LOCUS       NM_001395362            3451 bp    mRNA    linear   PRI 27-OCT-2024
DEFINITION  Homo sapiens retrotransposon Gag like 4 (RTL4), transcript variant
            2, mRNA.
ACCESSION   NM_001395362
VERSION     NM_001395362.2
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 3451)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   2  (bases 1 to 3451)
  AUTHORS   Irie,M., Koga,A., Kaneko-Ishino,T. and Ishino,F.
  TITLE     An LTR Retrotransposon-Derived Gene Displays Lineage-Specific
            Structural and Putative Species-Specific Functional Variations in
            Eutherians
  JOURNAL   Front Chem 4, 26 (2016)
   PUBMED   27446905
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 3451)
  AUTHORS   Zemunik,T., Boban,M., Lauc,G., Jankovic,S., Rotim,K., Vatavuk,Z.,
            Bencic,G., Dogas,Z., Boraska,V., Torlak,V., Susac,J., Zobic,I.,
            Rudan,D., Pulanic,D., Modun,D., Mudnic,I., Gunjaca,G., Budimir,D.,
            Hayward,C., Vitart,V., Wright,A.F., Campbell,H. and Rudan,I.
  TITLE     Genome-wide association study of biochemical traits in Korcula
            Island, Croatia
  JOURNAL   Croat Med J 50 (1), 23-33 (2009)
   PUBMED   19260141
  REMARK    GeneRIF: Observational study and genome-wide association study of
            gene-disease association. (HuGE Navigator)
REFERENCE   4  (bases 1 to 3451)
  AUTHORS   Brandt,J., Schrauth,S., Veith,A.M., Froschauer,A., Haneke,T.,
            Schultheis,C., Gessler,M., Leimeister,C. and Volff,J.N.
  TITLE     Transposable elements as a source of genetic innovation: expression
            and evolution of a family of retrotransposon-derived neogenes in
            mammals
  JOURNAL   Gene 345 (1), 101-111 (2005)
   PUBMED   15716091
REFERENCE   5  (bases 1 to 3451)
  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
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AL031388.1, AL929583.5, AL031176.8 and BX088563.4.
            
            On Jun 30, 2021 this sequence version replaced NM_001395362.1.
            
            ##Evidence-Data-START##
            CDS exon combination :: SRR1803616.268559.1 [ECO:0000331]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000695839.1/ ENSP00000512211.1
            RefSeq Select criteria :: based on manual assertion, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-102               AL031388.1         61238-61339
            103-221             AL929583.5         4033-4151
            222-381             AL031176.8         69775-69934
            382-436             BX088563.4         27182-27236
            437-3451            BX088563.4         50568-53582
FEATURES             Location/Qualifiers
     source          1..3451
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="X"
                     /map="Xq23"
     gene            1..3451
                     /gene="RTL4"
                     /gene_synonym="Mar4; Mart4; SIRH1; SIRH11; ZCCHC16"
                     /note="retrotransposon Gag like 4"
                     /db_xref="GeneID:340595"
                     /db_xref="HGNC:HGNC:25214"
                     /db_xref="MIM:301131"
     exon            1..102
                     /gene="RTL4"
                     /gene_synonym="Mar4; Mart4; SIRH1; SIRH11; ZCCHC16"
                     /inference="alignment:Splign:2.1.0"
     exon            103..221
                     /gene="RTL4"
                     /gene_synonym="Mar4; Mart4; SIRH1; SIRH11; ZCCHC16"
                     /inference="alignment:Splign:2.1.0"
     exon            222..381
                     /gene="RTL4"
                     /gene_synonym="Mar4; Mart4; SIRH1; SIRH11; ZCCHC16"
                     /inference="alignment:Splign:2.1.0"
     exon            382..436
                     /gene="RTL4"
                     /gene_synonym="Mar4; Mart4; SIRH1; SIRH11; ZCCHC16"
                     /inference="alignment:Splign:2.1.0"
     exon            437..3451
                     /gene="RTL4"
                     /gene_synonym="Mar4; Mart4; SIRH1; SIRH11; ZCCHC16"
                     /inference="alignment:Splign:2.1.0"
     CDS             666..1598
                     /gene="RTL4"
                     /gene_synonym="Mar4; Mart4; SIRH1; SIRH11; ZCCHC16"
                     /note="zinc finger CCHC domain-containing protein 16; zinc
                     finger CCHC-type containing 16; Sushi-Ichi retrotransposon
                     homolog 11; mammalian retrotransposon-derived 4; mammalian
                     retrotransposon-derived protein 4; zinc finger, CCHC
                     domain containing 16"
                     /codon_start=1
                     /product="retrotransposon Gag-like protein 4"
                     /protein_id="NP_001382291.1"
                     /db_xref="CCDS:CCDS35369.1"
                     /db_xref="GeneID:340595"
                     /db_xref="HGNC:HGNC:25214"
                     /db_xref="MIM:301131"
                     /translation="MEKCTKSSSTMQVEPSFLQAENLILRLQMQHPTTENTAKRGQVM
                     PALATTVMPVPYSLEHLTQFHGDPANCSEFLTQVTTYLTALQISNPANDAQIKLFFDY
                     LSQQLESCGIISGPDKSTLLKQYENLILEFQQSFGKPTKQEINPLMNAKFDKGDNSSQ
                     QDPATFHLLAQNLICNETNQSGQFEKALADPNQDEESVTDMMDNLPDLITQCIQLDKK
                     HSDRPELLQSETQLPLLASLIQHQALFSPTDPPPKKGPIQLREGQLPLTPAKRARQQE
                     TQLCLYCSQSGHFTRDCLAKRSRAPATTNNTAHQ"
     regulatory      3434..3439
                     /regulatory_class="polyA_signal_sequence"
                     /gene="RTL4"
                     /gene_synonym="Mar4; Mart4; SIRH1; SIRH11; ZCCHC16"
                     /note="hexamer: AATAAA"
     polyA_site      3451
                     /gene="RTL4"
                     /gene_synonym="Mar4; Mart4; SIRH1; SIRH11; ZCCHC16"
                     /note="major polyA site"
ORIGIN      
        1 gccttctttg cagctccgcg gccaggggtg gaaggaagcc gcagccgcag ccccaagtca
       61 acccccgctg ccccgtccca ccgtctcatc tctcccccct cgcagagacg gggtttcacc
      121 atgttagcca ggatggtctc gatctcctga cctcgtgatc cacctgcctc ggcctcccaa
      181 actgctggga ttacaggcgt gagccactgc gccctgcctg gaatgtacat gcatgcaggg
      241 ctccaggaga agaatttacc atgtgtaatc tcacttaagc gtcatgaaat cctgtaagaa
      301 aggtcaattc tattatcctc attttacaag tgagaaaacg aagccttgga gagattccat
      361 gacctgcccg aggtcacaca ggtaccacag gatgactgaa ggggtttgga tttgtatatt
      421 tcccttctcc tacatgacca ttggcctttt ccatgaagaa gaggcaacat tgagtggcgg
      481 acaacacttt ttggcatctc tccaattcag ctgttagcat ctcctagtgt cttcttcaca
      541 gctaacagct ttggctactt gctcatgaca ctccgtctct gatcacagag caaatccact
      601 gtctccattg gtttccagta ctagtactca attctactca atcccacctg attccaggag
      661 acataatgga gaagtgcacg aaatcatcat ctaccatgca ggtagagcct tcctttcttc
      721 aggcagagaa tctgattctg cggcttcaaa tgcagcatcc aaccacggag aacactgcta
      781 aaaggggcca agtcatgcct gccctggcca ccacagtgat gcctgtacca tactcacttg
      841 agcatctcac ccagtttcat ggtgaccctg ccaattgctc agagttcctc actcaggtga
      901 ctacctactt gacagctctc caaatctcta atcctgcaaa tgatgcccag atcaaactct
      961 tttttgatta cctatctcag cagttagaaa gttgtgggat catatctggg cctgacaaga
     1021 gtaccttact gaagcaatat gagaatctta ttcttgagtt ccagcagtca tttggtaaac
     1081 ccacaaaaca ggaaatcaat cctctgatga atgctaagtt tgacaaagga gacaactcct
     1141 ctcagcagga ccctgctact ttccacctcc tcgctcaaaa tctgatctgt aatgaaacca
     1201 atcagagtgg tcagttcgaa aaggcactag ctgatcccaa ccaggatgaa gagagtgtca
     1261 ctgatatgat ggacaatctt ccagacctga tcactcagtg cattcagttg gacaagaaac
     1321 atagtgacag gccagagctc ctacagtcag agacccagct cccattgttg gcttccttga
     1381 tccaacacca agccctcttt agccccacag atccaccacc caagaaaggg cctatacagc
     1441 tgcgagaagg ccagctgcct ctcaccccag ccaaacgagc ccgccagcaa gaaactcagt
     1501 tgtgcctcta ctgcagccaa tctggtcact tcacaagaga ttgccttgcc aaacgttctc
     1561 gagctccggc aacgacaaat aacacagctc accagtaaga ggagaccagg aaagtcactt
     1621 tttaaactta catcccagcc ttactgattt ataacctgca ttaactttta aaatacagat
     1681 ggggaactgt gacaccactt tataggcagt tatgaactga cacgctttgg gggaatttaa
     1741 acaatcagat cttgttcatt ggcaaattac ccctcacgaa acctaacccg agaatgatga
     1801 aaacaattca caggcacttt ctgcagttgg gattaattct ccaagagcac caaaaacctg
     1861 caggcaaaac tttgcccagt ctgagccaat gaaaataacc gtggaagcac attgggaacc
     1921 ttatcctgac caatgggtga catctgggtt gagtttgtgt cccaaatcct gaatcttgtg
     1981 tgcctagaaa tgagcccaag acttttacct tcacctttat tggtctgtat cctagtttcc
     2041 tgttggctta ggacctttgg ctgaagtcca aatgacattc ctataatctg cttatattct
     2101 cctcctagag tttggaccat gcttcaccta ttgactacga tctaccttca gcataaatca
     2161 accttcctgg aaccacagct ctgccaccct tccatagagc tatatgtttt gtttccatct
     2221 aaagactcat gctttcccaa caaacagaac ctcctggcta tttacaaacc agattgaatg
     2281 ggcatttgaa tactgcttgg aactgttggt ccctttttct ttgcaggcta gcccatcagg
     2341 caggtgtatg cttttagcca agcccaccaa ttccaactta ttcctctctt ctccaacaac
     2401 cctacttgag gttccagcat gtcttatagc caagtcaata tgctctagga taaggatttc
     2461 tgaaaggtat ttagtgagag ttggggatgg tgtgtcataa ttactgtatc tgtagcatgt
     2521 ccttgctgcc ttggacaagg gacctggcca aataaatctc cactgaagac tgacagccag
     2581 accctgcagt agtttctaac tctagaagcc tcaatgtagt caccatctag gattactact
     2641 cattgctatt gagctctacc tttatggacc acctctgaag tccttcatct aattgaggat
     2701 cttaaaaaac aatgaatggc aaaaaacttc ctacactatc tcatctgaaa aatcctgggg
     2761 cacatacatt aaaaccattt gtgcacaaaa ctcaggaagt cgggatttta ttgcttatgt
     2821 tttactcttg gtacacacca gctttgtgta gattcctgat gcttctgaac aaaagtagtg
     2881 ttatgctaga aaggcaaaac tccctaaaat gttaaaactg ttcagcaatg atcactgctg
     2941 gtaattacca gccctctgtt ccctgcttct tgtttctgat gtatgtcccc aaaatggata
     3001 tcctggagaa atatcagtaa tcacatattc cctagcaacc atcaaggcct ctcagaacat
     3061 gaaatcccat tgtactttgg ctttgtttct ggagaattat gctaactttg acaatactta
     3121 aacctaacta ggaccttact actctgattc tgtagcacca ataaatagat attttcacct
     3181 tgtgccttgc tagccactgt aacaattctt atttgcattc acgaatggtt tcttttaaca
     3241 acggctcgct gcacaaccac attactctat atgctcccac aacagagacc tgagttaaca
     3301 tattccagtt atgctaagaa attccgacta tagtactggg attgtatgag atcctctaac
     3361 aagtagagct attgaacgta gagtgactct gaaattacct ggaagtatct tgttctacct
     3421 ccatcaattc tataataaag gactaacctc a
//
