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C14orf39 chromosome 14 open reading frame 39 [ Homo sapiens (human) ]

Gene ID: 317761, updated on 14-Nov-2024

Summary

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Official Symbol
C14orf39provided by HGNC
Official Full Name
chromosome 14 open reading frame 39provided by HGNC
Primary source
HGNC:HGNC:19849
See related
Ensembl:ENSG00000179008 MIM:617307; AllianceGenome:HGNC:19849
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
POF18; SPGF52; Six6os1
Summary
Involved in homologous chromosome pairing at meiosis. Predicted to be located in chromosome. Predicted to be active in central element. Implicated in primary ovarian insufficiency 18 and spermatogenic failure 52. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in testis (RPKM 4.3), salivary gland (RPKM 0.6) and 3 other tissues See more
Orthologs
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Genomic context

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See C14orf39 in Genome Data Viewer
Location:
14q23.1
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (60435956..60515544, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (54642261..54705881, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (60902674..60952781, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8476 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5811 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8477 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8478 Neighboring gene long intergenic non-protein coding RNA 2322 Neighboring gene GNRHR2 pseudogene 1 Neighboring gene RBM8A pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:60977732-60978503 Neighboring gene spalt like transcription factor 4 pseudogene 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:60981577-60982078 Neighboring gene SIX homeobox 6 Neighboring gene vomeronasal 1 receptor 59 pseudogene Neighboring gene ribosomal protein L37 pseudogene 5

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. In silico analysis of a novel pathogenic variant c.7G > A in C14orf39 gene identified by WES in a Pakistani family with azoospermia.
    Title: In silico analysis of a novel pathogenic variant c.7G > A in C14orf39 gene identified by WES in a Pakistani family with azoospermia.
  2. Variations of C14ORF39 and SYCE1 Identified in Idiopathic Premature Ovarian Insufficiency and Nonobstructive Azoospermia.
    Title: Variations of C14ORF39 and SYCE1 Identified in Idiopathic Premature Ovarian Insufficiency and Nonobstructive Azoospermia.
  3. Homozygous mutations in C14orf39/SIX6OS1 cause non-obstructive azoospermia and premature ovarian insufficiency in humans.
    Title: Homozygous mutations in C14orf39/SIX6OS1 cause non-obstructive azoospermia and premature ovarian insufficiency in humans.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Premature ovarian failure 18
MedGen: C5543095 OMIM: 619203 GeneReviews: Not available
Compare labs
Spermatogenic failure 52
MedGen: C5543094 OMIM: 619202 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia.
EBI GWAS Catalog
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
EBI GWAS Catalog
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
EBI GWAS Catalog

Variation

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See Variation Viewer (GRCh37.p13)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Clone Names

  • MGC149706

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
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 ISS
Inferred from Sequence or Structural Similarity
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 ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in oogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in oogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
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 ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in synaptonemal complex assembly IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in central element IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in central element ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in chromosome ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
protein SIX6OS1
Names
six6 opposite strand transcript 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_174978.3 → NP_777638.3  protein SIX6OS1

    Status: VALIDATED

    Source sequence(s)
    AL122057, AL132778
    Consensus CDS
    CCDS9746.1
    UniProtKB/Swiss-Prot
    Q08AQ4, Q8N1H7
    Related
    ENSP00000324920.3, ENST00000321731.8
    Conserved Domains (1) summary
    pfam15676
    Location:37 → 587
    S6OS1; Six6 opposite strand transcript 1 family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    60435956..60515544 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047431324.1 → XP_047287280.1  protein SIX6OS1 isoform X3

    UniProtKB/Swiss-Prot
    Q08AQ4, Q8N1H7

  2. XM_017021250.3 → XP_016876739.1  protein SIX6OS1 isoform X8

  3. XM_017021248.3 → XP_016876737.1  protein SIX6OS1 isoform X5

  4. XM_047431327.1 → XP_047287283.1  protein SIX6OS1 isoform X7

  5. XM_047431325.1 → XP_047287281.1  protein SIX6OS1 isoform X6

  6. XM_024449555.2 → XP_024305323.1  protein SIX6OS1 isoform X4

    Conserved Domains (1) summary
    pfam15676
    Location:37 → 586
    S6OS1; Six6 opposite strand transcript 1 family

  7. XM_017021247.2 → XP_016876736.1  protein SIX6OS1 isoform X2

  8. XM_011536690.4 → XP_011534992.1  protein SIX6OS1 isoform X1

    Conserved Domains (1) summary
    pfam15676
    Location:73 → 623
    S6OS1; Six6 opposite strand transcript 1 family

  9. XM_047431326.1 → XP_047287282.1  protein SIX6OS1 isoform X6

  10. XM_047431323.1 → XP_047287279.1  protein SIX6OS1 isoform X3

    UniProtKB/Swiss-Prot
    Q08AQ4, Q8N1H7

  11. XM_047431322.1 → XP_047287278.1  protein SIX6OS1 isoform X1

  12. XM_017021251.2 → XP_016876740.1  protein SIX6OS1 isoform X8

  13. XM_011536703.3 → XP_011535005.1  protein SIX6OS1 isoform X9

    Conserved Domains (1) summary
    pfam15676
    Location:73 → 429
    S6OS1; Six6 opposite strand transcript 1 family

RNA

  1. XR_007064008.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    54642261..54705881 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054375943.1 → XP_054231918.1  protein SIX6OS1 isoform X8

  2. XM_054375940.1 → XP_054231915.1  protein SIX6OS1 isoform X5

  3. XM_054375942.1 → XP_054231917.1  protein SIX6OS1 isoform X7

  4. XM_054375941.1 → XP_054231916.1  protein SIX6OS1 isoform X6

  5. XM_054375939.1 → XP_054231914.1  protein SIX6OS1 isoform X4

  6. XM_054375937.1 → XP_054231912.1  protein SIX6OS1 isoform X2

  7. XM_054375936.1 → XP_054231911.1  protein SIX6OS1 isoform X1

  8. XM_054375938.1 → XP_054231913.1  protein SIX6OS1 isoform X3

  9. XM_054375944.1 → XP_054231919.1  protein SIX6OS1 isoform X8

  10. XM_054375945.1 → XP_054231920.1  protein SIX6OS1 isoform X9

RNA

  1. XR_008488859.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N1H7.2 GenPept UniProtKB/Swiss-Prot:Q8N1H7

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