LOCUS       NM_001134888            5398 bp    mRNA    linear   PRI 07-APR-2024
DEFINITION  Homo sapiens retrotransposon Gag like 1 (RTL1), transcript variant
            1, mRNA.
ACCESSION   NM_001134888 XM_370776
VERSION     NM_001134888.3
KEYWORDS    RefSeq; MANE Select.
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 5398)
  AUTHORS   Mahmoudi,A.R., Ghods,R., Madjd,Z., Abolhasani,M., Saeednejad
            Zanjani,L., Safaei,M., Balaei Goli,L., Vafaei,S., Katouzian,L.,
            Soltanghoraei,H., Shekarabi,M. and Zarnani,A.H.
  TITLE     Expression profiling of RTL1 in human breast cancer tissues and
            cell lines
  JOURNAL   Exp Mol Pathol 121, 104654 (2021)
   PUBMED   34087231
  REMARK    GeneRIF: Expression profiling of RTL1 in human breast cancer
            tissues and cell lines.
REFERENCE   2  (bases 1 to 5398)
  AUTHORS   Kitazawa,M., Sutani,A., Kaneko-Ishino,T. and Ishino,F.
  TITLE     The role of eutherian-specific RTL1 in the nervous system and its
            implications for the Kagami-Ogata and Temple syndromes
  JOURNAL   Genes Cells 26 (3), 165-179 (2021)
   PUBMED   33484574
  REMARK    GeneRIF: The role of eutherian-specific RTL1 in the nervous system
            and its implications for the Kagami-Ogata and Temple syndromes.
REFERENCE   3  (bases 1 to 5398)
  AUTHORS   Prats-Puig,A., Carreras-Badosa,G., Bassols,J., Cavelier,P.,
            Magret,A., Sabench,C., de Zegher,F., Ibanez,L., Feil,R. and
            Lopez-Bermejo,A.
  TITLE     The placental imprinted DLK1-DIO3 domain: a new link to prenatal
            and postnatal growth in humans
  JOURNAL   Am J Obstet Gynecol 217 (3), 350 (2017)
   PUBMED   28502757
  REMARK    GeneRIF: We find that placental expression of DIO3 and RTL1)
            correlates with prenatal growth. Combined, these findings suggest
            that epigenetic programming and gene expression within the
            DLK1-DIO3 imprinted domain influence both prenatal and postnatal
            growth.
REFERENCE   4  (bases 1 to 5398)
  AUTHORS   Belot,M.P., Naderi,K., Mille,C., Boelle,P.Y., Benachi,A.,
            Bougneres,P. and Fradin,D.
  TITLE     Role of DNA methylation at the placental RTL1 gene locus in type 1
            diabetes
  JOURNAL   Pediatr Diabetes 18 (3), 178-187 (2017)
   PUBMED   27174469
  REMARK    GeneRIF: Data suggest that DNA is differentially methylated
            (hypomethylated) at a gene locus associated with regulation of
            expression of RTL1 and miR136 in type 1 diabetes; these studies
            were conducted using tissue bank placentas and whole blood cell DNA
            from children with type 1 diabetes. (RTL1 = retrotransposon-like
            protein 1; miR136 = microRNA 136)
REFERENCE   5  (bases 1 to 5398)
  AUTHORS   Bundo,M., Toyoshima,M., Okada,Y., Akamatsu,W., Ueda,J.,
            Nemoto-Miyauchi,T., Sunaga,F., Toritsuka,M., Ikawa,D., Kakita,A.,
            Kato,M., Kasai,K., Kishimoto,T., Nawa,H., Okano,H., Yoshikawa,T.,
            Kato,T. and Iwamoto,K.
  TITLE     Increased l1 retrotransposition in the neuronal genome in
            schizophrenia
  JOURNAL   Neuron 81 (2), 306-313 (2014)
   PUBMED   24389010
  REMARK    GeneRIF: The results of this study suggest that hyperactive
            retrotransposition of L1 in neurons triggered by environmental
            and/or genetic risk factors may contribute to the susceptibility
            and pathophysiology of schizophrenia.
REFERENCE   6  (bases 1 to 5398)
  AUTHORS   Kagami,M., Sekita,Y., Nishimura,G., Irie,M., Kato,F., Okada,M.,
            Yamamori,S., Kishimoto,H., Nakayama,M., Tanaka,Y., Matsuoka,K.,
            Takahashi,T., Noguchi,M., Tanaka,Y., Masumoto,K., Utsunomiya,T.,
            Kouzan,H., Komatsu,Y., Ohashi,H., Kurosawa,K., Kosaki,K.,
            Ferguson-Smith,A.C., Ishino,F. and Ogata,T.
  TITLE     Deletions and epimutations affecting the human 14q32.2 imprinted
            region in individuals with paternal and maternal upd(14)-like
            phenotypes
  JOURNAL   Nat Genet 40 (2), 237-242 (2008)
   PUBMED   18176563
  REMARK    GeneRIF: RTL1, a paternally expressed gene in a cluster of
            imprinted genes on chromosome 14q32.2, is associated with
            upd(14)pat-like and upd(14)mat-like phenotypes.
REFERENCE   7  (bases 1 to 5398)
  AUTHORS   Youngson,N.A., Kocialkowski,S., Peel,N. and Ferguson-Smith,A.C.
  TITLE     A small family of sushi-class retrotransposon-derived genes in
            mammals and their relation to genomic imprinting
  JOURNAL   J Mol Evol 61 (4), 481-490 (2005)
   PUBMED   16155747
REFERENCE   8  (bases 1 to 5398)
  AUTHORS   Davis,E., Caiment,F., Tordoir,X., Cavaille,J., Ferguson-Smith,A.,
            Cockett,N., Georges,M. and Charlier,C.
  TITLE     RNAi-mediated allelic trans-interaction at the imprinted Rtl1/Peg11
            locus
  JOURNAL   Curr Biol 15 (8), 743-749 (2005)
   PUBMED   15854907
  REMARK    Erratum:[Curr Biol. 2005 May 10;15(9):884]
REFERENCE   9  (bases 1 to 5398)
  AUTHORS   Brandt,J., Veith,A.M. and Volff,J.N.
  TITLE     A family of neofunctionalized Ty3/gypsy retrotransposon genes in
            mammalian genomes
  JOURNAL   Cytogenet Genome Res 110 (1-4), 307-317 (2005)
   PUBMED   16093683
REFERENCE   10 (bases 1 to 5398)
  AUTHORS   Seitz,H., Youngson,N., Lin,S.P., Dalbert,S., Paulsen,M.,
            Bachellerie,J.P., Ferguson-Smith,A.C. and Cavaille,J.
  TITLE     Imprinted microRNA genes transcribed antisense to a reciprocally
            imprinted retrotransposon-like gene
  JOURNAL   Nat Genet 34 (3), 261-262 (2003)
   PUBMED   12796779
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AL117190.6.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Mar 13, 2020 this sequence version replaced NM_001134888.2.
            
            Summary: This gene is a retrotransposon-derived, paternally
            expressed imprinted gene that is highly expressed at the late fetal
            stage in both the fetus and placenta. It has an overlapping
            maternally expressed antisense transcript, which contains several
            microRNAs targeting the transcripts of this gene through an RNA
            interference (RNAi) mechanism. This gene is essential for
            maintenance of the fetal capillaries. [provided by RefSeq, Jul
            2009].
            
            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##
            Transcript exon combination :: ERR4368409.166420.1,
                                           ERR4352444.390932.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2162568 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            imprinted gene         :: PMID: 18176563
            MANE Ensembl match     :: ENST00000649591.1/ ENSP00000497482.1
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression, longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-118               AL117190.6         143721-143838       c
            119-214             AL117190.6         143407-143502       c
            215-276             AL117190.6         133560-133621       c
            277-5398            AL117190.6         119869-124990       c
FEATURES             Location/Qualifiers
     source          1..5398
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="14"
                     /map="14q32.2-q32.31"
     gene            1..5398
                     /gene="RTL1"
                     /gene_synonym="HUR1; Mar1; MART1; PEG11; SIRH2"
                     /note="retrotransposon Gag like 1"
                     /db_xref="GeneID:388015"
                     /db_xref="HGNC:HGNC:14665"
                     /db_xref="MIM:611896"
     exon            1..118
                     /gene="RTL1"
                     /gene_synonym="HUR1; Mar1; MART1; PEG11; SIRH2"
                     /inference="alignment:Splign:2.1.0"
     exon            119..214
                     /gene="RTL1"
                     /gene_synonym="HUR1; Mar1; MART1; PEG11; SIRH2"
                     /inference="alignment:Splign:2.1.0"
     exon            215..276
                     /gene="RTL1"
                     /gene_synonym="HUR1; Mar1; MART1; PEG11; SIRH2"
                     /inference="alignment:Splign:2.1.0"
     exon            277..5398
                     /gene="RTL1"
                     /gene_synonym="HUR1; Mar1; MART1; PEG11; SIRH2"
                     /inference="alignment:Splign:2.1.0"
     CDS             363..4439
                     /gene="RTL1"
                     /gene_synonym="HUR1; Mar1; MART1; PEG11; SIRH2"
                     /note="mammalian retrotransposon derived protein 1;
                     paternally expressed gene 11 protein;
                     retrotransposon-derived protein PEG11; Sushi-Ichi
                     retrotransposon homolog 2; mammalian
                     retrotransposon-derived 1; paternally expressed 11;
                     retrotransposon-like 1"
                     /codon_start=1
                     /product="retrotransposon-like protein 1"
                     /protein_id="NP_001128360.1"
                     /db_xref="CCDS:CCDS53910.1"
                     /db_xref="GeneID:388015"
                     /db_xref="HGNC:HGNC:14665"
                     /db_xref="MIM:611896"
                     /translation="MIEPSEDSFETMMEHKNPSSKQMESSEGSSNTTEATSGSGVRGE
                     AGPASGPAQEKKEPPSGPLQEMEELPTDLLQDMEEPSSGPRKEIEDPPNDLLQDLEES
                     CNGSHQARGDPLSGASDRMKEASVNPSGAREEQEAHTDLKESGREETPQEQNQTEHST
                     AELMAMVRSIISLYFRMQDLKEQQRVAEEILIKGINAGQLPAPKHFSGDRREFHEFIV
                     LCQLTLQSYPRMFYNDRLRVGYVINHLSGLALEWAKALLQENSPLIGDFPAFLEAMSE
                     VFEYRQALRVAEEAMFTIRQGGRSATEYIDEFQSLVPILGWPDEVLQAHLCQGLNEEI
                     RHYLFRVPQPDSLDSLIVLILQIEEKLAERRAMLRLPPEARPRNLTWIDSPAPERWMV
                     SSWLPSEVHPDINRAHLFLLLMVRVNPYHSVAVQALVDSGADGNFMDEKFAQEHYVEL
                     YEKPYPQPVQSVDGSLIGNEPVWLYTEPLVCIHQNHQESIEFDIVPSPNFSVVLGIRW
                     LRVHAPEVDWIKGRCTFHSPYCLKNCFRPPPPCIALERHGMSLLPGLPHPYSDLADVF
                     NPKEADDETSDQPSSDGSDDLSESEPSELQQAGDSDHSETFYECPSTAPWEPVGARMQ
                     ERARLQEEYWDLQDMLTNRQDYIQMIPELFDQLHGAEWFTKLELRGTIVEESVNGHRT
                     EDVWKAAFGLELEEMKSYQPFALSPDPIIPQNVIHFILKDMLGFFVLSYGQEVLIYSM
                     SQEEHLHHVRQVLVRFRHHNVYCSLDKSQFHRQTVEFLGFVVTPKGVKLNKNVMTIIT
                     GYPTPGSKLSLRNFIEFVFPYRHFVERFSIIAEPLVRQLLSSYQFYWGVEEQEAFECL
                     KRAFRKAPLLHHPKPQNPFYLETGVTGTALHASLIQIDDQTGKRACCAFYSRNISPIE
                     VEYSQAEMKILPIRAAFMVWCRYLENTEEPIMILLNTEDLASLNNDRLTVLLPGHWVF
                     FFSHFNFDVMELPEQDGGRALPPVRNLRWRRAFQRNTAARQTLLLASRGFPRDPSTES
                     GEEENEEQDELNEQILRQELLAMIPIDQILNSFLAHFSMAQIRAVILHFFRGLLYWKN
                     TLALAAILVLLRVRQCLSLRPAPAMRVARPQPQRSLRLILDSSLIAGSSITTAITQLL
                     TQMPALVGANTIPAQELAELFLGPGRWQRNALHSQAHRGLQFTPGFWLTLCEFFGVRV
                     TPQEGHLPALRQNRYLELHVVGDEDVVLREALQDDLQRYRQCGLHDGLQDTSQDKQDN
                     DVQEAPPSHTAATHPPRPRHLMDPQVLEFLGSRLLHIHSADGQLHLLSREQAARALSQ
                     FLTLIYRRALPIPAWESQPREQARLEELPDEDEDANLD"
     regulatory      5379..5384
                     /regulatory_class="polyA_signal_sequence"
                     /gene="RTL1"
                     /gene_synonym="HUR1; Mar1; MART1; PEG11; SIRH2"
                     /note="hexamer: AATAAA"
     polyA_site      5398
                     /gene="RTL1"
                     /gene_synonym="HUR1; Mar1; MART1; PEG11; SIRH2"
                     /note="major polyA site"
ORIGIN      
        1 acaccccccc agcactcggc acagcctcgc tgagcagcct tcagcagcag ggtgtggtgg
       61 ggagcctcgg agagtctggg gttccatcct ggcccagcct cacaccagct gagagacgac
      121 cgactgagct tcgaggacag gaagccaccg gcatcactaa gccaccggca tcacttcatc
      181 cccagcctca cgcttgggac tgggcccggg gaagcaagca gcgaggatcg agtggcacag
      241 gacgggagga gatccacttg aacgcttgca gccaaggttc tgatctccac ggtcccagct
      301 actgactgga cgccatcaca accttaccaa tcttcagaat acactccttt ccatccgacg
      361 aaatgataga accctctgaa gactcatttg agacgatgat ggagcataag aatccatcat
      421 caaaacaaat ggagtcctcc gagggctcat ccaacaccac cgaggcgacg tcgggcagtg
      481 gagtgcgggg agaggcaggg ccagccagcg gcccagccca ggaaaagaag gagcccccca
      541 gtggcccact ccaggaaatg gaagagctgc ccactgatct actccaagac atggaggagc
      601 catccagtgg cccacgtaag gaaatagagg atccacccaa tgacctactc caagacctgg
      661 aggagtcatg caacggttca caccaggcaa ggggggatcc actcagtgga gcatctgata
      721 ggatgaaaga agcatcagtc aacccatcgg gagcccgaga agaacaagag gctcacactg
      781 acctgaagga atcgggaagg gaggagactc ctcaagagca aaaccagacc gagcactcaa
      841 ccgcagaact tatggccatg gtgaggtcca tcatctcgct gtacttccga atgcaagacc
      901 tcaaagagca acagagagta gcagaagaga tcttgatcaa agggatcaat gcaggccaac
      961 tgcccgcccc aaagcacttc tctggcgatc gcagagaatt ccacgagttc atcgtactct
     1021 gccaactgac cttacagagc tacccaagaa tgttctataa cgaccgtctg agagttggct
     1081 atgtcatcaa tcacctgtcc ggcttggcat tagaatgggc caaagctcta ctgcaggaaa
     1141 acagccccct gatcggagac ttcccagcct tcctggaggc catgtccgaa gtgtttgagt
     1201 accgccaggc actgcgtgtg gcagaagagg ccatgttcac catcaggcag ggcggccgct
     1261 ctgccactga gtacatcgat gagttccaga gcctggtacc catcttgggc tggccagatg
     1321 aagtcctgca ggcccacttg tgccaggggc tcaacgagga gatcaggcac tatctattcc
     1381 gggtccctca gccggattcc ctagacagtc tgattgtgct catcctgcaa atagaagaga
     1441 agctggcaga gagaagagct atgctcaggc tgccccccga ggcccgcccc cggaacctga
     1501 cctggatcga ctcacctgct ccagagaggt ggatggtcag cagctggttg cccagcgaag
     1561 tccatccgga catcaatcgc gcccacctct tcctgctgct catggtgaga gtgaacccct
     1621 accacagcgt cgcggtccag gccctggtgg attcgggagc tgacggcaac ttcatggatg
     1681 agaagttcgc ccaagagcac tacgtcgagc tctacgagaa gccgtaccca cagccggtcc
     1741 aatccgtgga cggctcgctg attggcaacg agcctgtctg gctctacacg gagcccctgg
     1801 tgtgtatcca ccagaaccac caggagtcca tcgaatttga catcgtacct tcaccgaact
     1861 tctctgtggt cctaggcatc cgctggctcc gagtccacgc ccccgaagtc gactggatca
     1921 aaggccgctg caccttccac tctccctact gcctgaagaa ctgcttccgc ccgcccccgc
     1981 catgcattgc cctagagagg cacggcatga gcctgctacc cggactgcca cacccatact
     2041 cagacctggc cgacgtgttt aacccgaagg aagcagatga tgagacttcc gaccagccaa
     2101 gctcagacgg atccgatgat ctttctgaat cagagccctc tgagcttcag caggctggag
     2161 acagtgatca cagcgagacc ttttacgagt gtccctccac cgcgccttgg gaacctgtgg
     2221 gtgccaggat gcaagaaaga gccaggctac aggaggaata ctgggacctg caggacatgc
     2281 tgaccaacag acaggactac atacagatga ttccggaact gtttgaccag ttacacggag
     2341 ccgagtggtt cacaaaactg gagctgcgtg ggaccattgt ggaggaaagc gtgaacgggc
     2401 accgcaccga agatgtgtgg aaagcagcgt ttggtttgga gcttgaagag atgaagagct
     2461 accagccgtt tgcgctctcc ccagacccta tcatacctca gaacgtgatt cacttcatcc
     2521 taaaggacat gctagggttc tttgtgcttt cttatggcca ggaagtcctg atctactcaa
     2581 tgagtcagga ggagcacctc caccacgtcc gccaagtcct ggtccgcttc cgccatcaca
     2641 acgtctactg ctccctggac aagagccagt tccaccgcca aaccgtggaa ttcctgggct
     2701 tcgtcgtcac ccccaaaggg gtgaaactga acaagaacgt catgaccatc ataacagggt
     2761 accctacccc tggctccaag ctatctctgc gaaacttcat cgaattcgtc ttcccctacc
     2821 gccacttcgt ggagcgcttc agcatcatcg cagagcccct ggtgcggcag ctgctgagct
     2881 cctaccagtt ctactgggga gtcgaggagc aagaggcctt cgagtgcctg aagagggctt
     2941 tccgcaaggc gcctctcctc caccacccca agccccagaa cccattctac ttggaaaccg
     3001 gcgtcaccgg cacggccctg cacgcctccc tgatccaaat cgacgaccaa accggcaaga
     3061 gagcctgctg cgctttctac tcccgcaaca tctcccctat cgaggttgag tactctcaag
     3121 cggagatgaa gattcttcca atacgggctg ccttcatggt gtggtgccgc tacctggaga
     3181 acaccgagga gcccatcatg atccttctca acacagagga tctagcctct ctgaataatg
     3241 acaggctcac cgtacttctc cccgggcatt gggtcttctt cttctcccac ttcaactttg
     3301 acgtcatgga gctgccagaa caagacggcg gccgagctct gccacctgtg agaaacctcc
     3361 ggtggaggag agccttccag aggaacactg ccgccaggca aaccctgctg ctggcctcaa
     3421 ggggattccc cagggatcca tcgacggaat ccggggaaga agagaatgaa gaacaggatg
     3481 agctcaatga acagatccta cggcaagagc tgctggccat gatacccatc gaccagatcc
     3541 tcaacagctt cctcgcccac ttcagcatgg cccagatcag ggccgtcatt ctgcacttct
     3601 tccgaggcct cctgtactgg aagaacaccc tagccctggc agccatcctc gtgctactgc
     3661 gcgtgaggca atgcctctcg ctgcggccgg cacccgccat gcgggtggct cggccccagc
     3721 cccagcgctc cctacgactc atcctggatt cgtccctcat cgcaggcagc agcatcacga
     3781 cagccatcac ccagctgctc acccagatgc ccgctctcgt aggtgcaaac accatcccag
     3841 cccaggagct ggctgagctg ttcctgggcc ctggccgctg gcagcgaaat gctctgcact
     3901 cccaggccca ccgaggcctg cagttcaccc ctggcttctg gctgacgctg tgtgagttct
     3961 tcggtgtcag agtcaccccc caggagggcc acctccctgc cctgcgtcag aaccgctacc
     4021 tggagctgca cgtcgttggt gatgaggatg tcgtcttgcg agaagccctg caagacgacc
     4081 tgcaacgtta ccgtcagtgt ggcctgcatg acggcctgca agacacctcg caggacaagc
     4141 aggacaacga cgtgcaggag gccccaccca gccacacagc agccacccac ccaccccgcc
     4201 cacgccacct gatggatccc caggtcctgg aattccttgg tagccgcctg ctccacatcc
     4261 acagtgcaga tggccagctg cacctgctca gccgggagca ggcagccagg gccctgagcc
     4321 agttcctgac cctgatctac aggcgggccc tgcccatccc cgcctgggag agccagccca
     4381 gggagcaggc aaggctagaa gagctgcctg atgaggacga agatgctaac ctcgactgaa
     4441 gacgcctccc tgtctccagc aaagagtccc ctctatttct caccccaaca cctcccgacg
     4501 tcccctggcc tccccgcgcc tcagcctgct tcgcttccct tcctgccact cctgacccaa
     4561 gaggaaccca cttgtgaagg gcaacaactt cttcaactca tcaaccagca atgccacctg
     4621 tgctaacgga ctacccagtc ctcagagacc cagcgccagc cctgggctac gagttctccg
     4681 ttctccaggt cccaagccca tgcccgggag tgacatccat gagggagaaa gcagtggtga
     4741 gcaggaagtg accccatgac gcgtggccag atgaagaagc aggcacagca ggcgcagcca
     4801 agcaagcagg tgacggggcc ccccacccgg cctggtgatg gccaccctgg gacactgacc
     4861 tcgggtgctc cactgacttc ttctacctcc actgccggtg ctcctgctcc cctgagctcc
     4921 cgcccccgcc ccccaacccc catcccccaa cctcccgaca tctgatgatg tggtgcctcc
     4981 ctcaccccca tcacaccctg caagcaaacc cacccccacc cccaccacat ctgcttcagc
     5041 ttttttgacc ccgccttcct cttgccctga gctctggact tacctggaca aagccgctct
     5101 ttggggcatc cggacgtacc agtgccactt accagacttg cacagcaaag agggcccctg
     5161 catgccttgg ggcgcctttc cctcccaaca ctgaacactg gacagtgcag gggtgcaggg
     5221 gcccctcata cagggatgga gtcccagaag gcacacagac acccagggga ccatgccgag
     5281 tcacagagag gctctggcca caccaccgct ttgcaagggg agtagaccct tccccacccc
     5341 ccgagctttc tcacccccca atctttttgc actcctcaaa taaagcaaac taaaagac
//
