Human Gene SYCP1 (ENST00000618516.4) from GENCODE V44
  Description: Major component of the transverse filaments of synaptonemal complexes (SCS), formed between homologous chromosomes during meiotic prophase. (from UniProt Q15431)
Gencode Transcript: ENST00000618516.4
Gencode Gene: ENSG00000198765.12
Transcript (Including UTRs)
   Position: hg38 chr1:114,854,868-114,995,019 Size: 140,152 Total Exon Count: 32 Strand: +
Coding Region
   Position: hg38 chr1:114,855,465-114,995,019 Size: 139,555 Coding Exon Count: 31 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:114,854,868-114,995,019)mRNA (may differ from genome)Protein (976 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGencodeGeneCardsHGNC
HPRDLynxMalacardsMGIneXtProtPubMed
ReactomeUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: SYCP1_HUMAN
DESCRIPTION: RecName: Full=Synaptonemal complex protein 1; Short=SCP-1; AltName: Full=Cancer/testis antigen 8; Short=CT8;
FUNCTION: Major component of the transverse filaments of synaptonemal complexes (SCS), formed between homologous chromosomes during meiotic prophase.
SUBUNIT: Found in a complex with SYCE1 and SYCE2. Interacts with SYCE1 and SYCE2 (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity). Chromosome (By similarity). Note=In tripartite segments of synaptonemal complexes, between lateral elements in the nucleus. Found only where the chromosome cores are synapsed. Its N-terminus is found towards the center of the synaptonemal complex while the C- terminus extends well into the lateral domain of the synaptonemal complex (By similarity).
TISSUE SPECIFICITY: Testis.
DOMAIN: Consists of an alpha-helical stretch of 700 AA residues, flanked by N- and C-terminal globular domains. The C-terminal domain has DNA-binding capacity (By similarity).

-  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


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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 21.33 RPKM in Testis
Total median expression: 21.61 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 -55.70178-0.313 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
IPR008827 - SCP-1

Pfam Domains:
PF05483 - Synaptonemal complex protein 1 (SCP-1)

ModBase Predicted Comparative 3D Structure on Q15431
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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
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:0003677 DNA binding

Biological Process:
GO:0000711 meiotic DNA repair synthesis
GO:0007049 cell cycle
GO:0007129 synapsis
GO:0007130 synaptonemal complex assembly
GO:0007131 reciprocal meiotic recombination
GO:0007283 spermatogenesis
GO:0032880 regulation of protein localization
GO:0035092 sperm chromatin condensation
GO:0051026 chiasma assembly
GO:0051301 cell division
GO:0051321 meiotic cell cycle
GO:0051878 lateral element assembly

Cellular Component:
GO:0000775 chromosome, centromeric region
GO:0000794 condensed nuclear chromosome
GO:0000795 synaptonemal complex
GO:0000801 central element
GO:0000802 transverse filament
GO:0001673 male germ cell nucleus
GO:0005634 nucleus
GO:0005694 chromosome


-  Descriptions from all associated GenBank mRNAs
  HM005504 - Homo sapiens clone HTL-T-191 testicular tissue protein Li 191 mRNA, complete cds.
LF383819 - JP 2014500723-A/191322: Polycomb-Associated Non-Coding RNAs.
MA619396 - JP 2018138019-A/191322: Polycomb-Associated Non-Coding RNAs.
BC026162 - Homo sapiens cDNA clone IMAGE:4827367, containing frame-shift errors.
AK315268 - Homo sapiens cDNA, FLJ96278.
AF273043 - Homo sapiens CTCL tumor antigen se2-1 mRNA, partial cds.
BC144020 - Homo sapiens cDNA clone IMAGE:9052540, containing frame-shift errors.
BC126266 - Homo sapiens synaptonemal complex protein 1, mRNA (cDNA clone MGC:161544 IMAGE:8991982), complete cds.
BC144019 - Homo sapiens synaptonemal complex protein 1, mRNA (cDNA clone MGC:177556 IMAGE:9052539), complete cds.
X95654 - H.sapiens mRNA for SCP1 protein.
D67035 - Homo sapiens mRNA for SCP-1, complete cds.
KJ892237 - Synthetic construct Homo sapiens clone ccsbBroadEn_01631 SYCP1 gene, encodes complete protein.
BC105299 - Homo sapiens synaptonemal complex protein 1, mRNA (cDNA clone IMAGE:6106106), complete cds.
BC065190 - Homo sapiens cDNA clone IMAGE:5164337, containing frame-shift errors.

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

Protein Q15431 (Reactome details) participates in the following event(s):

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: BC026162, ENST00000618516.1, ENST00000618516.2, ENST00000618516.3, O14963, Q15431, Q5VXJ6, SCP1, SYCP1_HUMAN, uc001efq.1, uc001efq.2, uc001efq.3, uc001efq.4, uc001efq.5
UCSC ID: ENST00000618516.4
RefSeq Accession: NM_001282541
Protein: Q15431 (aka SYCP1_HUMAN or SCP1_HUMAN)
CCDS: CCDS879.1, CCDS72840.1

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