U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

4930447C04Rik RIKEN cDNA 4930447C04 gene [ Mus musculus (house mouse) ]

Gene ID: 75801, updated on 5-Mar-2024

Summary

Go to the top of the page Help
Official Symbol
4930447C04Rikprovided by MGI
Official Full Name
RIKEN cDNA 4930447C04 geneprovided by MGI
Primary source
MGI:MGI:1923051
See related
Ensembl:ENSMUSG00000021098 AllianceGenome:MGI:1923051
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Six6OS; Six6as; Six6os1; 4921504I02Rik; A930035O15Rik
Summary
Involved in gamete generation and meiosis I. Located in central element. Is expressed in ovary; retina; and skeletal muscle. Human ortholog(s) of this gene implicated in primary ovarian insufficiency 18 and spermatogenic failure 52. Orthologous to human C14orf39 (chromosome 14 open reading frame 39). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in frontal lobe adult (RPKM 2.3), cortex adult (RPKM 1.7) and 11 other tissues See more
Orthologs
human all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See 4930447C04Rik in Genome Data Viewer
Location:
12 C3; 12 30.3 cM
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (72926967..72964742, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (72880193..72917957, complement)

Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 33785 Neighboring gene STARR-seq mESC enhancer starr_32453 Neighboring gene predicted gene, 40441 Neighboring gene STARR-seq mESC enhancer starr_32455 Neighboring gene sine oculis-related homeobox 6 Neighboring gene STARR-seq mESC enhancer starr_32458 Neighboring gene microRNA 9718 Neighboring gene sine oculis-related homeobox 1

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. Homozygous mutations in C14orf39/SIX6OS1 cause non-obstructive azoospermia and premature ovarian insufficiency in humans. Fan S, et al. Am J Hum Genet, 2021 Feb 4. PMID 33508233, Free PMC Article
  2. C14ORF39/SIX6OS1 is a constituent of the synaptonemal complex and is essential for mouse fertility. Gómez-H L, et al. Nat Commun, 2016 Oct 31. PMID 27796301, Free PMC Article
  3. The Zip4 protein directly couples meiotic crossover formation to synaptonemal complex assembly. Pyatnitskaya A, et al. Genes Dev, 2022 Jan 1. PMID 34969823, Free PMC Article
  4. SPO16 binds SHOC1 to promote homologous recombination and crossing-over in meiotic prophase I. Zhang Q, et al. Sci Adv, 2019 Jan. PMID 30746471, Free PMC Article
  5. Natural antisense transcripts associated with genes involved in eye development. Alfano G, et al. Hum Mol Genet, 2005 Apr 1. PMID 15703187

See all (20) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SIX6OS1 is essential for the appropriate processing of intermediate recombination nodules before crossover formation
    Title: C14ORF39/SIX6OS1 is a constituent of the synaptonemal complex and is essential for mouse fertility.
Submit: New GeneRIF Correction

Variation

Go to the top of the page Help

Alleles

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

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within DNA recombination IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in homologous chromosome pairing at meiosis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in homologous chromosome pairing at meiosis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in homologous chromosome pairing at meiosis ISO
Inferred from Sequence Orthology
more info
  
involved_in meiotic DNA double-strand break processing involved in reciprocal meiotic recombination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in meiotic DNA double-strand break processing involved in reciprocal meiotic recombination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in meiotic cell cycle IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
  
involved_in oogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in oogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of DNA-binding transcription factor activity NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in spermatogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in spermatogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in synaptonemal complex assembly IMP
Inferred from Mutant Phenotype
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 

General protein information

Go to the top of the page Help
Preferred Names
protein SIX6OS1
Names
Six6 antisense
six6 opposite strand transcript 1 homolog

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_029444.2 → NP_083720.1  protein SIX6OS1

    See identical proteins and their annotated locations for NP_083720.1

    Status: PROVISIONAL

    Source sequence(s)
    AK015397
    Consensus CDS
    CCDS25971.1
    UniProtKB/Swiss-Prot
    Q9CTN5, Q9D5F5, Q9D5Y9
    UniProtKB/TrEMBL
    B2RQE0
    Related
    ENSMUSP00000035376.6, ENSMUST00000044000.12
    Conserved Domains (1) summary
    pfam15676
    Location:37 → 574
    S6OS1; Six6 opposite strand transcript 1 family

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_000078.7 Reference GRCm39 C57BL/6J

    Range
    72926967..72964742 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011244201.3 → XP_011242503.1  protein SIX6OS1 isoform X1

    See identical proteins and their annotated locations for XP_011242503.1

    UniProtKB/TrEMBL
    B2RQE0
    Conserved Domains (1) summary
    pfam15676
    Location:37 → 577
    S6OS1; Six6 opposite strand transcript 1 family

  2. XM_017315237.1 → XP_017170726.1  protein SIX6OS1 isoform X2

    UniProtKB/TrEMBL
    B2RQE0
    Conserved Domains (1) summary
    pfam15676
    Location:37 → 576
    S6OS1; Six6 opposite strand transcript 1 family

  3. XM_017315239.1 → XP_017170728.1  protein SIX6OS1 isoform X4

    UniProtKB/TrEMBL
    B2RQE0
    Conserved Domains (1) summary
    pfam15676
    Location:37 → 540
    S6OS1; Six6 opposite strand transcript 1 family

  4. XM_017315238.1 → XP_017170727.1  protein SIX6OS1 isoform X3

    UniProtKB/TrEMBL
    B2RQE0, F8WHJ9
    Conserved Domains (1) summary
    pfam15676
    Location:37 → 575
    S6OS1; Six6 opposite strand transcript 1 family

  5. XM_011244200.2 → XP_011242502.1  protein SIX6OS1 isoform X1

    See identical proteins and their annotated locations for XP_011242502.1

    UniProtKB/TrEMBL
    B2RQE0
    Conserved Domains (1) summary
    pfam15676
    Location:37 → 577
    S6OS1; Six6 opposite strand transcript 1 family

  6. XM_011244203.3 → XP_011242505.1  protein SIX6OS1 isoform X1

    See identical proteins and their annotated locations for XP_011242505.1

    UniProtKB/TrEMBL
    B2RQE0
    Conserved Domains (1) summary
    pfam15676
    Location:37 → 577
    S6OS1; Six6 opposite strand transcript 1 family

  7. XM_011244202.2 → XP_011242504.1  protein SIX6OS1 isoform X1

    See identical proteins and their annotated locations for XP_011242504.1

    UniProtKB/TrEMBL
    B2RQE0
    Conserved Domains (1) summary
    pfam15676
    Location:37 → 577
    S6OS1; Six6 opposite strand transcript 1 family

  8. XM_011244205.3 → XP_011242507.1  protein SIX6OS1 isoform X5

    UniProtKB/TrEMBL
    B2RQE0
    Conserved Domains (1) summary
    pfam15676
    Location:1 → 468
    S6OS1; Six6 opposite strand transcript 1 family

  9. XM_011244206.2 → XP_011242508.1  protein SIX6OS1 isoform X6

    Conserved Domains (1) summary
    pfam15676
    Location:6 → 411
    S6OS1; Six6 opposite strand transcript 1 family

RNA

  1. XR_001780504.1 RNA Sequence

  2. XR_001780501.1 RNA Sequence

  3. XR_001780502.1 RNA Sequence

  4. XR_001780500.1 RNA Sequence

  5. XR_004937553.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9CTN5.2 GenPept UniProtKB/Swiss-Prot:Q9CTN5

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous