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SHOC1 shortage in chiasmata 1 [ Homo sapiens (human) ]

Gene ID: 158401, updated on 3-Apr-2024

Summary

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Official Symbol
SHOC1provided by HGNC
Official Full Name
shortage in chiasmata 1provided by HGNC
Primary source
HGNC:HGNC:26535
See related
Ensembl:ENSG00000165181 MIM:618038; AllianceGenome:HGNC:26535
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
ZIP2; MZIP2; ZIP2H; SPGF75; C9orf84
Summary
Enables single-stranded DNA binding activity. Predicted to be involved in resolution of meiotic recombination intermediates. Predicted to be located in chromosome. Predicted to be active in condensed nuclear chromosome. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Restricted expression toward testis (RPKM 5.2) See more
Orthologs
mouse all
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Genomic context

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Location:
9q31.3
Exon count:
32
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (111686171..111794937, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (123857529..123984501, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (114448451..114557217, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene DNAJC25-GNG10 readthrough Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20181 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28795 Neighboring gene FOXA motif-containing MPRA enhancer 227 Neighboring gene Sharpr-MPRA regulatory region 12797 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_105958 Neighboring gene DnaJ heat shock protein family (Hsp40) member C25 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28796 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20182 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20183 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28797 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28798 Neighboring gene Sharpr-MPRA regulatory region 3205 Neighboring gene G protein subunit gamma 10 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_105998 Neighboring gene uncharacterized LOC124902249 Neighboring gene RNA, U6 small nuclear 1013, pseudogene

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
  • 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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Related articles in PubMed

  1. Bi-allelic SHOC1 loss-of-function mutations cause meiotic arrest and non-obstructive azoospermia. Yao C, et al. J Med Genet, 2021 Oct. PMID 32900840, Free PMC Article
  2. Bi-allelic variants in SHOC1 cause non-obstructive azoospermia with meiosis arrest in humans and mice. Wang W, et al. Mol Hum Reprod, 2022 May 27. PMID 35485979
  3. SHOC1, an XPF endonuclease-related protein, is essential for the formation of class I meiotic crossovers. Macaisne N, et al. Curr Biol, 2008 Sep 23. PMID 18812090
  4. SHOC1 and PTD form an XPF-ERCC1-like complex that is required for formation of class I crossovers. Macaisne N, et al. J Cell Sci, 2011 Aug 15. PMID 21771883
  5. SHOC1 is a ERCC4-(HhH)2-like protein, integral to the formation of crossover recombination intermediates during mammalian meiosis. Guiraldelli MF, et al. PLoS Genet, 2018 May. PMID 29742103, Free PMC Article

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Bi-allelic variants in SHOC1 cause non-obstructive azoospermia with meiosis arrest in humans and mice.
    Title: Bi-allelic variants in SHOC1 cause non-obstructive azoospermia with meiosis arrest in humans and mice.
  2. Bi-allelic SHOC1 loss-of-function mutations cause meiotic arrest and non-obstructive azoospermia.
    Title: Bi-allelic SHOC1 loss-of-function mutations cause meiotic arrest and non-obstructive azoospermia.
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
Spermatogenic failure 75
MedGen: C5677014 OMIM: 619949 GeneReviews: Not available
not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ32779, FLJ44067, MGC43661

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP hydrolysis activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables single-stranded DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables single-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in reciprocal meiotic recombination ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in resolution of meiotic recombination intermediates IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in resolution of meiotic recombination intermediates ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in synaptonemal complex assembly ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in chromosome ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in condensed nuclear chromosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in condensed nuclear chromosome ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
protein shortage in chiasmata 1 ortholog
Names
Zip2 homolog
protein ZIP2 homolog
uncharacterized protein C9orf84

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_001080551.3 → NP_001074020.3  protein shortage in chiasmata 1 ortholog isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. It encodes isoform 2, which is shorter and has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AL135787, AL356491
    Consensus CDS
    CCDS43863.1
    Related
    ENSP00000378259.3, ENST00000394779.7
    Conserved Domains (1) summary
    pfam17825
    Location:46 → 1405
    DUF5587; Family of unknown function (DUF5587)

  2. NM_001378211.1 → NP_001365140.1  protein shortage in chiasmata 1 ortholog isoform 4

    Status: VALIDATED

    Source sequence(s)
    AL135787, AL354877, AL356491
    Consensus CDS
    CCDS94461.1
    UniProtKB/TrEMBL
    A0A804HLJ8
    Related
    ENSP00000508388.1, ENST00000682961.1
    Conserved Domains (1) summary
    pfam17825
    Location:65 → 1508
    DUF5587; Family of unknown function (DUF5587)

  3. NM_001378212.1 → NP_001365141.1  protein shortage in chiasmata 1 ortholog isoform 5

    Status: VALIDATED

    Source sequence(s)
    AL135787, AL356491
    Consensus CDS
    CCDS94459.1
    UniProtKB/TrEMBL
    A6PVK7
    Related
    ENSP00000378257.4, ENST00000394777.8
    Conserved Domains (1) summary
    pfam17825
    Location:46 → 1370
    DUF5587; Family of unknown function (DUF5587)

  4. NM_173521.5 → NP_775792.5  protein shortage in chiasmata 1 ortholog isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AL135787, AL354877, AL356491
    Consensus CDS
    CCDS6781.3
    UniProtKB/Swiss-Prot
    A2A2V3, Q2M1H8, Q5VXU9, Q96M73
    Related
    ENSP00000322108.4, ENST00000318737.8
    Conserved Domains (1) summary
    pfam17825
    Location:1 → 1444
    DUF5587; Family of unknown function (DUF5587)

RNA

  1. NR_109816.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains an alternate 5' exon structure compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL135787, AL354877, AL356491

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    111686171..111794937 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017014340.2 → XP_016869829.1  protein shortage in chiasmata 1 ortholog isoform X3

    Conserved Domains (1) summary
    pfam17825
    Location:74 → 1395
    DUF5587; Family of unknown function (DUF5587)

  2. XM_006716975.3 → XP_006717038.1  protein shortage in chiasmata 1 ortholog isoform X1

    Conserved Domains (1) summary
    pfam17825
    Location:65 → 1473
    DUF5587; Family of unknown function (DUF5587)

  3. XM_011518302.3 → XP_011516604.1  protein shortage in chiasmata 1 ortholog isoform X2

    See identical proteins and their annotated locations for XP_011516604.1

    UniProtKB/Swiss-Prot
    A2A2V3, Q2M1H8, Q5VXU9, Q96M73
    Conserved Domains (1) summary
    pfam17825
    Location:1 → 1444
    DUF5587; Family of unknown function (DUF5587)

  4. XM_011518303.2 → XP_011516605.1  protein shortage in chiasmata 1 ortholog isoform X2

    See identical proteins and their annotated locations for XP_011516605.1

    UniProtKB/Swiss-Prot
    A2A2V3, Q2M1H8, Q5VXU9, Q96M73
    Related
    ENSP00000363405.3, ENST00000374287.7
    Conserved Domains (1) summary
    pfam17825
    Location:1 → 1444
    DUF5587; Family of unknown function (DUF5587)

  5. XM_047422865.1 → XP_047278821.1  protein shortage in chiasmata 1 ortholog isoform X5

  6. XM_011518306.2 → XP_011516608.1  protein shortage in chiasmata 1 ortholog isoform X4

    Conserved Domains (1) summary
    pfam17825
    Location:10 → 1319
    DUF5587; Family of unknown function (DUF5587)

  7. XM_017014341.2 → XP_016869830.1  protein shortage in chiasmata 1 ortholog isoform X7

    Conserved Domains (1) summary
    pfam17825
    Location:65 → 1064
    DUF5587; Family of unknown function (DUF5587)

  8. XM_047422866.1 → XP_047278822.1  protein shortage in chiasmata 1 ortholog isoform X6

  9. XM_011518309.2 → XP_011516611.1  protein shortage in chiasmata 1 ortholog isoform X7

    Conserved Domains (1) summary
    pfam17825
    Location:65 → 1064
    DUF5587; Family of unknown function (DUF5587)

  10. XM_047422868.1 → XP_047278824.1  protein shortage in chiasmata 1 ortholog isoform X9

  11. XM_047422867.1 → XP_047278823.1  protein shortage in chiasmata 1 ortholog isoform X8

    UniProtKB/TrEMBL
    A0A804HK82
    Related
    ENSP00000507813.1, ENST00000683944.1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    123857529..123984501 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054362153.1 → XP_054218128.1  protein shortage in chiasmata 1 ortholog isoform X10

  2. XM_054362154.1 → XP_054218129.1  protein shortage in chiasmata 1 ortholog isoform X2

  3. XM_054362155.1 → XP_054218130.1  protein shortage in chiasmata 1 ortholog isoform X2

  4. XM_054362157.1 → XP_054218132.1  protein shortage in chiasmata 1 ortholog isoform X5

  5. XM_054362156.1 → XP_054218131.1  protein shortage in chiasmata 1 ortholog isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5VXU9.1 GenPept UniProtKB/Swiss-Prot:Q5VXU9

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