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

    Gene ID: 158401, updated on 5-May-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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    See SHOC1 in Genome Data Viewer
    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

    Gene LinkOut

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

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