Human Gene SYCP1 (uc001efr.3)
  Description: Homo sapiens synaptonemal complex protein 1 (SYCP1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr1:115,397,455-115,537,990 Size: 140,536 Total Exon Count: 32 Strand: +
Coding Region
   Position: hg19 chr1:115,398,086-115,537,640 Size: 139,555 Coding Exon Count: 31 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:115,397,455-115,537,990)mRNA (may differ from genome)Protein (976 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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OMIMPubMedReactomeTreefamUniProtKBWikipedia
BioGrid CRISPR DB

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SYCP1
CDC HuGE Published Literature: SYCP1
Positive Disease Associations: Body Composition , Body Mass Index , Heart Failure
Related Studies:
  1. Body Composition
    , , . [PubMed 0]
  2. Body Mass Index
    , , . [PubMed 0]
  3. Heart Failure
    , , . [PubMed 0]
           more ... click here to view the complete list

-  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: 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 -76.00209-0.364 Picture PostScript Text
3' UTR -69.60350-0.199 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
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  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.
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.
MA619396 - JP 2018138019-A/191322: Polycomb-Associated Non-Coding RNAs.
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.
JD469371 - Sequence 450395 from Patent EP1572962.

-  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: NM_003176, NP_003167, O14963, Q15431, Q5VXJ6, SCP1, SYCP1_HUMAN
UCSC ID: uc001efr.3
RefSeq Accession: NM_003176
Protein: Q15431 (aka SYCP1_HUMAN or SCP1_HUMAN)
CCDS: CCDS879.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_003176.2
exon count: 32CDS single in 3' UTR: no RNA size: 3503
ORF size: 2931CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 6059.00frame shift in genome: no % Coverage: 99.63
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.