LOCUS       XM_039095924            5269 bp    mRNA    linear   ROD 11-JUN-2023
DEFINITION  PREDICTED: Rattus norvegicus UPF2, regulator of nonsense mediated
            mRNA decay (Upf2), transcript variant X2, mRNA.
ACCESSION   XM_039095924
VERSION     XM_039095924.1
DBLINK      BioProject: PRJNA677964
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_051352.1) annotated using gene prediction method: Gnomon,
            supported by EST evidence.
            Also see:
                Documentation of NCBI's Annotation Process
            
            [WARNING] On Feb 22, 2024 this sequence was replaced by
            XM_039095924.2.
            
            ##Genome-Annotation-Data-START##
            Annotation Provider         :: NCBI RefSeq
            Annotation Status           :: Updated annotation
            Annotation Name             :: GCF_015227675.2-RS_2023_06
            Annotation Pipeline         :: NCBI eukaryotic genome annotation
                                           pipeline
            Annotation Software Version :: 10.1
            Annotation Method           :: Best-placed RefSeq; Gnomon;
                                           cmsearch; tRNAscan-SE
            Features Annotated          :: Gene; mRNA; CDS; ncRNA
            Annotation Date             :: 06/06/2023
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..5269
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN/NHsdMcwi"
                     /db_xref="taxon:10116"
                     /chromosome="17"
                     /sex="male"
                     /tissue_type="kidney"
                     /geo_loc_name="USA: Wisconsin, Milwaukee, Medical College
                     of Wisconsin"
                     /collection_date="2019-03-08"
                     /collected_by="Rebecca Schilling"
     gene            1..5269
                     /gene="Upf2"
                     /note="UPF2, regulator of nonsense mediated mRNA decay;
                     Derived by automated computational analysis using gene
                     prediction method: Gnomon. Supporting evidence includes
                     similarity to: 27 ESTs, and 100% coverage of the annotated
                     genomic feature by RNAseq alignments, including 88 samples
                     with support for all annotated introns"
                     /db_xref="GeneID:361271"
                     /db_xref="RGD:1309178"
     CDS             207..4016
                     /gene="Upf2"
                     /codon_start=1
                     /product="regulator of nonsense transcripts 2 isoform X1"
                     /protein_id="XP_038951852.1"
                     /db_xref="GeneID:361271"
                     /db_xref="RGD:1309178"
                     /translation="MPAERKKSASMEEKESLLNNKEKDCSERRPVSSKEKSKDDLKIT
                     AKKEVSKVPEDKKKKLEEDKRKKEDKERKKKEEEKVKAEEELKKKEEEEKKKQEEEER
                     KKQEEQAKRQQEEAAAQLKEKEESLQLHQEAWERHQLRKELRSKNQNAPDNRPEENFF
                     SRLDSSLKKNTAFVKKLKTITEQQRDSLSHDFNGLNLSKYIAEAVASIVEAKLKISDV
                     NCAVHLCSLFHQRYADFAPSLLQVWKKHFEARKEEKTPNITKLRTDLRFIAELTIVGI
                     FTDKEGLSLIYEQLKSIINADRESHTHVSVVISFCRHCGDDIAGLVPRKVKSAAEKFN
                     LNFPPSEIISPEKQQPFQNLLKEYFTSLTKHLKRDHRELQNTERQNRRILHSKGELSE
                     DRHKQYEEFAMSYQKLLANSQSLADLLDENMPDLPQDKPTPEEHGPGIDIFTPGKPGE
                     YDLEGGIWEDEDARNFYENLIDLKAFVPAILFKDNEKSQNKDSSKDDSKEAKEPKDNK
                     EASSPDDLELELENLEINDDTLELEGGDEAEDLTKKLLDEQEQEDEEASTGSHLKLIV
                     DAFLQQLPNCVNRDLIDKAAMDFCMNMNTKANRKKLVRALFIVPRQRLDLLPFYARLV
                     ATLHPCMSDVAEDLCSMLRGDFRFHVRKKDQINIETKNKTVRFIGELTKFKMFTKNDT
                     LHCLKMLLSDFSHHHIEMACTLLETCGRFLFRSPESHLRTSVLLEQMMRKKQAMHLDA
                     RYVTMVENAYYYCNPPPAEKTVRRKRPPLQEYVRKLLYKDLSKVTTEKVLRQMRKLPW
                     QDQEVKDYVICCMINIWNVKYNSIHCVANLLAGLVLYQEDVGIHVVDGVLEDIRLGME
                     VNQPKFNQRRISSAKFLGELYNYRMVESAVIFRTLYSFTSFGVNPDGSPSSLDPPEHL
                     FRIRLVCTILDTCGQYFDRGSSKRKLDCFLVYFQRYVWWKKSLEVWTKDHPFPIDIDY
                     MISDTLELLRPKIKLCNSLEESIRQVQDLEREFLIKLGLVNDKESKDSMTEGENLEED
                     EEEEEGGAETEEQSGNESEVNEPEEEEGSDDEDEGEEEEEENTDYLTDSNKENETDEE
                     NAEVMIKGGGLKHVPCVEDEDFIQALDKMMLENLQQRSGESVKVHQLDVAIPLHLKSQ
                     LRKGPPLGGGEGETESADTMPFVMLTRKGNKQQFKILNVPMSSQLAANHWNQQQAEQE
                     ERMRMKKLTLDINERQEQEDYQEMLQSLAQRPAPANTNRERRPRYQHPKGAPNADLIF
                     KTGGRRR"
ORIGIN      
        1 gggaaggcgg gccctcggct gcgagatagg tggggggagg ggaggggaga gcccgagctc
       61 tggagttggt gctgggaaac ccggggctaa tgttgacaac aggcactagt ttttaggtgt
      121 tcataaaagt cgtacaaatc atcgggcaag cctttattga gctgtggtga aatttctgaa
      181 aaatttgaat tgtcctgggt cacataatgc cagctgagcg gaaaaagtca gcaagtatgg
      241 aggaaaaaga atctttacta aacaacaagg aaaaagactg cagtgagagg cggccagtga
      301 gcagcaagga gaaatcaaaa gacgatctca agatcactgc caagaaggag gtcagtaagg
      361 tcccagaaga caaaaagaag aaactggaag aagataagag aaaaaaggaa gacaaggaac
      421 gtaagaaaaa agaggaagag aaggtgaagg cagaggaaga gttgaagaag aaggaagagg
      481 aagaaaagaa aaaacaggaa gaggaagaga ggaaaaagca ggaggagcag gccaagcggc
      541 agcaggaaga agcagctgcc cagctgaaag agaaagaaga atctcttcag cttcatcagg
      601 aggcgtggga acgccatcaa ctacgaaagg aactccgtag caaaaaccaa aatgctccag
      661 acaaccgacc agaggaaaat ttctttagcc gcctagattc gagcttaaag aaaaatactg
      721 cttttgtcaa gaaactaaaa acaattacag aacaacagag agactccttg tctcatgatt
      781 ttaatggcct gaatttaagc aaatatattg cagaagccgt agcttccatt gtggaagcaa
      841 aattaaaaat ctctgacgtg aactgtgccg tgcacctctg ctctctcttt caccagcggt
      901 acgctgactt tgcaccctca cttcttcagg tgtggaaaaa acattttgaa gcaaggaaag
      961 aggagaaaac gcccaacatt accaagctaa gaactgactt gcgtttcatt gcagaattga
     1021 caatagtggg aatcttcact gacaaggaag gtctttcctt aatctatgaa cagctaaaaa
     1081 gtattattaa tgctgatcga gaatcccaca ctcatgtgtc tgtggtgatt agtttctgtc
     1141 gtcattgtgg agatgatatt gctggacttg taccgaggaa agtaaagagt gctgcagaga
     1201 agtttaattt gaactttcct cctagtgaga taattagccc agagaagcag cagcctttcc
     1261 agaatctttt aaaagagtac tttacgtctc tgaccaaaca cctgaaaagg gaccacaggg
     1321 agcttcagaa tactgagagg caaaacaggc gtattctgca ctctaaaggc gagctaagtg
     1381 aagacaggca taaacagtat gaagagttcg ccatgtctta ccagaagctg ctggcaaatt
     1441 ctcaatcctt agccgacctt ttggatgaaa atatgccaga tcttcctcag gacaaaccga
     1501 caccagaaga gcatggacct ggaatcgata tatttacacc tggaaaacct ggagaatatg
     1561 acttagaagg tggcatatgg gaagacgaag acgctcggaa tttttatgaa aacctcatcg
     1621 atttgaaagc atttgttcca gccatcttgt ttaaagacaa tgaaaaaagt cagaacaaag
     1681 attctagcaa agatgattcc aaagaggcaa aagaaccaaa ggataataag gaagcatcaa
     1741 gtcccgatga tttggaactt gagttggaga atttagaaat taatgatgac acactggagt
     1801 tagaaggtgg agatgaagct gaagatctta caaagaaact ccttgatgaa caagaacaag
     1861 aagatgaaga agccagcact ggatctcacc tcaaactcat agtggatgct ttcctccagc
     1921 agctgcccaa ctgtgtcaac cgagacctga ttgacaaggc agccatggac ttttgcatga
     1981 acatgaacac aaaggcaaac aggaagaagt tggttcgggc gctcttcata gttcctaggc
     2041 aaaggttgga tttgctccca ttttatgcaa gattggttgc tacattgcat ccctgcatgt
     2101 ctgatgtagc agaggatctt tgttccatgc tgagggggga tttcagattt catgttcgaa
     2161 aaaaggacca gatcaacatt gaaacaaaga ataaaactgt ccgttttatt ggagaactaa
     2221 ccaagtttaa gatgttcacc aaaaatgata cactgcattg tctaaagatg cttctgtcag
     2281 acttttctca tcatcatatt gaaatggcat gtaccctact ggagacctgt ggacggtttc
     2341 ttttccgatc tccagaatca cacctgagga ccagtgtgct tttggagcaa atgatgagaa
     2401 agaagcaagc aatgcacctg gacgcgcgct acgttacaat ggtggagaac gcgtattact
     2461 actgcaaccc accaccagcc gagaagacag tgagaaggaa gcggcctcct cttcaggagt
     2521 atgtccgcaa acttctgtac aaggatctct ctaaggtcac cacggaaaag gttttgagac
     2581 agatgcgaaa gttgccctgg caggaccaag aagttaaaga ctatgtcatt tgttgtatga
     2641 taaacatttg gaatgtgaaa tacaatagta ttcactgtgt agccaacctc ctagcaggac
     2701 tagtgcttta ccaggaggat gttgggatcc acgttgtgga cggagtactt gaagatattc
     2761 gattgggaat ggaggttaat caacctaaat ttaaccagag gcgcatcagt agtgccaagt
     2821 tcttaggaga actttataat tacagaatgg tcgaatcggc tgttattttc agaactcttt
     2881 attcttttac ttcatttggt gtcaaccctg acgggtctcc aagttccctg gaccctcctg
     2941 agcatctgtt tagaattaga ctagtctgca ctattttgga tacctgtggc cagtactttg
     3001 acagaggttc cagtaaaaga aaacttgact gcttccttgt atattttcag cgttatgttt
     3061 ggtggaagaa aagtttggag gtttggacaa aagaccatcc atttcctatt gatatagatt
     3121 acatgatcag tgatacacta gaactgctaa gaccaaagat caaactctgt aattctctgg
     3181 aagaatccat caggcaggta caagacttgg aacgagaatt cttaataaaa ctaggcctag
     3241 taaatgacaa agagtccaaa gattctatga cagaagggga aaatcttgaa gaggatgaag
     3301 aagaagaaga aggaggagct gagacagagg aacagtctgg aaatgagagt gaagtaaacg
     3361 agccagaaga agaagagggt tctgatgatg aagacgaggg agaggaggag gaagaagaga
     3421 atacagatta cctcacagat tccaacaagg agaacgagac tgatgaagag aatgctgagg
     3481 tgatgattaa gggaggcgga ctgaagcatg ttccttgtgt agaagatgag gacttcattc
     3541 aagctctgga caaaatgatg ctagaaaacc ttcagcagcg aagtggtgaa tctgtgaaag
     3601 tacaccaact tgatgttgct attcctttgc atctcaaaag ccagctgagg aaagggcccc
     3661 cacttggtgg tggggaagga gagacagagt ctgcagacac gatgccgttt gtcatgctga
     3721 caaggaaagg caataaacag cagtttaaga ttctcaatgt gcccatgtca tcccaacttg
     3781 ctgcaaatca ctggaaccag caacaagcag aacaagagga gaggatgagg atgaaaaagc
     3841 tcaccttaga catcaacgaa cgacaagaac aagaagatta tcaagaaatg ttgcagtctc
     3901 tcgcacagcg cccagctcca gcgaacacta atcgtgagcg gcggcctcgt taccaacatc
     3961 caaagggagc gcctaatgca gatctaatct ttaagactgg tgggaggaga cgttgatcca
     4021 gcagcacgtg tcatttcatt aggtcctgta tctgatgttg tggatagtgg agtcctccag
     4081 caattgaatg agagcagcgg acacatctca gcatgtcggt ctagagagtt gcgaatctaa
     4141 acctgggaca ggctggggcc atgaggcaga aacaccagcc tctgccaaca ccggaacaag
     4201 ccgacgcttc cagacaaggc agaaaggcct tttgtaatgg aaatcacgtg agggttaatc
     4261 ttctcttgag aatggcagtc aagaaatgag aaggttcact tgactgctga gagctacacc
     4321 aggaagagcg tccgtgaggt gactgagccg gagaggaaac ggttgagatg ggatggtatg
     4381 ggggaaatga acttgagttt taaacttgat ttaagttaca gtgtctctga attgaacatc
     4441 ccatgttgga agaagataca tttgggggct ccaggactac agtagaacag tatagagcaa
     4501 gcagtaaaat cttctagtaa aacttccatg caggacagca aaatgatgca agatatccaa
     4561 atgccagaca agccgccagg aaaggtctgt gtaaggagtt tgtttcaaga gggacaaggg
     4621 atgagggaga aaaacctgtt ttaaccatca gagtcagtga tgtaaagttg cctattagag
     4681 tgaaagaaaa ctgaagactg ttaatatgca aagcattcat tcagatggct tagaaggtct
     4741 gacagcagcc taagaacggg gatgtagttg agcccattgt aagtatcatt gaaaacaagc
     4801 cgtgccagtg agcatgtcac agaagaagga aggacgacag aagtggatca gagtatttgg
     4861 ttgaccttca tgggtttaca gcctctgtgt ctaaacaagc tatggaaaca agtagagctt
     4921 ttactttgct tttgtttcgt ttccttttgt tccccttccc cagtagaaat gagggttctt
     4981 agtctgtttc tgacagtctg ttaatttatt aggataggtg tctttcattt gcttcccagt
     5041 aggcgtagtc atttagttaa cagacacatc tgtatgctac aacttgatta catctttttc
     5101 tattttgcat ctttctttta ccatgtttca gtttctgcat gtagatttca ataagaaaca
     5161 aaacttgtaa agttgtaaca tttcacatgg aaatgctgcc caatcttcac cagcttcaga
     5221 aatctgacct ttgccgatgc tgcaataaag tgttgtaatt tggatttgg
//
