U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

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

    Summary

    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 ATP hydrolysis activity and single-stranded DNA binding activity. Predicted to be involved in resolution of meiotic recombination intermediates and synaptonemal complex assembly. Predicted to be located in chromosome. Predicted to be active in condensed nuclear chromosome. Implicated in spermatogenic failure 75. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Restricted expression toward testis (RPKM 5.2) See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SHOC1 in Genome Data Viewer
    Location:
    9q31.3
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (111686171..111794937, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (123857529..123984501, complement)
    RS_2024_09 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

    Expression

    • 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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001080551.3NP_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:461405
      DUF5587; Family of unknown function (DUF5587)
    2. NM_001378211.1NP_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:651508
      DUF5587; Family of unknown function (DUF5587)
    3. NM_001378212.1NP_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:461370
      DUF5587; Family of unknown function (DUF5587)
    4. NM_173521.5NP_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:11444
      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_2024_08

    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_017014340.2XP_016869829.1  protein shortage in chiasmata 1 ortholog isoform X3

      Conserved Domains (1) summary
      pfam17825
      Location:741395
      DUF5587; Family of unknown function (DUF5587)
    2. XM_006716975.3XP_006717038.1  protein shortage in chiasmata 1 ortholog isoform X1

      Conserved Domains (1) summary
      pfam17825
      Location:651473
      DUF5587; Family of unknown function (DUF5587)
    3. XM_011518302.3XP_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:11444
      DUF5587; Family of unknown function (DUF5587)
    4. XM_011518303.2XP_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:11444
      DUF5587; Family of unknown function (DUF5587)
    5. XM_047422865.1XP_047278821.1  protein shortage in chiasmata 1 ortholog isoform X5

      UniProtKB/TrEMBL
      Q6ZU10
    6. XM_011518306.2XP_011516608.1  protein shortage in chiasmata 1 ortholog isoform X4

      Conserved Domains (1) summary
      pfam17825
      Location:101319
      DUF5587; Family of unknown function (DUF5587)
    7. XM_017014341.2XP_016869830.1  protein shortage in chiasmata 1 ortholog isoform X7

      Conserved Domains (1) summary
      pfam17825
      Location:651064
      DUF5587; Family of unknown function (DUF5587)
    8. XM_047422866.1XP_047278822.1  protein shortage in chiasmata 1 ortholog isoform X6

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

      Conserved Domains (1) summary
      pfam17825
      Location:651064
      DUF5587; Family of unknown function (DUF5587)
    10. XM_047422868.1XP_047278824.1  protein shortage in chiasmata 1 ortholog isoform X9

    11. XM_047422867.1XP_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_054362153.1XP_054218128.1  protein shortage in chiasmata 1 ortholog isoform X10

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

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

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

      UniProtKB/TrEMBL
      Q6ZU10
    5. XM_054362156.1XP_054218131.1  protein shortage in chiasmata 1 ortholog isoform X4