LOCUS       NM_001414938            2818 bp    mRNA    linear   ROD 31-MAR-2024
DEFINITION  Rattus norvegicus VPS9 domain containing 1 (Vps9d1), transcript
            variant 2, mRNA.
ACCESSION   NM_001414938 XM_006255767
VERSION     NM_001414938.1
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
REFERENCE   1  (bases 1 to 2818)
  AUTHORS   Gaudet,P., Livstone,M.S., Lewis,S.E. and Thomas,P.D.
  TITLE     Phylogenetic-based propagation of functional annotations within the
            Gene Ontology consortium
  JOURNAL   Brief Bioinform 12 (5), 449-462 (2011)
   PUBMED   21873635
REFERENCE   2  (bases 1 to 2818)
  AUTHORS   Strausberg,R.L., Feingold,E.A., Grouse,L.H., Derge,J.G.,
            Klausner,R.D., Collins,F.S., Wagner,L., Shenmen,C.M., Schuler,G.D.,
            Altschul,S.F., Zeeberg,B., Buetow,K.H., Schaefer,C.F., Bhat,N.K.,
            Hopkins,R.F., Jordan,H., Moore,T., Max,S.I., Wang,J., Hsieh,F.,
            Diatchenko,L., Marusina,K., Farmer,A.A., Rubin,G.M., Hong,L.,
            Stapleton,M., Soares,M.B., Bonaldo,M.F., Casavant,T.L.,
            Scheetz,T.E., Brownstein,M.J., Usdin,T.B., Toshiyuki,S.,
            Carninci,P., Prange,C., Raha,S.S., Loquellano,N.A., Peters,G.J.,
            Abramson,R.D., Mullahy,S.J., Bosak,S.A., McEwan,P.J.,
            McKernan,K.J., Malek,J.A., Gunaratne,P.H., Richards,S.,
            Worley,K.C., Hale,S., Garcia,A.M., Gay,L.J., Hulyk,S.W.,
            Villalon,D.K., Muzny,D.M., Sodergren,E.J., Lu,X., Gibbs,R.A.,
            Fahey,J., Helton,E., Ketteman,M., Madan,A., Rodrigues,S.,
            Sanchez,A., Whiting,M., Madan,A., Young,A.C., Shevchenko,Y.,
            Bouffard,G.G., Blakesley,R.W., Touchman,J.W., Green,E.D.,
            Dickson,M.C., Rodriguez,A.C., Grimwood,J., Schmutz,J., Myers,R.M.,
            Butterfield,Y.S., Krzywinski,M.I., Skalska,U., Smailus,D.E.,
            Schnerch,A., Schein,J.E., Jones,S.J. and Marra,M.A.
  CONSRTM   Mammalian Gene Collection Program Team
  TITLE     Generation and initial analysis of more than 15,000 full-length
            human and mouse cDNA sequences
  JOURNAL   Proc Natl Acad Sci U S A 99 (26), 16899-16903 (2002)
   PUBMED   12477932
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000019.1.
            
            On Dec 15, 2022 this sequence version replaced XM_006255767.3.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR26360186.130749.1,
                                           SRR26360176.1377200.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA5760383,
                                           SAMEA5760386 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-217               JAXUCZ010000019.1  68199028-68199244   c
            218-293             JAXUCZ010000019.1  68197633-68197708   c
            294-386             JAXUCZ010000019.1  68195178-68195270   c
            387-546             JAXUCZ010000019.1  68194931-68195090   c
            547-658             JAXUCZ010000019.1  68192329-68192440   c
            659-721             JAXUCZ010000019.1  68192178-68192240   c
            722-774             JAXUCZ010000019.1  68191303-68191355   c
            775-862             JAXUCZ010000019.1  68191117-68191204   c
            863-948             JAXUCZ010000019.1  68190864-68190949   c
            949-1433            JAXUCZ010000019.1  68189861-68190345   c
            1434-1563           JAXUCZ010000019.1  68189118-68189247   c
            1564-1769           JAXUCZ010000019.1  68188655-68188860   c
            1770-1866           JAXUCZ010000019.1  68188287-68188383   c
            1867-1971           JAXUCZ010000019.1  68186844-68186948   c
            1972-2818           JAXUCZ010000019.1  68185517-68186363   c
FEATURES             Location/Qualifiers
     source          1..2818
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="19"
                     /map="19q12"
     gene            1..2818
                     /gene="Vps9d1"
                     /gene_synonym="RGD1565149"
                     /note="VPS9 domain containing 1"
                     /db_xref="GeneID:307923"
                     /db_xref="RGD:1565149"
     exon            1..217
                     /gene="Vps9d1"
                     /gene_synonym="RGD1565149"
                     /inference="alignment:Splign:2.1.0"
     CDS             119..2065
                     /gene="Vps9d1"
                     /gene_synonym="RGD1565149"
                     /note="isoform 2 is encoded by transcript variant 2; VPS9
                     domain-containing protein 1; RBSC-thyroid hormone receptor
                     associated-like polypeptide"
                     /codon_start=1
                     /product="VPS9 domain-containing protein 1 isoform 2"
                     /protein_id="NP_001401867.1"
                     /db_xref="GeneID:307923"
                     /db_xref="RGD:1565149"
                     /translation="MAAAAGDGAAKPLQSAMKLANKAIELDTGNRPREAYMEYLRSIR
                     YISQVLLEDVENTTEAGETVPPETSKMLKLAEQCLERAQSTATKLGKICLKPAIPAAP
                     PVPLPSRHRRVCSDEGGKLSPFLPPEIFQKLQVAESHNSKKELTPLEKASLQNQKLRA
                     TYEARMARLDPSQAMQKTSLTLSLQRQMMENLVIAKAREETLQRKMEQRRLRLQEAAN
                     RRFCSQVALTPEEREQRALYAAILEYEQDHDWPKHWRAKLKRSPGDLSLVTSLVSHLL
                     SLPDHPISQLLKKLQCAVYSALYPVVSRAAICAVPAPGSCSLPPEANGLLAPGSRRLR
                     SSQSLYCMLSPSEPSAAPRALDGPPSTPSIPILHSGTLDREADGSPAGPSSPLVGALP
                     HLPDKDSSFEDLEQFLAMSEPQTPGAKREPLLECLKSTVKDIHNAIDRLLSLTLLAFE
                     SLNTATCKDRCLACIEEPFFSPLWPLLLALYRSVHRTREAAVSRSMELYRNALPTALG
                     IPTKLLPCVPEAQASTYPYCTAAQELGLLVLESCPQKKLECIVRTLRVICICAEDYCR
                     AQEARPEGGSQPPAAAIGADDLLPILSFVVLRSGLPQLVSECAALEEFTHEGYLIGEE
                     GYCLTSLQSALSYVELLSRGRLDK"
     exon            218..293
                     /gene="Vps9d1"
                     /gene_synonym="RGD1565149"
                     /inference="alignment:Splign:2.1.0"
     exon            294..386
                     /gene="Vps9d1"
                     /gene_synonym="RGD1565149"
                     /inference="alignment:Splign:2.1.0"
     exon            387..546
                     /gene="Vps9d1"
                     /gene_synonym="RGD1565149"
                     /inference="alignment:Splign:2.1.0"
     exon            547..658
                     /gene="Vps9d1"
                     /gene_synonym="RGD1565149"
                     /inference="alignment:Splign:2.1.0"
     exon            659..721
                     /gene="Vps9d1"
                     /gene_synonym="RGD1565149"
                     /inference="alignment:Splign:2.1.0"
     exon            722..774
                     /gene="Vps9d1"
                     /gene_synonym="RGD1565149"
                     /inference="alignment:Splign:2.1.0"
     exon            775..862
                     /gene="Vps9d1"
                     /gene_synonym="RGD1565149"
                     /inference="alignment:Splign:2.1.0"
     exon            863..948
                     /gene="Vps9d1"
                     /gene_synonym="RGD1565149"
                     /inference="alignment:Splign:2.1.0"
     exon            949..1433
                     /gene="Vps9d1"
                     /gene_synonym="RGD1565149"
                     /inference="alignment:Splign:2.1.0"
     exon            1434..1563
                     /gene="Vps9d1"
                     /gene_synonym="RGD1565149"
                     /inference="alignment:Splign:2.1.0"
     exon            1564..1769
                     /gene="Vps9d1"
                     /gene_synonym="RGD1565149"
                     /inference="alignment:Splign:2.1.0"
     exon            1770..1866
                     /gene="Vps9d1"
                     /gene_synonym="RGD1565149"
                     /inference="alignment:Splign:2.1.0"
     exon            1867..1971
                     /gene="Vps9d1"
                     /gene_synonym="RGD1565149"
                     /inference="alignment:Splign:2.1.0"
     exon            1972..2818
                     /gene="Vps9d1"
                     /gene_synonym="RGD1565149"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 gtatctgggt cccttccggc ggtgcgcggc tcccacagct ccttcagctg cgcactccgc
       61 gttccggtct ggaagcgtcc gccccgcccc tgctgcccgg cctcccccgc ccggcgccat
      121 ggccgctgcg gccggggacg gcgcggcgaa gccactgcaa agcgccatga aactggccaa
      181 caaggccatc gagctagaca ccggcaaccg gccccgggaa gcgtacatgg aatacctgag
      241 gagcatccgc tacatctccc aggtgttgct cgaagacgtg gaaaacacta cagaagctgg
      301 ggaaaccgtg ccccctgaga cctcaaagat gctgaagctg gctgaacagt gtctggagcg
      361 ggcccagtca acagctacca aacttgggaa aatatgcctg aagccagcca tacctgcagc
      421 ccctcccgtg cccttgccca gccgacaccg ccgagtgtgt tcagatgaag gggggaagct
      481 ctctcctttc ctgccccctg agatcttcca gaagctgcag gtggcagaat cgcacaactc
      541 taagaaggag ctaacaccac tggagaaggc ctccctacaa aaccagaagc tgagggccac
      601 atatgaggcc cggatggccc gtctggaccc cagccaggcc atgcagaaga catcactgac
      661 tctgtctcta cagcggcaga tgatggagaa tctggtgatc gccaaagcaa gagaagagac
      721 actgcagcgg aagatggagc agcgccgcct gcgacttcag gaggctgcca acaggaggtt
      781 ctgcagtcaa gttgctctga ccccagagga gcgggagcag cgagccctgt atgctgccat
      841 cttggaatat gagcaagacc atgactggcc aaagcactgg agagccaagc tcaagcggag
      901 cccaggggac ctgtcgctgg tgaccagcct ggtctcccac ctgctcagcc ttcctgatca
      961 ccccatttcc cagctcctga agaagctcca gtgtgcagta tacagtgcac tgtaccctgt
     1021 tgtgagccgg gctgctatct gtgctgtgcc tgccccaggc agctgctccc tgcccccaga
     1081 agccaatggc ctcctagctc ctgggagccg gcgacttcgg tcctcccaga gcctctactg
     1141 catgctctcc ccctcagagc ccagtgcagc cccgagagct ctggacggac ctccttccac
     1201 accttctatc cccatactcc actcaggcac cctggacaga gaggcagatg gcagcccagc
     1261 agggccctcc tcacccctgg tgggtgcttt accccacctg ccagacaagg acagctcctt
     1321 tgaggacctg gaacagtttt tggctatgtc tgagccacag accccaggag caaagaggga
     1381 gcccttgctg gaatgtctga agagcacagt aaaggacatt cacaatgcca tcgacagact
     1441 gctctcgctg accctattgg ccttcgaaag cctgaataca gccacctgca aagaccgctg
     1501 cctggcatgc atcgaggagc ccttcttctc cccactgtgg cccctgctgc tagccctcta
     1561 caggagtgtg caccgtaccc gggaggctgc tgtgagcagg agcatggagc tgtacaggaa
     1621 cgcactccct acagcccttg gcatccccac caagctcctc ccatgcgtcc ctgaggctca
     1681 agcctccacc tacccctact gcactgcagc ccaggaactg gggctgctgg tcttggagag
     1741 ctgccctcag aagaagctgg agtgcatcgt gcggactctg cgggtcatct gcatctgtgc
     1801 agaagactac tgccgtgccc aagaggccag gcctgagggt ggatcccagc ccccggctgc
     1861 tgccattggt gctgatgact tgctgcccat tctgtccttt gtggtgctga gaagtggcct
     1921 cccccaacta gtatcagagt gcgcagccct ggaggaattc actcatgaag ggtacttgat
     1981 tggagaagaa gggtactgtc tgacatcact gcagagtgct ctgagctatg tggaactttt
     2041 gtcccgggga cggctggaca agtagtggtg gctggacctc acagaccaaa ggagccacag
     2101 agcctccaca ctgttctttg tatctggttt ggggacaccg gaggccagcc tgctgtggtg
     2161 gtaatctagc ttgcccacct tctttaccat agatctgacc tggaggccta ggacagtgcc
     2221 tcttggcagg acatggctgc tgaatcaggc ttgctctgtc ttgagcctgc ctctcaaacc
     2281 ccataggaga aatctgtagc tgctgctcct tggggagcct gcaacactga aggggctcca
     2341 gtaaacctga tgttcttgtg gacactgggc agcccctata gggtaccagc agagaaatgg
     2401 cattgggagc cttgccaggc caatctgatt ttacccccct ccagtctcct gagacagccc
     2461 gtttgtgtga gccagtgtct tgttaataac aagtgggctt taccctgccc ccgagtgcgg
     2521 gtgtaggtag tgtgaggcta tgctgtttat ttaccaggca gcaactgctc tgttcgcttt
     2581 tgctggcccg ggtatcactg cacaggcccg ggatgtgagc ctttctccta ccgaggtcca
     2641 ggacatcctg ccctgggctg gtcctggttg gggacagtga actccattca ggacactagc
     2701 taacaaatac agttgaacag actcttcggt gtcagaatct aaagcttagc ccctggactg
     2761 atgtctccca gtggccacca accaactcag actaaaataa agaagtcact ccatctaa
//
