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Sycp3 synaptonemal complex protein 3 [ Mus musculus (house mouse) ]

Gene ID: 20962, updated on 8-Feb-2024

Summary

Official Symbol
Sycp3provided by MGI
Official Full Name
synaptonemal complex protein 3provided by MGI
Primary source
MGI:MGI:109542
See related
Ensembl:ENSMUSG00000020059 AllianceGenome:MGI:109542
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Cor1; Scp3
Summary
Predicted to enable DNA binding activity. Involved in meiotic chromosome segregation and spermatogenesis. Acts upstream of or within several processes, including cellular response to leukemia inhibitory factor; meiosis I cell cycle process; and sperm chromatin condensation. Located in condensed chromosome and male germ cell nucleus. Is expressed in several structures, including adrenal gland; alimentary system; brain; genitourinary system; and primordial germ cell. Used to study azoospermia. Human ortholog(s) of this gene implicated in spermatogenic failure 4. Orthologous to human SYCP3 (synaptonemal complex protein 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in testis adult (RPKM 5.3), kidney adult (RPKM 2.4) and 12 other tissues See more
Orthologs
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Genomic context

See Sycp3 in Genome Data Viewer
Location:
10 C1; 10 43.94 cM
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 10 NC_000076.7 (88295449..88309098)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 10 NC_000076.6 (88459587..88473236)

Chromosome 10 - NC_000076.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E2332 Neighboring gene STARR-positive B cell enhancer ABC_E11453 Neighboring gene predicted gene, 40733 Neighboring gene N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits Neighboring gene STARR-positive B cell enhancer ABC_E5162 Neighboring gene STARR-positive B cell enhancer mm9_chr10:87872706-87873007 Neighboring gene STARR-positive B cell enhancer ABC_E2333 Neighboring gene STARR-positive B cell enhancer ABC_E3906 Neighboring gene choline phosphotransferase 1 Neighboring gene STARR-seq mESC enhancer starr_27496 Neighboring gene myosin binding protein C, slow-type Neighboring gene STARR-seq mESC enhancer starr_27498 Neighboring gene STARR-positive B cell enhancer ABC_E6897 Neighboring gene STARR-seq mESC enhancer starr_27500 Neighboring gene STARR-seq mESC enhancer starr_27501 Neighboring gene ribosomal protein L7A pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within cell cycle IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within cell division IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within cellular response to leukemia inhibitory factor IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in chiasma assembly IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within chiasma assembly IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in female meiosis chromosome segregation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in female meiosis chromosome separation NAS
Non-traceable Author Statement
more info
PubMed 
involved_in female meiosis sister chromatid cohesion IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within homologous chromosome pairing at meiosis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within lateral element assembly IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within meiotic DNA repair synthesis IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in meiotic cell cycle IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within meiotic cell cycle IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within mitotic cell cycle IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within sperm DNA condensation IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in sperm DNA condensation ISO
Inferred from Sequence Orthology
more info
 
involved_in spermatid development IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within spermatogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in spermatogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in synaptonemal complex assembly IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within synaptonemal complex assembly IGI
Inferred from Genetic Interaction
more info
PubMed 
Component Evidence Code Pubs
located_in chromosome IDA
Inferred from Direct Assay
more info
PubMed 
located_in chromosome, centromeric region IDA
Inferred from Direct Assay
more info
PubMed 
located_in condensed chromosome IDA
Inferred from Direct Assay
more info
PubMed 
located_in condensed chromosome, centromeric region IDA
Inferred from Direct Assay
more info
PubMed 
located_in condensed nuclear chromosome IDA
Inferred from Direct Assay
more info
PubMed 
located_in female germ cell nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in lateral element IDA
Inferred from Direct Assay
more info
PubMed 
located_in lateral element ISO
Inferred from Sequence Orthology
more info
 
located_in male germ cell nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 
is_active_in synaptonemal complex IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in synaptonemal complex IDA
Inferred from Direct Assay
more info
PubMed 
located_in synaptonemal complex ISO
Inferred from Sequence Orthology
more info
PubMed 
located_in transverse filament IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
synaptonemal complex protein 3
Names
SCP-3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_011517.2NP_035647.2  synaptonemal complex protein 3

    See identical proteins and their annotated locations for NP_035647.2

    Status: VALIDATED

    Source sequence(s)
    BC138509, BY386732
    Consensus CDS
    CCDS24111.1
    UniProtKB/Swiss-Prot
    P70281, Q3V2A4, Q549A7
    UniProtKB/TrEMBL
    A2RSE7
    Related
    ENSMUSP00000020252.4, ENSMUST00000020252.10
    Conserved Domains (1) summary
    pfam04803
    Location:103222
    Cor1; Cor1/Xlr/Xmr conserved region

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000076.7 Reference GRCm39 C57BL/6J

    Range
    88295449..88309098
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)