LOCUS       NM_001346303            3737 bp    mRNA    linear   ROD 09-APR-2024
DEFINITION  Rattus norvegicus Smg5 nonsense mediated mRNA decay factor like 1
            (Smg5l1), transcript variant 2, mRNA.
ACCESSION   NM_001346303
VERSION     NM_001346303.1
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     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000007.1.
            
            Transcript Variant: This variant (2) differs in the 5' UTR, lacks a
            portion of the 5' coding region and initiates translation at a
            downstream start site compared to variant 1. The encoded isoform
            (2) has a shorter N-terminus than isoform 1.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR26360190.2170939.1,
                                           SRR26360194.1044639.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN12840105, SAMN12840106
                                           [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-108               JAXUCZ010000007.1  77802221-77802328
            109-198             JAXUCZ010000007.1  77816831-77816920
            199-325             JAXUCZ010000007.1  77909039-77909165
            326-3737            JAXUCZ010000007.1  77933075-77936486
FEATURES             Location/Qualifiers
     source          1..3737
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="7"
                     /map="7q31"
     gene            1..3737
                     /gene="Smg5l1"
                     /gene_synonym="RGD1309489"
                     /note="Smg5 nonsense mediated mRNA decay factor like 1"
                     /db_xref="GeneID:314915"
                     /db_xref="RGD:1309489"
     exon            1..108
                     /gene="Smg5l1"
                     /gene_synonym="RGD1309489"
                     /inference="alignment:Splign:2.1.0"
     exon            109..198
                     /gene="Smg5l1"
                     /gene_synonym="RGD1309489"
                     /inference="alignment:Splign:2.1.0"
     exon            199..325
                     /gene="Smg5l1"
                     /gene_synonym="RGD1309489"
                     /inference="alignment:Splign:2.1.0"
     exon            326..3737
                     /gene="Smg5l1"
                     /gene_synonym="RGD1309489"
                     /inference="alignment:Splign:2.1.0"
     CDS             364..3285
                     /gene="Smg5l1"
                     /gene_synonym="RGD1309489"
                     /note="isoform 2 is encoded by transcript variant 2"
                     /codon_start=1
                     /product="similar to Est1p-like protein B isoform 2"
                     /protein_id="NP_001333232.1"
                     /db_xref="GeneID:314915"
                     /db_xref="RGD:1309489"
                     /translation="MEKNQEETLRATFLYQEVCLAAQRLDIFLQKENAHKEVFKPHVL
                     ALREMLQQACIKLMFLHPVVYGRKAEELLWRKIYSDIVMLLMKTNKKQMDTFQHWGEP
                     LQAHLKAGLKFYEHLFLFLQGHYELRLQSYIDWPHNAIHLIGCKKVGPTSVEEASWAR
                     MACHRCLLYLGDLFRYQHEFLDLATKNLAERCYYRALSVAPNMGMPFNQLGALMGSKY
                     YDLEATYYYQRCLHAEVPFKGAAWNLKRLYDHAGKRYSCLKRYQGRKLSHSQRQCWDN
                     KRLLVSFLYLQSLLQPKRKFKAARLIALCQLVLDDFRLCLSYRPYQSGLCQASIEDKP
                     PKGYLFLPDFLIFHMVVLCLMNVHSLRKSGSKQQKPAVIFTLTLFSYLVQHVNTRIQA
                     ELQKRKLTPEEAALRDGCWDKEPGKEHQDFPSPGLQNNHSQKSHKWSGICRESEASFH
                     SCCDSDETEEDENSSLSSQAQSDTGSETSHSDTTDEEGSGSLGSDEIQKSGGSPKPKR
                     AHSRNKLKAYVPPDSLLDLLKTTISSSLPAPLSQKLQGKHASPLAPVFSHNVLTPPTD
                     PTPTVALSSSLGTEGEISSFPETEFYMGSSWEQRSFITQNNLQTTQWKLDILSAEGLL
                     PTIKVILSWLRSNHSLLLSHWRSVCSLWDHLSVLLNLLPSVGDLQHPGLCLSHHLQDL
                     LQSCQWPNTPKYLQLPEDIALFQQSSPQVSQDREGLGQDPPQLTNQEEVIVRICFFRS
                     FGHFATRLPGQFLRFDSKLGIFVSSTLERSESAPQQFPRTTPRIRLSKDIVQLWLQRE
                     VALLEKTLRSPQTRSVLTPYLFPDPRALCEHLSVIQKLATSAKFFLIIPKIVVDTLYI
                     LKWEDRRALAAITFLEDELKRRNQYILCQSFVSKRLVRPRMTKPDSDAWDLYNILEFC
                     KSLLDSSRPGILDPSSMVMIITGVCLEHPRNFSYPLQLVLGMATEAGVEIKNILSFHK
                     E"
ORIGIN      
        1 aaaagaaact gcattctggg gcatcctggg attttttttt gtggtggggt ggagacccat
       61 atttttctta ccagggagag agctgcctgt tttcctgtaa gagcttgtgc catttctgcc
      121 aaatatgaat gtgttttaga agactacagg atgaatgcat gaatgcagtt cagactgagg
      181 caaggccatg ctgagacgat attcagtcat cagtgagcat ctgctgcatg aagaaaactg
      241 taattattga ctttggactt aatttggatg ttcacacagc cgtagtcaga cagtgctttg
      301 atattttttc tcctggacag cctgggaaac actgtaagca ttgctcaaaa agaatctggc
      361 ctcatggaga aaaaccagga ggaaaccctg agagccacat tcctctacca ggaggtctgc
      421 ttggcagctc agagactaga tatcttcctt caaaaagaaa atgcccacaa agaggttttt
      481 aagcctcatg tcctggctct cagagagatg cttcagcaag cctgtattaa actcatgttc
      541 ctccatccgg tggtttatgg taggaaggct gaagagctct tatggaggaa aatatactct
      601 gacattgtca tgctgctcat gaagaccaac aagaaacaaa tggacacttt ccaacattgg
      661 ggagagcctc tccaggctca cctgaaggct ggcctcaagt tctatgagca tctcttcctg
      721 ttccttcagg gccactatga attgaggtta cagagctaca ttgattggcc tcacaatgcc
      781 atccacttga ttggatgtaa gaaagtggga cccacatcag tggaagaggc ttcctgggcc
      841 cgcatggcct gtcatcgctg cctgctctac ctgggagact tgttccggta tcagcatgag
      901 ttcctagacc tggctactaa gaacttggca gagagatgct actacagagc cttgtcagtg
      961 gccccgaata tgggaatgcc cttcaatcaa ctaggtgctc tcatggggag taagtattat
     1021 gatctggaag ccacatatta ctatcagcgt tgcctccacg ctgaagtgcc ttttaaagga
     1081 gcagcttgga acctcaaacg actctatgat catgctggaa agaggtacag ctgtctgaag
     1141 aggtaccagg gaaggaaact gtctcatagc caaaggcagt gttgggacaa caaaaggctt
     1201 ctggttagct tcctgtacct tcagagcctc ctgcagccta agagaaaatt caaagctgca
     1261 aggcttatag ccctgtgcca actcgttctt gatgacttcc gtctctgtct ttcctaccgg
     1321 ccataccaat ctggcttgtg ccaggcttcc atagaagata agcctcctaa aggctatctg
     1381 tttctcccag acttcctcat cttccacatg gtggttcttt gtctcatgaa tgtgcacagc
     1441 ctgaggaaat caggctcaaa acagcaaaaa ccagctgtta tcttcaccct gactcttttc
     1501 tcttatttag tacaacatgt gaacacacga atccaggctg agctgcagaa gaggaagttg
     1561 actccagaag aggctgcttt aagagatgga tgctgggaca aagagcctgg aaaggaacat
     1621 caagatttcc catctcctgg gctccagaac aaccactctc agaaaagcca caagtggtct
     1681 ggtatttgca gagaaagtga ggccagtttt cattcctgtt gtgactcaga tgagacagag
     1741 gaagatgaaa actcatcctt aagttcccag gcacaatcag acacaggcag tgagacatcc
     1801 cactctgata caacagatga agaagggagt ggatctttgg gttcagatga aattcagaag
     1861 agtggaggtt cacccaaacc taaaagagct cattccagaa acaaattgaa ggcatatgta
     1921 cctcctgaca gtctccttga tctcttgaaa acaactattt cttccagcct gccagctcct
     1981 ttgagtcaaa aactccaagg aaaacatgcc tcgccattgg ctcctgtctt cagtcacaat
     2041 gttctgacac ctccaactga tccaacccct actgttgctc tcagcagttc cttgggcact
     2101 gagggtgaga taagcagctt tcctgagaca gaattctaca tgggttcctc ttgggagcaa
     2161 aggtccttca tcacccagaa caatctccag accactcaat ggaaactgga cattctttct
     2221 gcagagggac tgttgcctac catcaaggtg atcctgagct ggctccgcag taatcacagc
     2281 ctcctcctgt cacattggag gagtgtgtgt agcttatggg accacctctc tgtgttgctg
     2341 aacctgttgc cttcagttgg agaccttcag catcccggtc tttgtctgtc tcaccatctc
     2401 caggacttgc tgcagagttg tcaatggccg aatactccta agtaccttca actccctgag
     2461 gacattgccc tgttccaaca gtcttctcct caagtgtccc aggataggga aggcttaggg
     2521 caggatccac ctcaactcac caaccaagag gaagttatcg tgcgtatttg tttcttcaga
     2581 agttttgggc actttgcaac aagactccca ggacagtttc tgagatttga ctctaagctg
     2641 ggtatctttg tgagcagtac ccttgaaagg tcagaaagtg cacctcagca gtttccaaga
     2701 acaactccaa gaatcagact ttccaaagac atagtccagc tctggttaca acgtgaagtg
     2761 gcattgctag agaagactct tagaagtccc cagactcggt cagtgttgac cccgtacctg
     2821 ttccctgatc ccagagccct ctgtgagcat ctttcagtca tacagaaact agccactagt
     2881 gctaagtttt ttcttatcat accgaagatt gtagttgaca cactgtatat cctaaaatgg
     2941 gaagaccgca gggccttggc ggccatcact tttctagagg atgagttaaa gagaaggaat
     3001 cagtacattc tctgccagtc ctttgtgtcc aagaggttgg tgaggcccag gatgactaaa
     3061 ccagactctg atgcctggga tctctacaat attcttgagt tctgcaaaag tctgctggac
     3121 tcatccagac cagggattct ggatcccagc agcatggtga tgattattac tggtgtctgt
     3181 ttggaacacc ctagaaattt ctcatacccc ttgcaactag tgctggggat ggcaacagaa
     3241 gctggtgtgg aaatcaagaa cattctgagt ttccacaaag aatgaaaggt gatcagttga
     3301 aatgctcaca cattctgtcc ttgttttgcc agtgtttatc attcaaattc aatgtgctct
     3361 ccctcgtaag cacctaatgc tgaggtagga attgtgtaca tgaatatttc tgtctacccg
     3421 taggtagaat tgtagtgtaa tagctttctg aggccttcct gtttcctttc tagccatcgt
     3481 atctctgtat tatgcttatc ttggaaaaaa ggtcaacatt agctcattgt ttagtgattt
     3541 tctggcaaag caccaaattc acacatcact tctgtgtcca aatacagctt catggacatt
     3601 ctgtgattta atccagtctg ttttgtgaca tgtgactttt atgtatgttg ttttattata
     3661 gtgaggtcaa gtttattatt gatggcaaac ctctaccatc tattaaactc aataaatatg
     3721 aagataaaat tccatga
//
