SHOC1 Gene (Protein Coding)

Shortage In Chiasmata 1

GC09M111689
GIFtS:
22
See more...

Aliases for SHOC1 Gene

Aliases for SHOC1 Gene

  • Shortage In Chiasmata 1 2 3 5
  • MZIP2 2 3 4
  • Protein Shortage In Chiasmata 1 Ortholog 3 4
  • C9orf84 3 4
  • ZIP2 3 4
  • Chromosome 9 Open Reading Frame 84 2
  • Uncharacterized Protein C9orf84 3
  • Protein ZIP2 Homolog 4
  • EC 3.6.-.- 4
  • FLJ32779 2
  • ZIP2H 3
  • SHOC1 5
  • Zip2 2

External Ids for SHOC1 Gene

Previous HGNC Symbols for SHOC1 Gene

  • C9orf84

Previous GeneCards Identifiers for SHOC1 Gene

  • GC09M111687
  • GC09M111688

Summaries for SHOC1 Gene

GeneCards Summary for SHOC1 Gene

SHOC1 (Shortage In Chiasmata 1) is a Protein Coding gene.

UniProtKB/Swiss-Prot Summary for SHOC1 Gene

  • ATPase required during meiosis for the formation of crossover recombination intermediates (By similarity). Binds DNA: preferentially binds to single-stranded DNA and DNA branched structures (PubMed:29742103). Does not show nuclease activity in vitro, but shows ATPase activity, which is stimulated by the presence of single-stranded DNA (PubMed:29742103). Plays a key role in homologous recombination and crossing-over in meiotic prophase I in male and female germ cells (By similarity). Requiref for recruitment TEX11 and MSH4 to recombination intermediates (By similarity).

Additional gene information for SHOC1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SHOC1 Gene

Genomics for SHOC1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for SHOC1 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
GH09J111804 Promoter/Enhancer 1.2 EPDnew Ensembl ENCODE 264.3 -9.9 -9880 3.7 CEBPB EP300 STAT3 FOSL1 PRDM10 JUND FOXA1 CTCF ATF2 DPF2 SHOC1 GNG10 RNU6-1013P ENSG00000224067 HSALNG0073715 lnc-UGCG-1 UGCG
GH09J111794 Promoter/Enhancer 1.1 EPDnew Ensembl ENCODE 263.9 +0.9 868 1 MAX USF2 RAD51 ZBTB33 POLR2A USF1 SHOC1 HSALNG0073715 GNG10
GH09J111783 Promoter 0.3 EPDnew 250.4 +12.4 12436 0.1 SHOC1 RNU6-1013P RF00994-1152 HSALNG0073713 lnc-PTGR1-3 HSALNG0073712-002 GNG10
GH09J111838 Enhancer 1.1 Ensembl ENCODE dbSUPER 19.8 -45.7 -45651 7.2 BCL11A CEBPA ZNF217 CEBPB IRF4 EP300 EBF1 CTBP1 BATF SMARCE1 RF00026-1141 RNU6-1013P SHOC1 ENSG00000224067 GNG10 PTGR1 HSALNG0073722 lnc-C9orf84-2 HSALNG0073724 UGCG
GH09J111759 Enhancer 0.9 Ensembl ENCODE 23.8 +35.1 35148 2.4 ZNF217 CTCF ELF1 ARNT REST IRF4 TRIM22 SMC3 RAD21 RFX5 SHOC1 ENSG00000224067 GNG10 RF00017-7819 RF00017-7820 HSALNG0073712-002
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SHOC1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SHOC1

Genomic Locations for SHOC1 Gene

Latest Assembly
chr9:111,686,171-111,795,949
(GRCh38/hg38)
Size:
109,779 bases
Orientation:
Minus strand

Previous Assembly
chr9:114,448,451-114,557,217
(GRCh37/hg19 by Entrez Gene)
Size:
108,767 bases
Orientation:
Minus strand

chr9:114,448,453-114,557,288
(GRCh37/hg19 by Ensembl)
Size:
108,836 bases
Orientation:
Minus strand

Genomic View for SHOC1 Gene

Genes around SHOC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SHOC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SHOC1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for SHOC1 Gene

Proteins for SHOC1 Gene

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  1. Antibodies for research
  2. Protein products for research
  3. Assay products for research

  • Protein details for SHOC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5VXU9-SHOC1_HUMAN
    Recommended name:
    Protein shortage in chiasmata 1 ortholog
    Protein Accession:
    Q5VXU9
    Secondary Accessions:
    • A2A2V3
    • Q2M1H8
    • Q96M73

    Protein attributes for SHOC1 Gene

    Size:
    1444 amino acids
    Molecular mass:
    165202 Da
    Quaternary structure:
    • Interacts with TEX11 (PubMed:29742103). Interacts with SPO16 (By similarity).

    Alternative splice isoforms for SHOC1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SHOC1 Gene

Post-translational modifications for SHOC1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SHOC1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SHOC1 Gene

Domains & Families for SHOC1 Gene

Gene Families for SHOC1 Gene

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

Protein Domains for SHOC1 Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

Q5VXU9

UniProtKB/Swiss-Prot:

SHOC1_HUMAN :
  • Belongs to the XPF family. Highly divergent.
Family:
  • Belongs to the XPF family. Highly divergent.
genes like me logo Genes that share domains with SHOC1: view

No data available for Suggested Antigen Peptide Sequences for SHOC1 Gene

Function for SHOC1 Gene

Products:

  1. Animal Models for research
  2. CRISPR products for research
  3. miRNA products for research
  4. Inhibitory RNAs for research
  5. Clone products for research
  6. Cell Lines for research

Molecular function for SHOC1 Gene

UniProtKB/Swiss-Prot Function:
ATPase required during meiosis for the formation of crossover recombination intermediates (By similarity). Binds DNA: preferentially binds to single-stranded DNA and DNA branched structures (PubMed:29742103). Does not show nuclease activity in vitro, but shows ATPase activity, which is stimulated by the presence of single-stranded DNA (PubMed:29742103). Plays a key role in homologous recombination and crossing-over in meiotic prophase I in male and female germ cells (By similarity). Requiref for recruitment TEX11 and MSH4 to recombination intermediates (By similarity).

Enzyme Numbers (IUBMB) for SHOC1 Gene

Phenotypes From GWAS Catalog for SHOC1 Gene

Gene Ontology (GO) - Molecular Function for SHOC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003697 single-stranded DNA binding IBA,IDA 29742103
GO:0016787 hydrolase activity IEA --
GO:0016887 ATPase activity IBA,IDA 29742103
genes like me logo Genes that share ontologies with SHOC1: view
genes like me logo Genes that share phenotypes with SHOC1: view

Animal Models for SHOC1 Gene

MGI Knock Outs for SHOC1:

miRNA for SHOC1 Gene

miRTarBase miRNAs that target SHOC1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SHOC1

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SHOC1 Gene

Localization for SHOC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SHOC1 Gene

Chromosome. Note=Localizes to meiotic chromosomes; associates with mid-stage meiotic recombination intermediates. Localization requires meiotic double-strand breaks (DSBs) recombination intermediates catalyzed by DMC1. {ECO:0000250 UniProtKB:A2ALV5}.

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 SHOC1 gene
Compartment Confidence
nucleus 4
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SHOC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000794 condensed nuclear chromosome IBA,ISS --
GO:0005694 chromosome ISS --
genes like me logo Genes that share ontologies with SHOC1: view

Pathways & Interactions for SHOC1 Gene

PathCards logo

SuperPathways for SHOC1 Gene

No Data Available

Interacting Proteins for SHOC1 Gene

Gene Ontology (GO) - Biological Process for SHOC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000712 resolution of meiotic recombination intermediates ISS --
GO:0007131 reciprocal meiotic recombination IEA,ISS --
GO:0051321 meiotic cell cycle IEA --
genes like me logo Genes that share ontologies with SHOC1: view

No data available for Pathways by source and SIGNOR curated interactions for SHOC1 Gene

Drugs & Compounds for SHOC1 Gene

Products:

  1. Drug products for research
No Compound Related Data Available

Transcripts for SHOC1 Gene

Products:

  1. CRISPR products for research
  2. miRNA products for research
  3. Inhibitory RNAs for research
  4. Clone products for research

mRNA/cDNA for SHOC1 Gene

4 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SHOC1

Alternative Splicing Database (ASD) splice patterns (SP) for SHOC1 Gene

No ASD Table

Relevant External Links for SHOC1 Gene

GeneLoc Exon Structure for
SHOC1

Expression for SHOC1 Gene

Products:

  1. Primer products for research

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SHOC1

SOURCE GeneReport for Unigene cluster for SHOC1 Gene:

Hs.428209
genes like me logo Genes that share expression patterns with SHOC1: view

Primer products for research

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for SHOC1 Gene

Orthologs for SHOC1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SHOC1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia C9H9orf84 30
  • 99.4 (n)
C9orf84 31
  • 98 (a)
 OneToOne
Dog
(Canis familiaris)
 Mammalia C11H9orf84 30
  • 85.53 (n)
C9orf84 31
  • 74 (a)
 OneToOne
Cow
(Bos Taurus)
 Mammalia LOC617568 30
  • 84.96 (n)
C9orf84 31
  • 74 (a)
 OneToOne
Mouse
(Mus musculus)
 Mammalia AI481877 30 31
  • 74.51 (n)
 OneToOne
Shoc1 17
Rat
(Rattus norvegicus)
 Mammalia LOC686050 30
  • 72.97 (n)
Oppossum
(Monodelphis domestica)
 Mammalia C9orf84 31
  • 49 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia C9orf84 31
  • 27 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves CZH9orf84 30
  • 59.1 (n)
C9orf84 31
  • 43 (a)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia C9orf84 31
  • 53 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia LOC100487050 30
  • 51.82 (n)
Species where no ortholog for SHOC1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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 Vase (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 SHOC1 Gene

ENSEMBL:
Gene Tree for SHOC1 (if available)
TreeFam:
Gene Tree for SHOC1 (if available)

Paralogs for SHOC1 Gene

No data available for Paralogs for SHOC1 Gene

Variants for SHOC1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SHOC1 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
rs10981009 - p.Arg1425Cys
rs10981047 - p.Thr226Ser
rs11791445 - p.Met734Leu
rs1322254 - p.Asn1380Lys
rs1322257 - p.Ile649Thr

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SHOC1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SHOC1 Gene

Variant ID Type Subtype PubMed ID
dgv7700n100 CNV gain 25217958
esv1003380 CNV deletion 20482838
esv1650763 CNV deletion 17803354
esv2420162 CNV deletion 18987734
esv2738937 CNV deletion 23290073
esv2738938 CNV deletion 23290073
esv2761550 CNV gain 21179565
nsv1110050 CNV deletion 24896259
nsv466486 CNV gain 19166990
nsv615193 CNV gain 21841781
nsv615194 CNV loss 21841781
nsv6667 CNV insertion 18451855
nsv831690 CNV loss 17160897

Variation tolerance for SHOC1 Gene

Residual Variation Intolerance Score: 92.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 19.37; 98.84% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SHOC1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SHOC1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SHOC1 Gene

Disorders for SHOC1 Gene

Additional Disease Information for SHOC1

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

No disorders were found for SHOC1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SHOC1 Gene

Publications for SHOC1 Gene

  1. SHOC1 is a ERCC4-(HhH)2-like protein, integral to the formation of crossover recombination intermediates during mammalian meiosis. (PMID: 29742103) Guiraldelli MF … Pezza RJ (PLoS genetics 2018) 2 3 4
  2. SHOC1 and PTD form an XPF-ERCC1-like complex that is required for formation of class I crossovers. (PMID: 21771883) Macaisne N … Mercier R (Journal of cell science 2011) 2 3
  3. DNA sequence and analysis of human chromosome 9. (PMID: 15164053) Humphray SJ … Dunham I (Nature 2004) 3 4
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. Estrogen-regulated feedback loop limits the efficacy of estrogen receptor-targeted breast cancer therapy. (PMID: 29987050) Xiao T … Brown M (Proceedings of the National Academy of Sciences of the United States of America 2018) 3

ExternalLinks

View latest publications for SHOC1 gene in Mastermind

Products for SHOC1 Gene

Sources for SHOC1 Gene