LOCUS       NM_001164835            3942 bp    mRNA    linear   PRI 13-MAY-2024
DEFINITION  Homo sapiens LINE1 type transposase domain containing 1 (L1TD1),
            transcript variant 1, mRNA.
ACCESSION   NM_001164835
VERSION     NM_001164835.2
KEYWORDS    RefSeq.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 3942)
  AUTHORS   Jin,S.W., Seong,Y., Yoon,D., Kwon,Y.S. and Song,H.
  TITLE     Dissolution of ribonucleoprotein condensates by the embryonic stem
            cell protein L1TD1
  JOURNAL   Nucleic Acids Res 52 (6), 3310-3326 (2024)
   PUBMED   38165001
  REMARK    GeneRIF: Dissolution of ribonucleoprotein condensates by the
            embryonic stem cell protein L1TD1.
REFERENCE   2  (bases 1 to 3942)
  AUTHORS   Bandesh,K., Traurig,M., Chen,P., Hsueh,W.C., Hanson,R.L., Piaggi,P.
            and Baier,L.J.
  TITLE     Identification and characterization of the long non-coding RNA
            NFIA-AS2 as a novel locus for body mass index in American Indians
  JOURNAL   Int J Obes (Lond) 47 (6), 434-442 (2023)
   PUBMED   36806387
  REMARK    GeneRIF: Identification and characterization of the long non-coding
            RNA NFIA-AS2 as a novel locus for body mass index in American
            Indians.
REFERENCE   3  (bases 1 to 3942)
  AUTHORS   Casarotto,M., Lupato,V., Giurato,G., Guerrieri,R., Sulfaro,S.,
            Salvati,A., D'Angelo,E., Furlan,C., Menegaldo,A., Baboci,L.,
            Montico,B., Turturici,I., Dolcetti,R., Romeo,S., Baggio,V.,
            Corrado,S., Businello,G., Guido,M., Weisz,A., Giacomarra,V.,
            Franchin,G., Steffan,A., Sigalotti,L., Vaccher,E.,
            Boscolo-Rizzo,P., Jerry,P., Fanetti,G. and Fratta,E.
  TITLE     LINE-1 hypomethylation is associated with poor outcomes in
            locoregionally advanced oropharyngeal cancer
  JOURNAL   Clin Epigenetics 14 (1), 171 (2022)
   PUBMED   36503584
  REMARK    GeneRIF: LINE-1 hypomethylation is associated with poor outcomes in
            locoregionally advanced oropharyngeal cancer.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3942)
  AUTHORS   Kuriyama,Y., Shimizu,A., Kim,J., Yasuda,M. and Motegi,S.I.
  TITLE     The differential expression of long interspersed nuclear elements-1
            as a marker for hypomethylation in Merkel cell carcinoma
  JOURNAL   Clin Exp Dermatol 47 (9), 1726-1728 (2022)
   PUBMED   35596537
  REMARK    GeneRIF: The differential expression of long interspersed nuclear
            elements-1 as a marker for hypomethylation in Merkel cell
            carcinoma.
REFERENCE   5  (bases 1 to 3942)
  AUTHORS   Huang,Y., Xu,F., Mei,S., Liu,X., Zhao,F., Wei,L., Fan,Z., Hu,Y.,
            Wang,L., Ai,B., Cen,S., Liang,C. and Guo,F.
  TITLE     MxB inhibits long interspersed element type 1 retrotransposition
  JOURNAL   PLoS Genet 18 (2), e1010034 (2022)
   PUBMED   35171907
  REMARK    GeneRIF: MxB inhibits long interspersed element type 1
            retrotransposition.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 3942)
  AUTHORS   Shigaki,H., Baba,Y., Watanabe,M., Murata,A., Iwagami,S., Miyake,K.,
            Ishimoto,T., Iwatsuki,M. and Baba,H.
  TITLE     LINE-1 hypomethylation in gastric cancer, detected by bisulfite
            pyrosequencing, is associated with poor prognosis
  JOURNAL   Gastric Cancer 16 (4), 480-487 (2013)
   PUBMED   23179365
  REMARK    GeneRIF: LINE-1 hypomethylation in gastric cancer is associated
            with shorter survival, suggesting that it has potential for use as
            a prognostic biomarker.
REFERENCE   7  (bases 1 to 3942)
  AUTHORS   Cash,H.L., Tao,L., Yuan,J.M., Marsit,C.J., Houseman,E.A.,
            Xiang,Y.B., Gao,Y.T., Nelson,H.H. and Kelsey,K.T.
  TITLE     LINE-1 hypomethylation is associated with bladder cancer risk among
            nonsmoking Chinese
  JOURNAL   Int J Cancer 130 (5), 1151-1159 (2012)
   PUBMED   21445976
  REMARK    GeneRIF: there was no significant association of LINE-1 methylation
            with case status, although reduced LINE-1 methylation was
            associated with increased risk of bladder cancer among never
            smokers
REFERENCE   8  (bases 1 to 3942)
  AUTHORS   Narva,E., Rahkonen,N., Emani,M.R., Lund,R., Pursiheimo,J.P.,
            Nasti,J., Autio,R., Rasool,O., Denessiouk,K., Lahdesmaki,H., Rao,A.
            and Lahesmaa,R.
  TITLE     RNA-binding protein L1TD1 interacts with LIN28 via RNA and is
            required for human embryonic stem cell self-renewal and cancer cell
            proliferation
  JOURNAL   Stem Cells 30 (3), 452-460 (2012)
   PUBMED   22162396
  REMARK    GeneRIF: L1TD1 is part of the L1TD1-RHA-LIN28 complex that could
            influence levels of OCT4, suggesting that L1TD1 has an important
            role in the regulation of stemness.
REFERENCE   9  (bases 1 to 3942)
  AUTHORS   Wong,R.C., Ibrahim,A., Fong,H., Thompson,N., Lock,L.F. and
            Donovan,P.J.
  TITLE     L1TD1 is a marker for undifferentiated human embryonic stem cells
  JOURNAL   PLoS One 6 (4), e19355 (2011)
   PUBMED   21559406
  REMARK    GeneRIF: L1TD1 is a downstream target of Nanog and represents a
            useful marker for identifying undifferentiated hESC
            Publication Status: Online-Only
REFERENCE   10 (bases 1 to 3942)
  AUTHORS   Yamamoto,E., Toyota,M., Suzuki,H., Kondo,Y., Sanomura,T.,
            Murayama,Y., Ohe-Toyota,M., Maruyama,R., Nojima,M., Ashida,M.,
            Fujii,K., Sasaki,Y., Hayashi,N., Mori,M., Imai,K., Tokino,T. and
            Shinomura,Y.
  TITLE     LINE-1 hypomethylation is associated with increased CpG island
            methylation in Helicobacter pylori-related enlarged-fold gastritis
  JOURNAL   Cancer Epidemiol Biomarkers Prev 17 (10), 2555-2564 (2008)
   PUBMED   18842996
  REMARK    GeneRIF: LINE-1 hypomethylation is significantly associated with
            CpG island hypermethylation in EF+ gastritis.
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            CX167172.1, CX166941.1, DR005055.1, AK001973.1, AB211065.1,
            CN428323.1, BX382228.2 and BU677875.1.
            
            On May 31, 2019 this sequence version replaced NM_001164835.1.
            
            Transcript Variant: This variant (1) represents the longer
            transcript. Both variants 1 and 2 encode the same protein.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            CDS exon combination :: AK001746.1, CX781700.1 [ECO:0000331]
            RNAseq introns       :: single sample supports all introns
                                    SAMEA2142853 [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-40                CX167172.1         48-87
            41-633              CX166941.1         1-593
            634-736             DR005055.1         457-559
            737-1908            AK001973.1         599-1770
            1909-2553           AB211065.1         1783-2427
            2554-3238           CN428323.1         149-833
            3239-3560           BX382228.2         347-668             c
            3561-3586           BU677875.1         374-399             c
            3587-3942           BU677875.1         17-372              c
FEATURES             Location/Qualifiers
     source          1..3942
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="1"
                     /map="1p31.3"
     gene            1..3942
                     /gene="L1TD1"
                     /gene_synonym="ECAT11"
                     /note="LINE1 type transposase domain containing 1"
                     /db_xref="GeneID:54596"
                     /db_xref="HGNC:HGNC:25595"
     exon            1..73
                     /gene="L1TD1"
                     /gene_synonym="ECAT11"
                     /inference="alignment:Splign:2.1.0"
     exon            74..167
                     /gene="L1TD1"
                     /gene_synonym="ECAT11"
                     /inference="alignment:Splign:2.1.0"
     exon            168..278
                     /gene="L1TD1"
                     /gene_synonym="ECAT11"
                     /inference="alignment:Splign:2.1.0"
     exon            279..1396
                     /gene="L1TD1"
                     /gene_synonym="ECAT11"
                     /inference="alignment:Splign:2.1.0"
     CDS             389..2986
                     /gene="L1TD1"
                     /gene_synonym="ECAT11"
                     /note="ES cell-associated protein 11; LINE-1 type
                     transposase domain containing 1"
                     /codon_start=1
                     /product="LINE-1 type transposase domain-containing
                     protein 1"
                     /protein_id="NP_001158307.1"
                     /db_xref="CCDS:CCDS619.1"
                     /db_xref="GeneID:54596"
                     /db_xref="HGNC:HGNC:25595"
                     /translation="MSDVSTSVQSKFARLAKKKENITYMKREQLTETDKDIAPVLDLK
                     CKDVSAIMNKFKVLMEIQDLMFEEMRETLKNDLKAVLGGKATIPEVKNSENSSSRTEF
                     QQIINLALQKTGMVGKIEGENSKIGDDNENLTFKLEVNELSGKLDNTNEYNSNDGKKL
                     PQGESRSYEVMGSMEETLCNIDDRDGNRNVHLEFTERESRKDGEDEFVKEMREERKFQ
                     KLKNKEEVLKASREEKVLMDEGAVLTLVADLSSATLDISKQWSNVFNILRENDFEPKF
                     LCEVKLAFKCDGEIKTFSDLQSLRKFASQKSSVKELLKDVLPQKEEINQGGRKYGIQE
                     KRDKTLIDSKHRAGEITSDGLSFLFLKEVKVAKPEEMKNLETQEEEFSELEELDEEAS
                     GMEDDEDTSGLEEEEEEPSGLEEEEEEEASGLEEDEASGLEEEEEQTSEQDSTFQGHT
                     LVDAKHEVEITSDGMETTFIDSVEDSESEEEEEGKSSETGKVKTTSLTEKKASRRQKE
                     IPFSYLVGDSGKKKLVKHQVVHKTQEEEETAVPTSQGTGTPCLTLCLASPSKSLEMSH
                     DEHKKHSHTNLSISTGVTKLKKTEEKKHRTLHTEELTSKEADLTEETEENLRSSVINS
                     IREIKEEIGNLKSSHSGVLEIENSVDDLSSRMDILEERIDSLEDQIEEFSKDTMQMTK
                     QIISKERQRDIEERSRSCNIRLIGIPEKESYENRAEDIIKEIIDENFAELKKGSSLEI
                     VSACRVPSKIDEKRLTPRHILVKFWNSSDKEKIIRASRERREITYQGTRIRLTADLSL
                     DTLDARSKWSNVFKVLLEKGFNPRILYPAKMAFDFRGKTKVFLSIEEFRDYVLHMPTL
                     RELLGNNIP"
     exon            1397..3942
                     /gene="L1TD1"
                     /gene_synonym="ECAT11"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3922..3927
                     /regulatory_class="polyA_signal_sequence"
                     /gene="L1TD1"
                     /gene_synonym="ECAT11"
                     /note="hexamer: ATTAAA"
     polyA_site      3942
                     /gene="L1TD1"
                     /gene_synonym="ECAT11"
                     /note="major polyA site"
ORIGIN      
        1 agtccttagt tacaaggctc catcctcact ttgttcgctc ctcagtcgtc caggcggatt
       61 cctttttcgc caggcaccaa ggcacagctt agagtagacc cgagtcctgc tctgcggagt
      121 tcgtcttccc agcgaaggta cagaggcgga tgaactgctg agacttgggt ctcactctgt
      181 cgcccggtac agtggcgtga tcttggctca ctgcaacctc cacctcccag gttcaagtga
      241 ttcttatacc tcagcctcct gagtagctgg gactacagat tgacgtattt taagattttt
      301 ttaacttctg aagtctagca ggcctgtaag aacaaaaatc attctgtagg aattaaaaac
      361 agaatccagt cttgacaaca tatccacaat gtctgatgta tctactagtg tacaatcaaa
      421 atttgctaga cttgcaaaga aaaaggaaaa tatcacctat atgaaaagag agcagttaac
      481 agaaactgat aaggacatag ctccggtatt agatttaaaa tgcaaggacg tatcagcaat
      541 tatgaataag tttaaggtct taatggaaat tcaagacctg atgtttgagg agatgaggga
      601 aactcttaaa aatgacctaa aagcagtttt agggggaaaa gctacaatac ctgaggtaaa
      661 gaattcagag aactccagta gtaggacaga gtttcagcaa ataatcaatt tagcattaca
      721 aaaaacaggg atggtaggga aaatagaagg agaaaactct aaaataggtg atgataatga
      781 aaatttaacc tttaaattag aagtaaatga gctgagtggt aaattagaca acactaacga
      841 atacaatagt aatgatggta agaaattacc ccagggtgaa tcacgaagtt acgaagtcat
      901 gggaagtatg gaagaaacct tatgcaatat agatgacaga gatggaaatc gcaatgtcca
      961 tttagaattt acagaaagag agagtaggaa ggatggagag gatgaatttg tcaaagaaat
     1021 gagagaggaa agaaaatttc agaaattgaa gaataaagag gaggttttaa aagcctccag
     1081 agaagaaaaa gtgttgatgg atgaaggagc agtacttacc ctggtagccg acctttcatc
     1141 agcaacactg gatattagta agcaatggag taatgtcttc aacattctga gagaaaatga
     1201 ttttgaacct aaatttctgt gtgaagttaa attagcattt aaatgtgatg gtgaaataaa
     1261 gacattttca gatctgcaaa gccttagaaa atttgccagc caaaaatctt ctgtgaaaga
     1321 attactgaaa gatgtactcc cacaaaagga agaaataaat caaggaggaa gaaaatatgg
     1381 aattcaagaa aaaagggata aaaccctaat agactcaaag catagagctg gagaaataac
     1441 cagtgatggc ttgagcttcc tatttcttaa agaagtaaaa gttgctaagc cagaggagat
     1501 gaaaaactta gagactcaag aggaagagtt ttccgagcta gaggagctgg atgaagaggc
     1561 ctcagggatg gaggatgatg aagatacctc agggctggag gaggaggagg aagagccctc
     1621 agggctggag gaggaagaag aagaagaggc ttcagggttg gaggaggatg aggcctcagg
     1681 gctagaggag gaagaggaac agacttcaga acaggactca acctttcagg gtcatacttt
     1741 ggtagatgca aagcatgaag ttgagataac cagtgatggc atggaaacta ctttcattga
     1801 ctctgtagag gattctgaat cagaggagga agaagaagga aagagctctg aaacaggaaa
     1861 ggtaaagact acctccctga ctgagaaaaa agcctcacgt agacaaaaag aaattccctt
     1921 tagttatttg gttggggact ctgggaagaa aaagttggtg aaacaccagg tggtgcacaa
     1981 aacccaggag gaagaggaaa cagctgtgcc cacaagtcaa ggaactggca caccctgtct
     2041 gaccttatgt ttggcctctc cctcaaagtc actagagatg agtcatgatg agcataaaaa
     2101 gcattcacat acaaatttga gtatttcaac aggagtcacc aaacttaaga aaacagaaga
     2161 aaagaaacac agaactctgc acacagaaga actaacatcc aaagaagcag acttaacaga
     2221 ggaaacagaa gaaaacttga gaagtagtgt gattaatagc atcagagaga taaaagagga
     2281 gattggaaat ttgaaaagtt cccattcagg tgtcttggaa attgaaaatt cagtagatga
     2341 tctgagtagc agaatggaca tacttgaaga aagaatagac agtctagaag atcaaattga
     2401 agaattctct aaggatacaa tgcaaatgac caaacagata attagtaaag aaaggcaaag
     2461 agatatagag gagagatcta gaagttgcaa cattcgtttg ataggaattc cagaaaagga
     2521 gagttatgag aatagggcag aggacataat taaagaaata attgatgaaa actttgcaga
     2581 actaaagaaa ggttcaagtc ttgagattgt cagtgcttgt cgagtaccta gtaaaattga
     2641 tgaaaagaga ctgactccta gacacatctt ggtgaaattt tggaattcta gtgataaaga
     2701 gaaaataata agggcttcta gagagagaag agaaattacc taccaaggaa caagaatcag
     2761 gttgacagca gacttatcac tggacacact ggatgctaga agtaaatgga gcaatgtctt
     2821 caaagttctg ctggaaaaag gctttaatcc tagaatccta tatccagcca aaatggcatt
     2881 tgattttagg ggtaaaacaa aggtatttct tagtattgaa gaatttagag attatgtttt
     2941 gcatatgccc accttgagag aattactggg gaataatata ccttagcacg ccagggtgac
     3001 tacaaacaat atgctttcct cccccagcat gcatccaaaa atcaacaagt aaaacgaaaa
     3061 tacacttcta cccagaagga tggacagcta atagcgtact tggggatgag gagcaaggaa
     3121 tattacagat attacctaga tgttaataaa gggtatgttt aaaaaaaata ggctggtctc
     3181 aatgtagtga gttatttcag ttgatcacag tcagttacag atagaattcc ttgttttact
     3241 tcccccccac cacctcccta ctgcagttga ctagtctttt tagaatttat attatctggc
     3301 tgggcacggt ggctcacacc tgtaatccca gcactttggg aggccgaggc gggtggatca
     3361 cgaggtcagg agatcgagac catcctggct aacacagtga aaccccgtct ctactaaaaa
     3421 taaaaaaaat tagccgggca tggtggcggg cgcctgtagt cccagctact tgggaggctg
     3481 aggcaggaga atggcgtgaa cccaggaggc ggagcttgca gtgagccgag atcacaccac
     3541 tgcactccag ccggagccac agagcgacac tccgtctcaa aaaaaagtat attgtgctag
     3601 cttgtctaag aataaacttc tatactgttg ggggagggct gcacctgtca agataacctg
     3661 tcaatgtagt aggaaaacag gaggggacag taacagaaaa gcacgggaaa agatggcaag
     3721 gttagttaaa atagaaaagt gctcagttcc tcatacctgt aatcccagca gtttaggggg
     3781 ccaaggcagg tgggtcactt gagcccaaga gttcaaggcc atcctgggca atgtggcgaa
     3841 agtgtctaca aaaaaataca aaaagaggaa gaaatgatat ttcacaagtt tgtatcattt
     3901 gtcatgatgt gactcgaata tattaaatct ttttcctttg aa
//
