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

Gene ID: 158401, updated on 13-Oct-2018

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; Vega:OTTHUMG00000020495
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; ZIP2H; C9orf84
Expression
Restricted expression toward testis (RPKM 5.2) See more
Orthologs

Genomic context

See SHOC1 in Genome Data Viewer
Location:
9q31.3
Exon count:
32
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 9 NC_000009.12 (111686175..111795949, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (114448901..114557556, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene DNAJC25-GNG10 readthrough Neighboring gene FOXA motif-containing MPRA enhancer 227 Neighboring gene DnaJ heat shock protein family (Hsp40) member C25 Neighboring gene G protein subunit gamma 10 Neighboring gene RNA, U6 small nuclear 1013, pseudogene Neighboring gene UDP-glucose ceramide glucosyltransferase Neighboring gene microRNA 4668

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 Jun 15 11:32:44 2016

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ32779, FLJ44067, MGC43661

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATPase activity IDA
Inferred from Direct Assay
more info
PubMed 
single-stranded DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
resolution of meiotic recombination intermediates ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
condensed nuclear chromosome ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
protein shortage in chiasmata 1 ortholog; uncharacterized protein C9orf84

NCBI Reference Sequences (RefSeq)

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_001080551.2NP_001074020.2  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)
    AK126055, BC041858, BC144680, DB088747
    Consensus CDS
    CCDS43863.1
    UniProtKB/TrEMBL
    Q6ZU10
    Related
    ENSP00000378259.3, OTTHUMP00000161933, ENST00000394779.7, OTTHUMT00000053658
  2. NM_173521.4NP_775792.4  protein shortage in chiasmata 1 ortholog isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AL833535, BC144680, DB066382
    Consensus CDS
    CCDS6781.3
    Related
    ENSP00000322108.4, OTTHUMP00000021923, ENST00000318737.8, OTTHUMT00000053656

RNA

  1. NR_109816.1 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)
    AK057341, AL704322, BC144680

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p12 Primary Assembly

    Range
    111686175..111795949 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017014340.1XP_016869829.1  uncharacterized protein C9orf84 isoform X4

  2. XM_006716975.2XP_006717038.1  uncharacterized protein C9orf84 isoform X2

  3. XM_006716974.2XP_006717037.1  uncharacterized protein C9orf84 isoform X1

  4. XM_011518302.2XP_011516604.1  uncharacterized protein C9orf84 isoform X3

    See identical proteins and their annotated locations for XP_011516604.1

    UniProtKB/Swiss-Prot
    Q5VXU9
  5. XM_011518303.1XP_011516605.1  uncharacterized protein C9orf84 isoform X3

    See identical proteins and their annotated locations for XP_011516605.1

    UniProtKB/Swiss-Prot
    Q5VXU9
  6. XM_011518306.1XP_011516608.1  uncharacterized protein C9orf84 isoform X5

  7. XM_011518309.1XP_011516611.1  uncharacterized protein C9orf84 isoform X6

  8. XM_017014341.1XP_016869830.1  uncharacterized protein C9orf84 isoform X6

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