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    L1TD1 LINE1 type transposase domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 54596, updated on 5-Mar-2024

    Summary

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    Official Symbol
    L1TD1provided by HGNC
    Official Full Name
    LINE1 type transposase domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:25595
    See related
    Ensembl:ENSG00000240563 AllianceGenome:HGNC:25595
    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
    ECAT11
    Summary
    Predicted to enable single-stranded RNA binding activity. Predicted to be involved in transposition, RNA-mediated. Located in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in placenta (RPKM 6.2), testis (RPKM 4.7) and 4 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See L1TD1 in Genome Data Viewer
    Location:
    1p31.3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (62194849..62212328)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (62073453..62090943)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (62660521..62678000)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:62659664-62660520 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:62660521-62661376 Neighboring gene ribosomal protein S15a pseudogene 7 Neighboring gene phosphatidylinositol glycan anchor biosynthesis class P pseudogene 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:62698440-62698940 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:62698941-62699441 Neighboring gene KN motif and ankyrin repeat domains 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:62733748-62734248 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1115 Neighboring gene RNA, U6 small nuclear 371, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:62774147-62774833 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:62783698-62784422 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:62784423-62785145 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:62802114-62802779 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:62816983-62817483 Neighboring gene Sharpr-MPRA regulatory region 10636 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:62866517-62867293 Neighboring gene uncharacterized LOC105378768

    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. LINE-1 hypomethylation is associated with poor outcomes in locoregionally advanced oropharyngeal cancer. Casarotto M, et al. Clin Epigenetics, 2022 Dec 12. PMID 36503584, Free PMC Article
    2. The differential expression of long interspersed nuclear elements-1 as a marker for hypomethylation in Merkel cell carcinoma. Kuriyama Y, et al. Clin Exp Dermatol, 2022 Sep. PMID 35596537
    3. MxB inhibits long interspersed element type 1 retrotransposition. Huang Y, et al. PLoS Genet, 2022 Feb. PMID 35171907, Free PMC Article
    4. LINE-1 expression in cancer correlates with p53 mutation, copy number alteration, and S phase checkpoint. McKerrow W, et al. Proc Natl Acad Sci U S A, 2022 Feb 22. PMID 35169076, Free PMC Article
    5. Maternal LINE-1 DNA Methylation in Early Spontaneous Preterm Birth. Barišić A, et al. Biol Res Nurs, 2022 Jan. PMID 34727781

    See all (36) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification and characterization of the long non-coding RNA NFIA-AS2 as a novel locus for body mass index in American Indians.
      Title: Identification and characterization of the long non-coding RNA NFIA-AS2 as a novel locus for body mass index in American Indians.
    2. LINE-1 hypomethylation is associated with poor outcomes in locoregionally advanced oropharyngeal cancer.
      Title: LINE-1 hypomethylation is associated with poor outcomes in locoregionally advanced oropharyngeal cancer.
    3. The differential expression of long interspersed nuclear elements-1 as a marker for hypomethylation in Merkel cell carcinoma.
      Title: The differential expression of long interspersed nuclear elements-1 as a marker for hypomethylation in Merkel cell carcinoma.
    4. Maternal LINE-1 DNA Methylation in Early Spontaneous Preterm Birth.
      Title: Maternal LINE-1 DNA Methylation in Early Spontaneous Preterm Birth.
    5. LINE-1 expression in cancer correlates with p53 mutation, copy number alteration, and S phase checkpoint.
      Title: LINE-1 expression in cancer correlates with p53 mutation, copy number alteration, and S phase checkpoint.
    6. MxB inhibits long interspersed element type 1 retrotransposition.
      Title: MxB inhibits long interspersed element type 1 retrotransposition.
    7. Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease.
      Title: Structural dissection of sequence recognition and catalytic mechanism of human LINE-1 endonuclease.
    8. The Rhox gene cluster suppresses germline LINE1 transposition.
      Title: The Rhox gene cluster suppresses germline LINE1 transposition.
    9. Hepatitis C virus infection restricts human LINE-1 retrotransposition in hepatoma cells.
      Title: Hepatitis C virus infection restricts human LINE-1 retrotransposition in hepatoma cells.
    10. Study results identify increased expression of L1TD1 as a prognostic marker predicting longer disease-free survival in colon cancer patients.
      Title: L1TD1 - a prognostic marker for colon cancer.
    Submit: New GeneRIF Correction See all GeneRIFs (23)

    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

    • FLJ10884, MGC133253

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables single-stranded RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in retrotransposition IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    part_of ribonucleoprotein complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    LINE-1 type transposase domain-containing protein 1
    Names
    ES cell-associated protein 11
    LINE-1 type transposase domain containing 1

    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_001164835.2 → NP_001158307.1  LINE-1 type transposase domain-containing protein 1

      See identical proteins and their annotated locations for NP_001158307.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AB211065, AK001973, BU677875, BX382228, CN428323, CX166941, CX167172, DR005055
      Consensus CDS
      CCDS619.1
      UniProtKB/Swiss-Prot
      Q5T7N2, Q8NDA1, Q9NUV8, Q9NV78
      Conserved Domains (1) summary
      pfam02994
      Location:600 → 863
      Transposase_22; L1 transposable element

    2. NM_019079.5 → NP_061952.3  LINE-1 type transposase domain-containing protein 1

      See identical proteins and their annotated locations for NP_061952.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AB211065, AK001973, BU677875, BX382228, CN428323, CX167172, DR005055
      Consensus CDS
      CCDS619.1
      UniProtKB/Swiss-Prot
      Q5T7N2, Q8NDA1, Q9NUV8, Q9NV78
      Related
      ENSP00000419901.1, ENST00000498273.2
      Conserved Domains (1) summary
      pfam02994
      Location:600 → 863
      Transposase_22; L1 transposable element

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      62194849..62212328
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      62073453..62090943
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5T7N2.1 GenPept UniProtKB/Swiss-Prot:Q5T7N2

    Gene LinkOut

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

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