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GIN1 gypsy retrotransposon integrase 1 [ Homo sapiens (human) ]

Gene ID: 54826, updated on 5-Mar-2024

Summary

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Official Symbol
GIN1provided by HGNC
Official Full Name
gypsy retrotransposon integrase 1provided by HGNC
Primary source
HGNC:HGNC:25959
See related
Ensembl:ENSG00000145723 AllianceGenome:HGNC:25959
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
GIN-1; TGIN1; ZH2C2
Summary
Predicted to enable nucleic acid binding activity. Predicted to be involved in DNA integration. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 1.7), thyroid (RPKM 1.6) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
5q21.1
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (103086000..103120138, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (103594035..103628240, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (102421704..102455842, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 7406 Neighboring gene uncharacterized LOC105379105 Neighboring gene eukaryotic translation initiation factor 3 subunit K pseudogene 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:102454978-102455479 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:102455480-102455980 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22858 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22859 Neighboring gene diphosphoinositol pentakisphosphate kinase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:102477431-102477932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22860 Neighboring gene uncharacterized LOC124901037

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. A mammalian gene evolved from the integrase domain of an LTR retrotransposon. Lloréns C, et al. Mol Biol Evol, 2001 Aug. PMID 11470852
  2. HAUSP regulates c-MYC expression via de-ubiquitination of TRRAP. Bhattacharya S, et al. Cell Oncol (Dordr), 2015 Aug. PMID 25925205
  3. Hepatitis B Virus HBx Protein Mediates the Degradation of Host Restriction Factors through the Cullin 4 DDB1 E3 Ubiquitin Ligase Complex. Minor MM, et al. Cells, 2020 Mar 30. PMID 32235678, Free PMC Article
  4. Systematic identification of pathological lamin A interactors. Dittmer TA, et al. Mol Biol Cell, 2014 May. PMID 24623722, Free PMC Article
  5. SUMOylation of DDX39A Alters Binding and Export of Antiviral Transcripts to Control Innate Immunity. Shi P, et al. J Immunol, 2020 Jul 1. PMID 32393512

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

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

  • FLJ20125

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in DNA integration IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
gypsy retrotransposon integrase-like protein 1
Names
Ty3/Gypsy integrase 1
zinc finger H2C2 domain-containing protein

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_001317954.2 → NP_001304883.1  gypsy retrotransposon integrase-like protein 1 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in the 5' region and initiates translation at a downstream start codon compared to variant 1. The encoded isoform (2) has a shorter N-terminus than isoform 1.
    Source sequence(s)
    AK225572, CR627424, DB101499
    UniProtKB/Swiss-Prot
    Q9NXP7
    Conserved Domains (1) summary
    cl21549
    Location:12 → 101
    rve; Integrase core domain

  2. NM_017676.2 → NP_060146.2  gypsy retrotransposon integrase-like protein 1 isoform 1

    See identical proteins and their annotated locations for NP_060146.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC008447, AK225572, DB101499
    Consensus CDS
    CCDS43349.1
    UniProtKB/Swiss-Prot
    B2RXF7, B4DIV4, Q6AI03, Q96BR2, Q9NXP7
    Related
    ENSP00000381970.2, ENST00000399004.7
    Conserved Domains (1) summary
    cl21549
    Location:154 → 248
    rve; Integrase core domain

RNA

  1. NR_134299.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks three internal exon compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region found in variant 1.
    Source sequence(s)
    AK225572, BC015325, CR627424, DB101499

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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    103086000..103120138 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017009599.2 → XP_016865088.1  gypsy retrotransposon integrase-like protein 1 isoform X1

    UniProtKB/Swiss-Prot
    B2RXF7, B4DIV4, Q6AI03, Q96BR2, Q9NXP7
    Conserved Domains (1) summary
    cl21549
    Location:154 → 248
    rve; Integrase core domain

  2. XM_047417343.1 → XP_047273299.1  gypsy retrotransposon integrase-like protein 1 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    103594035..103628240 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054352864.1 → XP_054208839.1  gypsy retrotransposon integrase-like protein 1 isoform X1

  2. XM_054352865.1 → XP_054208840.1  gypsy retrotransposon integrase-like protein 1 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NXP7.3 GenPept UniProtKB/Swiss-Prot:Q9NXP7

Gene LinkOut

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