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    RTL5 retrotransposon Gag like 5 [ Homo sapiens (human) ]

    Gene ID: 340526, updated on 17-Sep-2024

    Summary

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    Official Symbol
    RTL5provided by HGNC
    Official Full Name
    retrotransposon Gag like 5provided by HGNC
    Primary source
    HGNC:HGNC:29430
    See related
    Ensembl:ENSG00000242732 AllianceGenome:HGNC:29430
    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
    MAR5; MART5; RGAG4; SIRH8; 6430402L03Rik
    Expression
    Broad expression in brain (RPKM 6.6), testis (RPKM 6.2) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RTL5 in Genome Data Viewer
    Location:
    Xq13.1
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (72127110..72131915, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (70560716..70565521, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (71346960..71351765, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene NHS like 2 Neighboring gene RNA, U6 small nuclear 1078, pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:71216621-71217222 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29753 Neighboring gene Sharpr-MPRA regulatory region 1584 Neighboring gene ribosomal protein S26 pseudogene 11 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:71289659-71290216 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20901 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20902 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20903 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29754 Neighboring gene TPT1-like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29755 Neighboring gene RNA, 7SL, cytoplasmic 388, pseudogene Neighboring gene peptidylprolyl cis/trans isomerase, NIMA-interacting 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 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. Characterization of size-fractionated cDNA libraries generated by the in vitro recombination-assisted method. Ohara O, et al. DNA Res, 2002 Apr 30. PMID 12056414
    2. 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
    3. A family of neofunctionalized Ty3/gypsy retrotransposon genes in mammalian genomes. Brandt J, et al. Cytogenet Genome Res, 2005. PMID 16093683
    4. Spindle Assembly Checkpoint Inhibition Can Resensitize p53-Null Stem Cells to Cancer Chemotherapy. Liu C, et al. Cancer Res, 2019 May 1. PMID 30862715, Free PMC Article
    5. Genome-wide CRISPR screening reveals genetic modifiers of mutant EGFR dependence in human NSCLC. Zeng H, et al. Elife, 2019 Nov 19. PMID 31741433, Free PMC Article

    See all (8) 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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of retrotransposon gag domain containing 4 (RGAG4) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA2001

    General protein information

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    Preferred Names
    retrotransposon Gag-like protein 5
    Names
    Sushi-Ichi retrotransposon homolog 8
    mammalian retrotransposon-derived 5
    retrotransposon gag domain containing 4
    retrotransposon gag domain-containing protein 4

    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.

    Genomic

    1. NG_021352.1 RefSeqGene

      Range
      4987..9792
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001024455.4 → NP_001019626.1  retrotransposon Gag-like protein 5

      See identical proteins and their annotated locations for NP_001019626.1

      Status: VALIDATED

      Source sequence(s)
      AB082532, BC151224, BX119917
      Consensus CDS
      CCDS55446.1
      UniProtKB/Swiss-Prot
      A7E2W7, Q5HYW3, Q8NCM4, Q9NPX1
      Related
      ENSP00000418667.1, ENST00000479991.1
      Conserved Domains (2) summary
      pfam03732
      Location:190 → 282
      Retrotrans_gag; Retrotransposon gag protein
      pfam16297
      Location:151 → 228
      DUF4939; Domain of unknown function (DUF4939)

    2. NM_001405151.1 → NP_001392080.1  retrotransposon Gag-like protein 5

      Status: VALIDATED

      Source sequence(s)
      BX119917
      UniProtKB/Swiss-Prot
      A7E2W7, Q5HYW3, Q8NCM4, Q9NPX1
      Related
      ENSP00000476792.1, ENST00000609883.3

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      72127110..72131915 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      70560716..70565521 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5HYW3.1 GenPept UniProtKB/Swiss-Prot:Q5HYW3

    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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