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Sycp2 synaptonemal complex protein 2 [ Mus musculus (house mouse) ]

Gene ID: 320558, updated on 12-May-2024

Summary

Official Symbol
Sycp2provided by MGI
Official Full Name
synaptonemal complex protein 2provided by MGI
Primary source
MGI:MGI:1933281
See related
Ensembl:ENSMUSG00000060445 AllianceGenome:MGI:1933281
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
3830402K23Rik; 4930518F03Rik
Summary
Predicted to enable DNA binding activity. Acts upstream of or within several processes, including fertilization; male genitalia morphogenesis; and meiotic nuclear division. Located in lateral element. Is expressed in meiotic germ cell of ovary and primary oocyte. Human ortholog(s) of this gene implicated in spermatogenic failure 1. Orthologous to human SYCP2 (synaptonemal complex protein 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in testis adult (RPKM 6.1) and CNS E18 (RPKM 0.3) See more
Orthologs
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Genomic context

See Sycp2 in Genome Data Viewer
Location:
2 H4; 2 99.81 cM
Exon count:
43
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (177987088..178051580, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (178345295..178407776, complement)

Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_06699 Neighboring gene zinc finger protein 931 Neighboring gene phosphatase and actin regulator 3 Neighboring gene GC-rich promoter binding protein 1 pseudogene Neighboring gene protein phosphatase 1, regulatory subunit 3D Neighboring gene family with sequence similarity 217, member B Neighboring gene predicted gene, 35532

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)
  • Endonuclease-mediated (1) 
  • Targeted (3)  1 citation

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 animal organ morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
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 ectopic germ cell programmed cell death IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in female meiotic nuclear division IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within female meiotic nuclear division IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within fertilization IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within male genitalia morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in male meiotic nuclear division IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within male meiotic nuclear division IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within meiotic cell cycle IEA
Inferred from Electronic Annotation
more info
 
involved_in mitotic G1 phase IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within mitotic G1 phase IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within negative regulation of apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within negative regulation of developmental process IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within negative regulation of reproductive process IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
located_in chromosome IEA
Inferred from Electronic Annotation
more info
 
is_active_in condensed chromosome, centromeric region IBA
Inferred from Biological aspect of Ancestor
more info
 
is_active_in lateral element IBA
Inferred from Biological aspect of Ancestor
more info
 
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 nucleoplasm TAS
Traceable Author Statement
more info
 
located_in nucleus IEA
Inferred from Electronic Annotation
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
 

General protein information

Preferred Names
synaptonemal complex protein 2
Names
SCP-2
synaptonemal complex lateral element protein

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_177191.3NP_796165.2  synaptonemal complex protein 2

    See identical proteins and their annotated locations for NP_796165.2

    Status: VALIDATED

    Source sequence(s)
    AL772217, DQ103262
    Consensus CDS
    CCDS38370.1
    UniProtKB/Swiss-Prot
    A2AJW2, Q1G7B6, Q9CUU3
    Related
    ENSMUSP00000079909.4, ENSMUST00000081134.10
    Conserved Domains (1) summary
    COG4399
    Location:43236
    YheB; Uncharacterized membrane protein YheB, UPF0754 family [Function unknown]

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_000068.8 Reference GRCm39 C57BL/6J

    Range
    177987088..178051580 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006500664.4XP_006500727.1  synaptonemal complex protein 2 isoform X2

    Conserved Domains (1) summary
    pfam18584
    Location:53164
    SYCP2_SLD; Synaptonemal complex 2 Spt16M-like domain
  2. XM_017319020.3XP_017174509.1  synaptonemal complex protein 2 isoform X1

    Conserved Domains (2) summary
    pfam18581
    Location:185
    SYCP2_ARLD; Synaptonemal complex 2 armadillo-repeat-like domain
    pfam18584
    Location:179290
    SYCP2_SLD; Synaptonemal complex 2 Spt16M-like domain

RNA

  1. XR_003953467.2 RNA Sequence