LOCUS       XM_008773476            5365 bp    mRNA    linear   ROD 22-FEB-2024
DEFINITION  PREDICTED: Rattus norvegicus retrotransposon Gag like 9 (Rtl9),
            transcript variant X1, mRNA.
ACCESSION   XM_008773476
VERSION     XM_008773476.2
DBLINK      BioProject: PRJNA1074393
KEYWORDS    RefSeq.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
COMMENT     MODEL REFSEQ:  This record is predicted by automated computational
            analysis. This record is derived from a genomic sequence
            (NC_086039) annotated using gene prediction method: Gnomon,
            supported by EST evidence.
            Also see:
                Documentation of NCBI's Annotation Process
            
            On Jan 21, 2021 this sequence version replaced XM_008773476.1.
            
            ##Genome-Annotation-Data-START##
            Annotation Provider         :: NCBI RefSeq
            Annotation Status           :: Full annotation
            Annotation Name             :: GCF_036323735.1-RS_2024_02
            Annotation Pipeline         :: NCBI eukaryotic genome annotation
                                           pipeline
            Annotation Software Version :: 10.2
            Annotation Method           :: Best-placed RefSeq; Gnomon;
                                           cmsearch; tRNAscan-SE
            Features Annotated          :: Gene; mRNA; CDS; ncRNA
            Annotation Date             :: 02/09/2024
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..5365
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN/NHsdMcwi"
                     /bio_material="RGD 61498"
                     /db_xref="taxon:10116"
                     /chromosome="X"
                     /sex="male"
                     /tissue_type="kidney, spleen, liver"
                     /geo_loc_name="USA: Wisconsin, Milwaukee"
                     /lat_lon="43.05 N 88.04 W"
                     /collected_by="Rebecca Schilling, Melinda Dwinell"
     gene            1..5365
                     /gene="Rtl9"
                     /gene_synonym="Rgag1"
                     /note="retrotransposon Gag like 9; Derived by automated
                     computational analysis using gene prediction method:
                     Gnomon. Supporting evidence includes similarity to: 2
                     ESTs, 5 long SRA reads, 3 Proteins"
                     /db_xref="GeneID:100912526"
                     /db_xref="RGD:6486824"
     CDS             220..4341
                     /gene="Rtl9"
                     /gene_synonym="Rgag1"
                     /codon_start=1
                     /product="retrotransposon Gag-like protein 9 isoform X1"
                     /protein_id="XP_008771698.1"
                     /db_xref="GeneID:100912526"
                     /db_xref="RGD:6486824"
                     /translation="MADMSIPLHSLRFNNMMKEESGDPQNRGATFPRPMTETRAEVQI
                     LHSQLQLPTVSTSTSDPEGTSTQLTTSPAFDSLSTPLMGASHSGTVSPPLMSASDSGT
                     LSPLLMTASDSGTLSPLLMPVSDSGTLSPLLMPTSDSGTLSPLLSTSDYGLMSPGMMT
                     IPDFGTMSTSLMAAPDSAEMSPLAMPVPSAGVMSAPIMSTSPSEASLMLGSDPGEMSP
                     LLIPDMNPGVTSTPPMTAPGSEAMSPLQITDEDTEAMSKVLMTALASGEISSLLMSGT
                     DSEVISSLIMSALASGETSTQPTNPQDSEGIPSVLMPGSDSGVMSSLPMPASGSGAMP
                     APLLSIPDAGEITLPKPVPDAEAMSPLLMTALTSTVMPSQLMSASGSGVMSPDVTQNI
                     NSEVMTAPPLRVAASGLMSTLPTRTSDTEAAPIQLMRVPASGNMSTSQKTVPVSGSMS
                     TPLMAVSSPVAMFTEEMSNTTSGMMSTHLTMPQTSGMMPIGFMKATANGAVSAQQMRG
                     SASGMMPTQPVIATASEIMSVSQSTVPTSGSVSTQKTRAPVSGPMSTTQIRTTASGLT
                     STPQMKATASGTMSIPLMTAKTSGSASTLLMRDTASGVISVPQMRAPSSGSLSKPLMT
                     SKASGMFMQQMTTAAFGATPTSLIRDTASGGLSMPQMTDPASGGMSTLLTRATASGAT
                     STSQMTATTSGGMSMLQTRLSGPGATATSLMRATASEMIPSQPVNMQDSGGVAIPLMR
                     PVALGGMQMRSQGSGTMSTPLLRASDSSEMSTLLTKAPSSGERPLLLMRPPASGEIVP
                     PPRTPVYGTISAPHMTTTASGVMTMSPMKASVPASESTALQRSTDSGGMSTPLMRTAV
                     SRTKPIPQMMTTACGDVCPCPVRAAATAGISPSPVRPLASSTVSTPLRRPSDGAGTAE
                     LERVLGPGIMSSAQLAAMTSGEMSKPLMRASAPGTTPMPLMSPMTSGEMSMPLMKTMP
                     SGTMSTLQTKVMSSRATSLPQPINAASGGIANPPLRAPASGAVSTPLMRVSGSGMMPM
                     PLLRATASGGISVPQVTAPSSGDVSSPLLRAPTPGIMSTPQTAFGMTPALNIKVTDSG
                     EASTSHTRVTAPGYKSTPHTTSTVPEVKTPPPKEVPSFGMLTPALCYLLEEQEAARGS
                     SSVEEDEEEIDEEKQMKGFLDDSEKMAFLVSLHLGAAERWSILQMEVGNPVSSENKAF
                     LRRSQGLYDSLSEIDILSAVLCHPKQGKKSVRQYATDFLLLARHLSWSDAILRTRFLE
                     GLSEAVTTKMGRIFLKVAGSLKELIDRSLYTECQLAEEKDSSGNASQVVPTACKRNNE
                     EAMENELGCQQQTEEHQHVPKRCYYLKEHGDPQESLHDHLRQSAGLPKAPTNK"
     polyA_site      5365
                     /gene="Rtl9"
                     /gene_synonym="Rgag1"
                     /experiment="COORDINATES: polyA evidence [ECO:0006239]"
ORIGIN      
        1 tcaagtctga cattcttgtc atctgtttga aacctaacta gcctaacttt gcagaatgga
       61 cactggccac cagatttctc tctgtcattg tcactggggc ataatgaatt ttgaaagtgc
      121 tcatgactat ggcttggcta ttaagatttc attgatttgt gggtttcatc agcgcctctg
      181 atgtcaacac aataaagtcc gaaacgctgc cttgtagcca tggcagatat gtcaatacca
      241 ttgcattcat tacgattcaa caacatgatg aaagaggaaa gtggtgaccc tcaaaacagg
      301 ggggcaactt tccctagacc aatgacggag accagagcag aggttcaaat cctgcattca
      361 cagttgcagt tgcctactgt ctcaacttca acctcagatc ctgaagggac atctacacag
      421 ctgacgacat cgccagcctt tgacagtctg tctacacctc tcatgggagc gtcacactct
      481 gggacagtgt ccccaccact gatgtcagcc tcagactctg ggacactgtc cccattgcta
      541 atgacagcct cagattcagg aacactgtcc ccacttctaa tgccagtctc agactctggg
      601 acactgtctc cactgctaat gccaacctca gattctggaa cactgtcccc attgttgtct
      661 acttcagact atgggttaat gtctccaggg atgatgacaa ttcctgactt tgggacaatg
      721 tcaacatcac taatggcagc cccagattcg gcagagatgt caccactggc gatgccagtt
      781 ccatccgctg gagtgatgtc tgcacctata atgagcactt caccttctga ggcatcgtta
      841 atgctagggt cagatcctgg tgagatgtca ccactcctga ttccagatat gaaccctgga
      901 gtgacatcca caccaccaat gacagctcca ggctcagaag caatgtcccc attgcaaatt
      961 accgatgagg acacagaagc aatgtccaaa gtgttaatga ctgccctagc ttctggagag
     1021 atatcatccc tgttgatgtc aggcacagac tctgaagtga tatcatccct gataatgtca
     1081 gccctagcct ctggagaaac atcgacccag ccaacaaacc ctcaagactc tgaagggata
     1141 ccttctgtgc tcatgccagg ctcggactct ggagtcatgt cttcactgcc tatgccagct
     1201 tctggctctg gagcaatgcc tgcaccactt ctgtccatcc cagatgctgg agaaatcaca
     1261 ttaccaaagc cggtcccaga tgctgaggca atgtccccac tgttaatgac agccctcacc
     1321 tctacagtga tgcccagtca actgatgtca gcatctggtt ctggagtgat gtccccagat
     1381 gtaacacaaa atatcaactc tgaggtcatg actgctccac cattaagagt tgcagccagt
     1441 ggattgatgt ccacactacc cacaagaact tctgatacag aggcagcacc catccagcta
     1501 atgagagtcc ctgcctcagg aaatatgtct acatcacaaa agacggttcc agtctctgga
     1561 tcaatgtcca ctccactgat ggctgtctca agccctgtag caatgttcac agaagaaatg
     1621 tcgaacacaa cctctggtat gatgtctaca catttaacaa tgccccaaac atctggaatg
     1681 atgcctatag gttttatgaa ggccacagca aatggagctg tctctgcaca gcaaatgaga
     1741 ggttcagctt ctgggatgat gcccacacag ccagttatag ctacagcctc tgaaataatg
     1801 tccgtgtcac aatcaacagt cccaacctct gggtcagtgt ccacacagaa aactcgagct
     1861 cctgtctctg gaccaatgtc tacaacccaa ataagaacca cagcctcagg attgacatct
     1921 acaccacaaa tgaaagccac agcctctgga acaatgtcta tcccactaat gacagccaaa
     1981 acctctggat cagcatccac actgttaatg agagacacag cctcaggagt gatatccgtg
     2041 ccacagatga gagctccaag ctctggatca ttgtccaagc cactaatgac atccaaagct
     2101 tctggaatgt tcatgcagca aatgacaact gcagcttttg gagcaacacc tacatcacta
     2161 ataagagaca cagcttctgg aggtctgtct atgccacaga tgacagatcc agcctcagga
     2221 ggcatgtcca cactgctaac gagagccaca gcttcgggag caacgtctac atcacagatg
     2281 acagccacca cctctggagg catgtccatg cttcaaacaa gactctcagg tcctggagca
     2341 acagccacat cactaatgag agccacagcc tctgagatga tacctagtca gccagtgaac
     2401 atgcaagact ctggaggggt ggccatacca ctcatgagac ctgttgcctt gggagggatg
     2461 caaatgagat cccagggctc tggaacaatg tccacacccc tcttgagagc ctcagactca
     2521 tcagagatgt ctacattgct cacaaaagcc ccatcctctg gggagcggcc tctgctacta
     2581 atgagacctc cagcatctgg ggagatagtt ccacctccta gaaccccagt ttatgggacg
     2641 atatctgctc cacacatgac aaccacagcc tcaggagtga tgacgatgtc tcctatgaag
     2701 gcttctgtcc ctgcatcaga gtcgacagct ctccagagat ccacagattc aggagggatg
     2761 tccacaccac tgatgagaac agcagtttct agaacaaagc ctatcccaca aatgatgacc
     2821 acagcttgtg gagacgtgtg tccgtgccca gtgcgagctg cagccactgc agggatctct
     2881 ccatcaccag tcagaccact agcttcttcg accgtgtcta caccacttag gagaccctct
     2941 gatggagctg ggaccgcaga gttagagaga gttctaggcc ctggaattat gtcctctgca
     3001 caattggcag ctatgacctc aggagagatg tccaagccac tgatgagggc ttcagcccct
     3061 ggaaccacac ccatgccttt gatgtccccc atgacttctg gagagatgtc tatgccacta
     3121 atgaaaacca tgccttctgg gacaatgtca actctacaaa ccaaagtcat gagctctaga
     3181 gctacatctt taccacagcc aataaatgca gcttctgggg gaatagctaa tcccccactg
     3241 agagccccag cctctggagc agtgtctaca ccacttatga gagtctcggg ttcaggaatg
     3301 atgcccatgc ctctactgag ggctacagcc tcaggaggaa tatctgtgcc acaagtgaca
     3361 gctccaagct ctggagatgt gtcctcacca ctattgaggg ccccgacacc tggaataatg
     3421 tccacaccac aaacagcctt tggaatgaca cccgctctga atatcaaagt cacagactca
     3481 ggagaggcat ctacctctca caccagagta acagcccctg gatacaagag cacaccacac
     3541 acaacaagca cagtccctga agtgaagacg ccaccaccaa aggaagtgcc gtcctttggt
     3601 atgttgaccc cggcactctg ttacctctta gaagagcaag aagcagcccg gggctcatcc
     3661 tcggtggagg aagatgaaga ggagattgat gaggagaaac aaatgaaggg ttttttagat
     3721 gattctgaga aaatggcatt tctagtgtcg cttcatctgg gggcagcaga gagatggtcc
     3781 atcttgcaga tggaagtagg aaaccccgta tccagtgaaa ataaagcttt cttgagaaga
     3841 tcacagggct tatatgactc cctgtctgag atagacatcc taagtgctgt tctttgccat
     3901 cccaagcagg gcaaaaagtc agtaaggcag tatgccactg acttcctgct gctggcccga
     3961 catttgtctt ggtctgatgc cattctacgg accaggtttc tggaaggact ctcagaagct
     4021 gttaccacca aaatgggccg tatcttcctg aaggtggccg gcagcctgaa ggagctgata
     4081 gataggtctc tgtacaccga gtgccagctg gcggaagaga aggattcctc aggcaatgca
     4141 agccaagttg tgccaacagc ctgtaagcga aacaacgagg aggccatgga gaatgaactg
     4201 ggctgtcagc agcagactga ggagcaccag catgttccca aacgctgtta ctacttgaaa
     4261 gaacatggag acccccagga aagtcttcat gaccaccttc gacagagtgc aggccttccg
     4321 aaggccccta ccaacaagta gtactccttg gaatcttatg tggtttctga cttggctgct
     4381 aacttgagga ctggttcctg gacccattcc attcaacata aaacgtgttg ccttcaccct
     4441 tcagccttcc cctccaggca catcccactt tatctccctt ttggttgcct tgacattttt
     4501 tcacctacat gcctgtgacc tgccctgaca atcagtgtga actttaagag tgtgtggtgt
     4561 atgagcttct gaactcccat cattgtcatt aagaccagtt ccaattcttg gtccagggag
     4621 aagtctaggc aggagaaatc atgtcctacc tcaaaacacc ttagagtgtc ttgccatatg
     4681 tcatcaggca aacttgagga aaccctggta ctattacacc tggcagggaa gcctataaag
     4741 agagagatac ccactcctat accatccttt cagccagtag acttgccctt atatgtccca
     4801 gttcatagta tctaaatggg tctccagggc ctttgccctg tttatagtct caatcctaaa
     4861 ccatttgttt tgacccatga tattaatagt agtgatagta atggctaaca atgtggtgtt
     4921 gttggtactt gccatgtgat tgttggtaat gtgccatgtg acaggtactg ggttaaacct
     4981 ttgacaaaca ccatctcact acagcgttat agtaacctaa cttgttcttg tgttgttagc
     5041 ttctgatctc ttgatctgtt gcttatggcc cttgttcatc agtgtggaat ctctagctat
     5101 gacctctggg tgatcccctc agttgttaat tacccttgct ccccttggct gttgtgcttc
     5161 atggccaaca ctcttcataa gggccttggt gtctaaacag gtgtaggtag ttagaacata
     5221 atatgaacag tgtttgccta caggtggtgg gttatgggta tttttttatt ttctttttac
     5281 tgttctctgt actttccaga ttcaccacag taagcatgta ttacatttgt aatcataaaa
     5341 ataaaggtta tttgtggaaa atgaa
//
