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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
    mouse all
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    Genomic context

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    See GIN1 in Genome Data Viewer
    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

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

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