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

Gene ID: 54596, updated on 2-Nov-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 retrotransposition. Located in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in placenta (RPKM 6.2), testis (RPKM 4.7) and 4 other tissues See more
Orthologs
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (62194849..62212328)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (62073453..62090943)
RS_2024_09 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 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 bladder cancer risk among nonsmoking Chinese. Cash HL, et al. Int J Cancer, 2012 Mar 1. PMID 21445976, Free PMC Article
  2. Embryonic Stem Cell-Related Protein L1TD1 Is Required for Cell Viability, Neurosphere Formation, and Chemoresistance in Medulloblastoma. Santos MC, et al. Stem Cells Dev, 2015 Nov 15. PMID 26159230
  3. Positive selection and multiple losses of the LINE-1-derived L1TD1 gene in mammals suggest a dual role in genome defense and pluripotency. McLaughlin RN Jr, et al. PLoS Genet, 2014 Sep. PMID 25211013, Free PMC Article
  4. RNase H2, mutated in Aicardi-Goutières syndrome, promotes LINE-1 retrotransposition. Benitez-Guijarro M, et al. EMBO J, 2018 Aug 1. PMID 29959219, Free PMC Article
  5. L1TD1 - a prognostic marker for colon cancer. Chakroborty D, et al. BMC Cancer, 2019 Jul 23. PMID 31337362, Free PMC Article

See all (37) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Dissolution of ribonucleoprotein condensates by the embryonic stem cell protein L1TD1.
    Title: Dissolution of ribonucleoprotein condensates by the embryonic stem cell protein L1TD1.
  2. 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.
  3. 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.
  4. 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.
  5. Maternal LINE-1 DNA Methylation in Early Spontaneous Preterm Birth.
    Title: Maternal LINE-1 DNA Methylation in Early Spontaneous Preterm Birth.
  6. 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.
  7. MxB inhibits long interspersed element type 1 retrotransposition.
    Title: MxB inhibits long interspersed element type 1 retrotransposition.
  8. 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.
  9. The Rhox gene cluster suppresses germline LINE1 transposition.
    Title: The Rhox gene cluster suppresses germline LINE1 transposition.
  10. 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.
Submit: New GeneRIF Correction See all GeneRIFs (24)

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_2024_08

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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