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    TIGD6 tigger transposable element derived 6 [ Homo sapiens (human) ]

    Gene ID: 81789, updated on 5-Mar-2024

    Summary

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    Official Symbol
    TIGD6provided by HGNC
    Official Full Name
    tigger transposable element derived 6provided by HGNC
    Primary source
    HGNC:HGNC:18332
    See related
    Ensembl:ENSG00000164296 AllianceGenome:HGNC:18332
    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
    Summary
    The protein encoded by this gene belongs to the tigger subfamily of the pogo superfamily of DNA-mediated transposons in humans. These proteins are related to DNA transposons found in fungi and nematodes, and more distantly to the Tc1 and mariner transposases. They are also very similar to the major mammalian centromere protein B. [provided by RefSeq, Oct 2009]
    Expression
    Ubiquitous expression in prostate (RPKM 1.9), testis (RPKM 1.8) and 25 other tissues See more
    Orthologs
    all
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    Genomic context

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    See TIGD6 in Genome Data Viewer
    Location:
    5q32
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (149993118..150000654, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (150529664..150537200, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (149372681..149380217, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene phosphodiesterase 6A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149318171-149318672 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149318673-149319172 Neighboring gene Sharpr-MPRA regulatory region 12514 Neighboring gene MFF pseudogene 2 Neighboring gene NANOG hESC enhancer GRCh37_chr5:149338737-149339340 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16504 Neighboring gene solute carrier family 26 member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23393 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:149379441-149380229 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23394 Neighboring gene HMG-box containing 3 Neighboring gene small nucleolar RNA U13 Neighboring gene ribosomal protein S20 pseudogene 4

    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. Health and population effects of rare gene knockouts in adult humans with related parents. Narasimhan VM, et al. Science, 2016 Apr 22. PMID 26940866, Free PMC Article
    2. Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity. Saleheen D, et al. Nature, 2017 Apr 12. PMID 28406212, Free PMC Article
    3. A systematic survey of loss-of-function variants in human protein-coding genes. MacArthur DG, et al. Science, 2012 Feb 17. PMID 22344438, Free PMC Article
    4. Identification of a large set of rare complete human knockouts. Sulem P, et al. Nat Genet, 2015 May. PMID 25807282
    5. Common homozygosity for predicted loss-of-function variants reveals both redundant and advantageous effects of dispensable human genes. Rausell A, et al. Proc Natl Acad Sci U S A, 2020 Jun 16. PMID 32487729, Free PMC Article

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2021-02-03)

    ClinGen Genome Curation Page
    Haploinsufficency

    Dosage sensitivity unlikely (Last evaluated 2021-02-03)

    ClinGen Genome Curation PagePubMed

    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

    • DKFZp761E2110

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    tigger transposable element-derived protein 6

    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_001243253.2 → NP_001230182.1  tigger transposable element-derived protein 6 isoform 1

      See identical proteins and their annotated locations for NP_001230182.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. This variant represents the allele encoded by the GRCh38 reference genome and encodes isoform (1). Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC011406, AL136539, BC033641
      Consensus CDS
      CCDS4301.1
      UniProtKB/Swiss-Prot
      B3KTZ8, Q17RP2, Q96MQ4, Q9H0X7
      Related
      ENSP00000425318.2, ENST00000515406.2
      Conserved Domains (4) summary
      COG2963
      Location:5 → 57
      InsE; Transposase and inactivated derivatives [Mobilome: prophages, transposons]
      pfam03221
      Location:75 → 134
      HTH_Tnp_Tc5; Tc5 transposase DNA-binding domain
      cl21459
      Location:7 → 54
      HTH; Helix-turn-helix domains
      cl21549
      Location:207 → 372
      rve; Integrase core domain

    2. NM_001412170.1 → NP_001399099.1  tigger transposable element-derived protein 6 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses the same splicing as variant 1 but represents the allele encoded by the T2T genome assembly. The encoded isoform (2) is shorter and has a frameshifted C-terminus compared to isoform 1.
      Source sequence(s)
      CP068273

    3. NM_001412171.1 → NP_001399100.1  tigger transposable element-derived protein 6 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses the same splicing as variant 1 but represents the allele encoded by the T2T genome assembly. The encoded isoform (2) is shorter and has a frameshifted C-terminus compared to isoform 1.
      Source sequence(s)
      CP068273

    4. NM_001412172.1 → NP_001399101.1  tigger transposable element-derived protein 6 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) represents the allele encoded by the GRCh38 reference genome and encodes isoform (1).
      Source sequence(s)
      AC011406
      UniProtKB/Swiss-Prot
      B3KTZ8, Q17RP2, Q96MQ4, Q9H0X7

    5. NM_001412173.1 → NP_001399102.1  tigger transposable element-derived protein 6 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) uses the same splicing as variant 5 but represents the allele encoded by the T2T genome assembly. The encoded isoform (2) is shorter and has a frameshifted C-terminus compared to isoform 1.
      Source sequence(s)
      CP068273

    6. NM_030953.4 → NP_112215.1  tigger transposable element-derived protein 6 isoform 1

      See identical proteins and their annotated locations for NP_112215.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the allele encoded by the GRCh38 reference genome and encodes isoform (1). Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC011406, AK096325, AL136539
      Consensus CDS
      CCDS4301.1
      UniProtKB/Swiss-Prot
      B3KTZ8, Q17RP2, Q96MQ4, Q9H0X7
      Related
      ENSP00000296736.3, ENST00000296736.4
      Conserved Domains (4) summary
      COG2963
      Location:5 → 57
      InsE; Transposase and inactivated derivatives [Mobilome: prophages, transposons]
      pfam03221
      Location:75 → 134
      HTH_Tnp_Tc5; Tc5 transposase DNA-binding domain
      cl21459
      Location:7 → 54
      HTH; Helix-turn-helix domains
      cl21549
      Location:207 → 372
      rve; Integrase core domain

    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
      149993118..150000654 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      150529664..150537200 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q17RP2.2 GenPept UniProtKB/Swiss-Prot:Q17RP2

    Gene LinkOut

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

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