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Syce2 synaptonemal complex central element protein 2 [ Mus musculus (house mouse) ]

Gene ID: 71846, updated on 8-Feb-2024

Summary

Official Symbol
Syce2provided by MGI
Official Full Name
synaptonemal complex central element protein 2provided by MGI
Primary source
MGI:MGI:1919096
See related
Ensembl:ENSMUSG00000003824 AllianceGenome:MGI:1919096
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
Cesc1; 1700013H19Rik
Summary
Predicted to act upstream of or within synaptonemal complex assembly. Located in central element. Is expressed in primary spermatocyte and spermatocyte. Orthologous to human SYCE2 (synaptonemal complex central element protein 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in testis adult (RPKM 31.9), liver E14 (RPKM 10.9) and 11 other tissues See more
Orthologs
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Genomic context

See Syce2 in Genome Data Viewer
Location:
8 C3; 8 41.25 cM
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 8 NC_000074.7 (85598740..85614075)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (84872111..84887446)

Chromosome 8 - NC_000074.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 1700122E12 gene Neighboring gene predicted gene 5911 Neighboring gene phenylalanyl-tRNA synthetase, alpha subunit Neighboring gene STARR-positive B cell enhancer ABC_E11391 Neighboring gene microRNA 7069 Neighboring gene glutaryl-Coenzyme A dehydrogenase Neighboring gene STARR-positive B cell enhancer ABC_E1763 Neighboring gene predicted gene, 39213 Neighboring gene CapStarr-seq enhancer MGSCv37_chr8:87427053-87427162 Neighboring gene Kruppel-like transcription factor 1 (erythroid)

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)
  • Gene trapped (1)  1 citation
  • Endonuclease-mediated (1) 

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
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 meiotic cell cycle IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within synaptonemal complex assembly IC
Inferred by Curator
more info
PubMed 
Component Evidence Code Pubs
is_active_in central element IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in central element IDA
Inferred from Direct Assay
more info
PubMed 
located_in chromosome IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in synaptonemal complex ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 

General protein information

Preferred Names
synaptonemal complex central element protein 2
Names
central element synaptonemal complex 1
central element synaptonemal complex protein 1

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_001168244.1NP_001161716.1  synaptonemal complex central element protein 2 isoform 3

    See identical proteins and their annotated locations for NP_001161716.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and 5' coding region and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AC161765, AK082833, AK167332
    UniProtKB/Swiss-Prot
    Q505B8
  2. NM_001168246.1NP_001161718.1  synaptonemal complex central element protein 2 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC161765
    Consensus CDS
    CCDS52620.1
    UniProtKB/TrEMBL
    A2RTK0, E9PYH4
    Related
    ENSMUSP00000131438.2, ENSMUST00000170296.2
  3. NM_027954.3NP_082230.2  synaptonemal complex central element protein 2 isoform 2

    See identical proteins and their annotated locations for NP_082230.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1
    Source sequence(s)
    AC161765, AK005954, AK082833, BY246600
    Consensus CDS
    CCDS22481.1
    UniProtKB/Swiss-Prot
    Q3TJR1, Q505B8, Q9DAC4
    UniProtKB/TrEMBL
    A2RTK0
    Related
    ENSMUSP00000122159.2, ENSMUST00000136026.8

RNA

  1. NR_031759.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC161765, AK082833, BY083329
    Related
    ENSMUST00000003922.6

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_000074.7 Reference GRCm39 C57BL/6J

    Range
    85598740..85614075
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)