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    RTL6 retrotransposon Gag like 6 [ Homo sapiens (human) ]

    Gene ID: 84247, updated on 6-Oct-2024

    Summary

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    Official Symbol
    RTL6provided by HGNC
    Official Full Name
    retrotransposon Gag like 6provided by HGNC
    Primary source
    HGNC:HGNC:13343
    See related
    Ensembl:ENSG00000188636 AllianceGenome:HGNC:13343
    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
    Mar6; Mart6; SIRH3; LDOC1L; dJ1033E15.2
    Expression
    Ubiquitous expression in brain (RPKM 18.2), ovary (RPKM 11.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RTL6 in Genome Data Viewer
    Location:
    22q13.31
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (44492583..44498233, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (44976418..44982051, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (44888463..44894113, complement)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44839807-44840536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44840537-44841266 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44843884-44844547 Neighboring gene long intergenic non-protein coding RNA 1656 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr22:44844727-44845926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19211 Neighboring gene MRPS18C pseudogene 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44891229-44892006 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44892007-44892784 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13867 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13868 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:44923943-44924102 Neighboring gene uncharacterized LOC105373059 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44939408-44939962 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44939963-44940517 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44941073-44941626 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:44946331-44946858 Neighboring gene keratin 18 pseudogene 23

    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 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. Transposable elements as a source of genetic innovation: expression and evolution of a family of retrotransposon-derived neogenes in mammals. Brandt J, et al. Gene, 2005 Jan 17. PMID 15716091
    2. A family of neofunctionalized Ty3/gypsy retrotransposon genes in mammalian genomes. Brandt J, et al. Cytogenet Genome Res, 2005. PMID 16093683
    3. The protein network surrounding the human telomere repeat binding factors TRF1, TRF2, and POT1. Giannone RJ, et al. PLoS One, 2010 Aug 25. PMID 20811636, Free PMC Article
    4. A genome annotation-driven approach to cloning the human ORFeome. Collins JE, et al. Genome Biol, 2004. PMID 15461802, Free PMC Article
    5. A protein-protein interaction map of the TNF-induced NF-κB signal transduction pathway. Van Quickelberghe E, et al. Sci Data, 2018 Dec 18. PMID 30561431, Free PMC Article

    See all (16) 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

    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

    • DKFZp761O17121

    General protein information

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    Preferred Names
    retrotransposon Gag-like protein 6
    Names
    LDOC1 like
    Sushi-Ichi retrotransposon homolog 3
    leucine zipper down-regulated in cancer 1 like
    leucine zipper protein down-regulated in cancer cells-like
    mammalian retrotransposon-derived 6
    mammalian retrotransposon-derived protein 6
    protein LDOC1L

    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_032287.3 → NP_115663.2  retrotransposon Gag-like protein 6

      See identical proteins and their annotated locations for NP_115663.2

      Status: VALIDATED

      Source sequence(s)
      AL136553, BC018713, BC030232, Z75407
      Consensus CDS
      CCDS33662.1
      UniProtKB/Swiss-Prot
      Q6ICC9, Q6ZTR1
      UniProtKB/TrEMBL
      B4DKA7
      Related
      ENSP00000340434.3, ENST00000341255.4
      Conserved Domains (1) summary
      pfam16297
      Location:98 → 177
      DUF4939; Domain of unknown function (DUF4939)

    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_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      44492583..44498233 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      44976418..44982051 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ICC9.1 GenPept UniProtKB/Swiss-Prot:Q6ICC9

    Gene LinkOut

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

    Chemical Information
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