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SYCP3 synaptonemal complex protein 3 [ Homo sapiens (human) ]

Gene ID: 50511, updated on 15-Jun-2019

Summary

Official Symbol
SYCP3provided by HGNC
Official Full Name
synaptonemal complex protein 3provided by HGNC
Primary source
HGNC:HGNC:18130
See related
Ensembl:ENSG00000139351 MIM:604759
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
COR1; SCP3; SPGF4; RPRGL4
Summary
This gene encodes an essential structural component of the synaptonemal complex. This complex is involved in synapsis, recombination and segregation of meiotic chromosomes. Mutations in this gene are associated with azoospermia in males and susceptibility to pregnancy loss in females. Alternate splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, May 2010]
Expression
Broad expression in testis (RPKM 35.2), duodenum (RPKM 4.0) and 14 other tissues See more
Orthologs

Genomic context

See SYCP3 in Genome Data Viewer
Location:
12q23.2
Exon count:
8
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (101728648..101739721, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (102122426..102133474, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene myosin binding protein C, slow type Neighboring gene uncharacterized LOC105369937 Neighboring gene choline phosphotransferase 1 Neighboring gene RNY1 pseudogene 16 Neighboring gene N-acetylglucosamine-1-phosphate transferase subunits alpha and beta Neighboring gene RNA, U6 small nuclear 101, pseudogene Neighboring gene ST13, Hsp70 interacting protein pseudogene 22

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Cell Cycle, organism-specific biosystem (from REACTOME)
    Cell Cycle, organism-specific biosystem
    Cell Cycle
  • Homologous recombination, organism-specific biosystem (from KEGG)
    Homologous recombination, organism-specific biosystemHomologous recombination (HR) is essential for the accurate repair of DNA double-strand breaks (DSBs), potentially lethal lesions. HR takes place in the late S-G2 phase of the cell cycle and involves...
  • Homologous recombination, conserved biosystem (from KEGG)
    Homologous recombination, conserved biosystemHomologous recombination (HR) is essential for the accurate repair of DNA double-strand breaks (DSBs), potentially lethal lesions. HR takes place in the late S-G2 phase of the cell cycle and involves...
  • Meiosis, organism-specific biosystem (from REACTOME)
    Meiosis, organism-specific biosystemDuring meiosis the replicated chromosomes of a single diploid cell are segregated into 4 haploid daughter cells by two successive divisions, meiosis I and meiosis II. In meiosis I, the distinguishing...
  • Meiotic synapsis, organism-specific biosystem (from REACTOME)
    Meiotic synapsis, organism-specific biosystemMeiotic synapsis is the stable physical pairing of homologous chromosomes that begins in leptonema of prophase I and lasts until anaphase of prophase I. First, short segments of axial elements form a...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC71888

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cell division IEA
Inferred from Electronic Annotation
more info
 
male meiosis I NAS
Non-traceable Author Statement
more info
PubMed 
meiotic cell cycle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
spermatid development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
spermatogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
spermatogenesis, exchange of chromosomal proteins IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
chromosome, centromeric region ISS
Inferred from Sequence or Structural Similarity
more info
 
lateral element ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
synaptonemal complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
synaptonemal complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
synaptonemal complex protein 3

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_021181.1 RefSeqGene

    Range
    4998..15822
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001177948.1NP_001171419.1  synaptonemal complex protein 3

    See identical proteins and their annotated locations for NP_001171419.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AC063950, AF517774
    Consensus CDS
    CCDS9087.1
    UniProtKB/Swiss-Prot
    Q8IZU3
    UniProtKB/TrEMBL
    A0A024RBF8
    Related
    ENSP00000266743.2, ENST00000266743.6
    Conserved Domains (1) summary
    pfam04803
    Location:83206
    Cor1; Cor1/Xlr/Xmr conserved region
  2. NM_001177949.2NP_001171420.1  synaptonemal complex protein 3

    See identical proteins and their annotated locations for NP_001171420.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AC063950, AF492003, BG201028
    Consensus CDS
    CCDS9087.1
    UniProtKB/Swiss-Prot
    Q8IZU3
    UniProtKB/TrEMBL
    A0A024RBF8
    Related
    ENSP00000376655.1, ENST00000392924.2
    Conserved Domains (1) summary
    pfam04803
    Location:83206
    Cor1; Cor1/Xlr/Xmr conserved region
  3. NM_153694.4NP_710161.1  synaptonemal complex protein 3

    See identical proteins and their annotated locations for NP_710161.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AC063950, BC062662, BG202454
    Consensus CDS
    CCDS9087.1
    UniProtKB/Swiss-Prot
    Q8IZU3
    UniProtKB/TrEMBL
    A0A024RBF8
    Related
    ENSP00000376658.3, ENST00000392927.7
    Conserved Domains (1) summary
    pfam04803
    Location:83206
    Cor1; Cor1/Xlr/Xmr conserved region

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    101728648..101739721 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011538421.3XP_011536723.2  synaptonemal complex protein 3 isoform X3

  2. XM_005268922.5XP_005268979.3  synaptonemal complex protein 3 isoform X1

  3. XM_017019368.2XP_016874857.1  synaptonemal complex protein 3 isoform X2

  4. XM_024448994.1XP_024304762.1  synaptonemal complex protein 3 isoform X5

    Conserved Domains (1) summary
    pfam04803
    Location:83206
    Cor1; Cor1/Xlr/Xmr conserved region
  5. XM_005268926.4XP_005268983.1  synaptonemal complex protein 3 isoform X4

    See identical proteins and their annotated locations for XP_005268983.1

    Conserved Domains (1) summary
    pfam04803
    Location:85204
    Cor1; Cor1/Xlr/Xmr conserved region
  6. XM_024448995.1XP_024304763.1  synaptonemal complex protein 3 isoform X5

    Conserved Domains (1) summary
    pfam04803
    Location:83206
    Cor1; Cor1/Xlr/Xmr conserved region
  7. XM_005268925.1XP_005268982.1  synaptonemal complex protein 3 isoform X4

    See identical proteins and their annotated locations for XP_005268982.1

    Conserved Domains (1) summary
    pfam04803
    Location:85204
    Cor1; Cor1/Xlr/Xmr conserved region
  8. XM_024448996.1XP_024304764.1  synaptonemal complex protein 3 isoform X5

    Conserved Domains (1) summary
    pfam04803
    Location:83206
    Cor1; Cor1/Xlr/Xmr conserved region
  9. XM_005268924.1XP_005268981.1  synaptonemal complex protein 3 isoform X4

    See identical proteins and their annotated locations for XP_005268981.1

    Conserved Domains (1) summary
    pfam04803
    Location:85204
    Cor1; Cor1/Xlr/Xmr conserved region
  10. XM_005268927.2XP_005268984.1  synaptonemal complex protein 3 isoform X4

    See identical proteins and their annotated locations for XP_005268984.1

    Conserved Domains (1) summary
    pfam04803
    Location:85204
    Cor1; Cor1/Xlr/Xmr conserved region
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