
R-HSA-1221632 Meiotic synapsis
R-HSA-1500620 Meiosis
R-HSA-1474165 Reproduction
R-HSA-1640170 Cell Cycle

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000392924.1, NM_153694, Q8IZU3, SCP3, SYCP3_HUMAN, uc318vma.1, uc318vma.2
UCSC ID: ENST00000392924.2_7
RefSeq Accession: NM_001177949.2
Protein: Q8IZU3 (aka SYCP3_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.