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Aliases for C14orf39 Gene

Aliases for C14orf39 Gene

  • Chromosome 14 Open Reading Frame 39 2 3 5
  • Six6 Opposite Strand Transcript 1 3 4
  • Protein SIX6OS1 3
  • Six6os1 3

External Ids for C14orf39 Gene

Previous GeneCards Identifiers for C14orf39 Gene

  • GC14M054696
  • GC14M058853
  • GC14M058892
  • GC14M059972
  • GC14M060863
  • GC14M041066
  • GC14M060396

Summaries for C14orf39 Gene

GeneCards Summary for C14orf39 Gene

C14orf39 (Chromosome 14 Open Reading Frame 39) is a Protein Coding gene.

UniProtKB/Swiss-Prot for C14orf39 Gene

  • Meiotic protein that localizes to the central element of the synaptonemal complex and is required for chromosome synapsis during meiotic recombination. Required for the appropriate processing of intermediate recombination nodules before crossover formation.

Additional gene information for C14orf39 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for C14orf39 Gene

Genomics for C14orf39 Gene

GeneHancer (GH) Regulatory Elements for C14orf39 Gene

Promoters and enhancers for C14orf39 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH14J060485 Promoter/Enhancer 1.3 EPDnew ENCODE 674 +29.6 29587 1.5 ATF1 NFRKB SIN3A POLR2B EGR1 ZHX1 EGR2 ZNF202 SP3 SMAD5 C14orf39 TRMT5 SIX6 SALL4P7 GNRHR2P1 GC14M060376
GH14J060514 Promoter/Enhancer 1.2 EPDnew ENCODE 656.8 +0.3 315 2.1 CTCF SAP130 ZBTB21 MAX SIN3A ZNF335 ZFHX2 GLIS2 POLR2A PATZ1 ENSG00000258670 C14orf39 GC14M060376
GH14J060515 Enhancer 0.2 ENCODE 650.7 +1.4 1429 0 C14orf39 ENSG00000258670 SIX6 GC14M060376
GH14J060640 Promoter/Enhancer 2.9 VISTA EPDnew Ensembl ENCODE dbSUPER 25.9 -134.6 -134641 19.2 PKNOX1 FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 SIX1 TRMT5 SLC38A6 PCNX4 C14orf39 LOC101927702 SIX4 TMEM30B MNAT1 SIX6
GH14J060330 Enhancer 1.3 Ensembl ENCODE dbSUPER 14.5 +183.9 183876 1.7 PKNOX1 CLOCK SMAD1 ARID4B SIN3A DMAP1 IRF4 YY1 ZNF143 ATF7 L3HYPDH C14orf39 PCNX4 SCOCP1 LOC101927702 PPM1A TRMT5 GC14P060353 LINC02322
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around C14orf39 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the C14orf39 gene promoter:
  • RP58
  • C/EBPalpha
  • FOXJ2
  • FOXJ2 (long isoform)
  • Nkx3-1
  • Nkx3-1 v1
  • Nkx3-1 v2
  • Nkx3-1 v3
  • Nkx3-1 v4
  • GCNF

Genomic Locations for C14orf39 Gene

Genomic Locations for C14orf39 Gene
chr14:60,353,122-60,515,543
(GRCh38/hg38)
Size:
162,422 bases
Orientation:
Minus strand
chr14:60,863,187-60,982,261
(GRCh37/hg19)
Size:
119,075 bases
Orientation:
Minus strand

Genomic View for C14orf39 Gene

Genes around C14orf39 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
C14orf39 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for C14orf39 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for C14orf39 Gene

Proteins for C14orf39 Gene

  • Protein details for C14orf39 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N1H7-S6OS1_HUMAN
    Recommended name:
    Protein SIX6OS1
    Protein Accession:
    Q8N1H7
    Secondary Accessions:
    • Q08AQ4

    Protein attributes for C14orf39 Gene

    Size:
    587 amino acids
    Molecular mass:
    68166 Da
    Quaternary structure:
    • Interacts with SYCE1.

neXtProt entry for C14orf39 Gene

Post-translational modifications for C14orf39 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for C14orf39 Gene

Domains & Families for C14orf39 Gene

Gene Families for C14orf39 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for C14orf39 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for C14orf39 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with C14orf39: view

No data available for UniProtKB/Swiss-Prot for C14orf39 Gene

Function for C14orf39 Gene

Molecular function for C14orf39 Gene

UniProtKB/Swiss-Prot Function:
Meiotic protein that localizes to the central element of the synaptonemal complex and is required for chromosome synapsis during meiotic recombination. Required for the appropriate processing of intermediate recombination nodules before crossover formation.

Phenotypes From GWAS Catalog for C14orf39 Gene

Gene Ontology (GO) - Molecular Function for C14orf39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
genes like me logo Genes that share ontologies with C14orf39: view
genes like me logo Genes that share phenotypes with C14orf39: view

Animal Model Products

miRNA for C14orf39 Gene

miRTarBase miRNAs that target C14orf39

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for C14orf39 Gene

Localization for C14orf39 Gene

Subcellular locations from UniProtKB/Swiss-Prot for C14orf39 Gene

Chromosome. Note=Component of the central element of the synaptonemal complex. In spermatocytes, detected from zygonema to pachynema and localizes along synapsed lateral elements. Loading to the central element of the synaptonemal complex is dependent on the assembly of the tripartite synaptonemal complex structure that occurs upon synapsis between homologous chromosomes. {ECO:0000250 UniProtKB:Q9CTN5}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for C14orf39 gene
Compartment Confidence
nucleus 5
cytoskeleton 3
extracellular 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for C14orf39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000801 central element ISS --
GO:0005575 cellular_component ND --
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with C14orf39: view

Pathways & Interactions for C14orf39 Gene

SuperPathways for C14orf39 Gene

No Data Available

Interacting Proteins for C14orf39 Gene

Gene Ontology (GO) - Biological Process for C14orf39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006310 DNA recombination IEA --
GO:0007129 synapsis ISS,IEA --
GO:0007275 multicellular organism development IEA --
GO:0007283 spermatogenesis ISS,IEA --
GO:0010705 meiotic DNA double-strand break processing involved in reciprocal meiotic recombination ISS,IEA --
genes like me logo Genes that share ontologies with C14orf39: view

No data available for Pathways by source and SIGNOR curated interactions for C14orf39 Gene

Drugs & Compounds for C14orf39 Gene

No Compound Related Data Available

Transcripts for C14orf39 Gene

mRNA/cDNA for C14orf39 Gene

(10) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(8) Selected AceView cDNA sequences:
(5) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for C14orf39 Gene

Chromosome 14 open reading frame 39:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for C14orf39 Gene

No ASD Table

Relevant External Links for C14orf39 Gene

GeneLoc Exon Structure for
C14orf39
ECgene alternative splicing isoforms for
C14orf39

Expression for C14orf39 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for C14orf39 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for C14orf39 Gene

This gene is overexpressed in Pituitary (x9.8), Testis (x8.5), and Muscle - Skeletal (x4.9).

Protein differential expression in normal tissues from HIPED for C14orf39 Gene

This gene is overexpressed in Frontal cortex (20.9), Breast (15.4), CD4 Tcells (13.6), and Fetal ovary (9.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for C14orf39 Gene



Protein tissue co-expression partners for C14orf39 Gene

NURSA nuclear receptor signaling pathways regulating expression of C14orf39 Gene:

C14orf39

SOURCE GeneReport for Unigene cluster for C14orf39 Gene:

Hs.335754

mRNA Expression by UniProt/SwissProt for C14orf39 Gene:

Q8N1H7-S6OS1_HUMAN
Tissue specificity: Highest expression in retina, skeletal muscle and colon.
genes like me logo Genes that share expression patterns with C14orf39: view

No data available for Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for C14orf39 Gene

Orthologs for C14orf39 Gene

This gene was present in the common ancestor of chordates.

Orthologs for C14orf39 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia C14H14orf39 33
  • 99.38 (n)
C14orf39 34
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia C8H14orf39 33
  • 87.74 (n)
C14orf39 34
  • 79 (a)
OneToOne
cow
(Bos Taurus)
Mammalia C10H14orf39 33
  • 87.04 (n)
C14orf39 34
  • 77 (a)
OneToOne
mouse
(Mus musculus)
Mammalia 4930447C04Rik 16 34 33
  • 82.35 (n)
rat
(Rattus norvegicus)
Mammalia Six6os1 33
  • 81.31 (n)
oppossum
(Monodelphis domestica)
Mammalia C14orf39 34
  • 52 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia C14orf39 34
  • 40 (a)
OneToOne
chicken
(Gallus gallus)
Aves LOC101748050 33
  • 63.14 (n)
C14orf39 34
  • 41 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100486324 33
  • 53.53 (n)
Species where no ortholog for C14orf39 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for C14orf39 Gene

ENSEMBL:
Gene Tree for C14orf39 (if available)
TreeFam:
Gene Tree for C14orf39 (if available)

Paralogs for C14orf39 Gene

(1) SIMAP similar genes for C14orf39 Gene using alignment to 4 proteins:

  • G3V257_HUMAN
  • G3V3U9_HUMAN
  • G3V493_HUMAN
  • H0YJQ0_HUMAN
genes like me logo Genes that share paralogs with C14orf39: view

No data available for Paralogs for C14orf39 Gene

Variants for C14orf39 Gene

Sequence variations from dbSNP and Humsavar for C14orf39 Gene

SNP ID Clin Chr 14 pos Variation AA Info Type
rs1000044481 -- 60,495,700(-) T/C genic_upstream_transcript_variant, intron_variant
rs1000100644 -- 60,448,497(-) G/T genic_downstream_transcript_variant, intron_variant
rs1000274959 -- 60,442,270(-) T/G genic_downstream_transcript_variant, intron_variant
rs1000333214 -- 60,493,534(-) G/A genic_upstream_transcript_variant, intron_variant
rs1000342994 -- 60,435,493(-) ACA/A downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for C14orf39 Gene

Variant ID Type Subtype PubMed ID
dgv1089n106 OTHER inversion 24896259
esv3892552 CNV loss 25118596
nsv1294 CNV deletion 18451855
nsv564880 CNV gain 21841781
nsv564881 CNV gain 21841781

Variation tolerance for C14orf39 Gene

Residual Variation Intolerance Score: 80.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.51; 88.80% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for C14orf39 Gene

Human Gene Mutation Database (HGMD)
C14orf39
SNPedia medical, phenotypic, and genealogical associations of SNPs for
C14orf39

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for C14orf39 Gene

Disorders for C14orf39 Gene

Additional Disease Information for C14orf39

No disorders were found for C14orf39 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for C14orf39 Gene

Publications for C14orf39 Gene

  1. C14ORF39/SIX6OS1 is a constituent of the synaptonemal complex and is essential for mouse fertility. (PMID: 27796301) Gómez-H L … Pendas AM (Nature communications 2016) 2 3 58
  2. Natural antisense transcripts associated with genes involved in eye development. (PMID: 15703187) Alfano G … Banfi S (Human molecular genetics 2005) 3 4 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. (PMID: 25231870) Perry JR … Ong KK (Nature 2014) 3 58
  5. Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. (PMID: 23563607) Berndt SI … Ingelsson E (Nature genetics 2013) 3 58

Products for C14orf39 Gene

Sources for C14orf39 Gene

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