LOCUS       NM_139040               2055 bp    mRNA    linear   ROD 19-NOV-2024
DEFINITION  Rattus norvegicus phagophore assembly factor 1 (Phaf1), mRNA.
ACCESSION   NM_139040
VERSION     NM_139040.2
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 2055)
  AUTHORS   Stricker,N.L. and Huganir,R.L.
  TITLE     The PDZ domains of mLin-10 regulate its trans-Golgi network
            targeting and the surface expression of AMPA receptors
  JOURNAL   Neuropharmacology 45 (6), 837-848 (2003)
   PUBMED   14529721
  REMARK    GeneRIF: Lin-10 is enriched in the trans-Golgi network and present
            in dendrites and spines of whole brain and cultured neurons--where
            protein sorting and synaptic delivery are known to
            occur--suggesting that Lin-10 may regulate AMPA receptor
            trafficking in vivo.
REFERENCE   2  (bases 1 to 2055)
  AUTHORS   Ide,N., Hata,Y., Hirao,K., Irie,M., Deguchi,M., Yao,I., Satoh,A.,
            Wada,M., Takahashi,K., Nakanishi,H. and Takai,Y.
  TITLE     Interaction of rat lin-10 with brain-enriched F-actin-binding
            protein, neurabin-II/spinophilin
  JOURNAL   Biochem Biophys Res Commun 244 (1), 258-262 (1998)
   PUBMED   9514910
REFERENCE   3  (bases 1 to 2055)
  AUTHORS   Ide,N., Hirao,K., Hata,Y., Takeuchi,M., Irie,M., Yao,I.,
            Deguchi,M., Toyoda,A., Nishioka,H., Mizoguchi,A. and Takai,Y.
  TITLE     Molecular cloning and characterization of rat lin-10
  JOURNAL   Biochem Biophys Res Commun 243 (2), 634-638 (1998)
   PUBMED   9480860
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000019.1.
            
            On Dec 3, 2020 this sequence version replaced NM_139040.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: U92010.1, SRR26643291.41632.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA5760383, SAMEA5760386
                                           [ECO:0000348]
            ##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
            1-260               JAXUCZ010000019.1  50011438-50011697
            261-343             JAXUCZ010000019.1  50018749-50018831
            344-427             JAXUCZ010000019.1  50021999-50022082
            428-471             JAXUCZ010000019.1  50025483-50025526
            472-551             JAXUCZ010000019.1  50026377-50026456
            552-646             JAXUCZ010000019.1  50026695-50026789
            647-744             JAXUCZ010000019.1  50027422-50027519
            745-857             JAXUCZ010000019.1  50027600-50027712
            858-991             JAXUCZ010000019.1  50032542-50032675
            992-1075            JAXUCZ010000019.1  50032971-50033054
            1076-1158           JAXUCZ010000019.1  50034991-50035073
            1159-1202           JAXUCZ010000019.1  50035665-50035708
            1203-1246           JAXUCZ010000019.1  50036147-50036190
            1247-1305           JAXUCZ010000019.1  50036325-50036383
            1306-1378           JAXUCZ010000019.1  50037809-50037881
            1379-2055           JAXUCZ010000019.1  50038626-50039302
FEATURES             Location/Qualifiers
     source          1..2055
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="19"
                     /map="19q11"
     gene            1..2055
                     /gene="Phaf1"
                     /gene_synonym="Lin-10; Lin10; RGD621098"
                     /note="phagophore assembly factor 1"
                     /db_xref="GeneID:207123"
                     /db_xref="RGD:621098"
     exon            1..260
                     /gene="Phaf1"
                     /gene_synonym="Lin-10; Lin10; RGD621098"
                     /inference="alignment:Splign:2.1.0"
     CDS             197..1465
                     /gene="Phaf1"
                     /gene_synonym="Lin-10; Lin10; RGD621098"
                     /note="lin-10 homolog; UPF0183 protein C16orf70 homolog"
                     /codon_start=1
                     /product="phagosome assembly factor 1"
                     /protein_id="NP_620609.2"
                     /db_xref="GeneID:207123"
                     /db_xref="RGD:621098"
                     /translation="MLDLEVVPERSLGNEQWEFTLGMPLAQAVAILQKHCRIIKNVQV
                     LYSEQSPLSHDLILNLTQDGIKLLFDAFNQRLKVIEVYDLTKVKLKYCGVHFNSQAIA
                     PTIEQIDQSFGATHPGVYNSAEQLFHLNFRGLSFSFQLDSWTEAPKYEPNFAHGLASL
                     QIPHGATVKRMYIYSGNSLQDTKAPMMPLSCFLGNVYAESVDVLRDGTGPSGLRLRLL
                     AAGCGPGVLADAKMRVFERAVYFGDSCQDVLSMLGSPHKVFYKSEDKMKIHSPSPHKQ
                     VPSKCNDYFFNYFTLGVDILFDANTHKVKKFVLHTNYPGHYNFNIYHRCEFKIPLAIK
                     KENAGGQTEICTTYSKWDSIQELLGHPVEKPVVLHRSSSPNNTNPFGSTFCFGLQRMI
                     FEVMQNNHIASVTLYGPPRPGAHLRTAELP"
     exon            261..343
                     /gene="Phaf1"
                     /gene_synonym="Lin-10; Lin10; RGD621098"
                     /inference="alignment:Splign:2.1.0"
     exon            344..427
                     /gene="Phaf1"
                     /gene_synonym="Lin-10; Lin10; RGD621098"
                     /inference="alignment:Splign:2.1.0"
     exon            428..471
                     /gene="Phaf1"
                     /gene_synonym="Lin-10; Lin10; RGD621098"
                     /inference="alignment:Splign:2.1.0"
     exon            472..551
                     /gene="Phaf1"
                     /gene_synonym="Lin-10; Lin10; RGD621098"
                     /inference="alignment:Splign:2.1.0"
     exon            552..646
                     /gene="Phaf1"
                     /gene_synonym="Lin-10; Lin10; RGD621098"
                     /inference="alignment:Splign:2.1.0"
     exon            647..744
                     /gene="Phaf1"
                     /gene_synonym="Lin-10; Lin10; RGD621098"
                     /inference="alignment:Splign:2.1.0"
     exon            745..857
                     /gene="Phaf1"
                     /gene_synonym="Lin-10; Lin10; RGD621098"
                     /inference="alignment:Splign:2.1.0"
     exon            858..991
                     /gene="Phaf1"
                     /gene_synonym="Lin-10; Lin10; RGD621098"
                     /inference="alignment:Splign:2.1.0"
     exon            992..1075
                     /gene="Phaf1"
                     /gene_synonym="Lin-10; Lin10; RGD621098"
                     /inference="alignment:Splign:2.1.0"
     exon            1076..1158
                     /gene="Phaf1"
                     /gene_synonym="Lin-10; Lin10; RGD621098"
                     /inference="alignment:Splign:2.1.0"
     exon            1159..1202
                     /gene="Phaf1"
                     /gene_synonym="Lin-10; Lin10; RGD621098"
                     /inference="alignment:Splign:2.1.0"
     exon            1203..1246
                     /gene="Phaf1"
                     /gene_synonym="Lin-10; Lin10; RGD621098"
                     /inference="alignment:Splign:2.1.0"
     exon            1247..1305
                     /gene="Phaf1"
                     /gene_synonym="Lin-10; Lin10; RGD621098"
                     /inference="alignment:Splign:2.1.0"
     exon            1306..1378
                     /gene="Phaf1"
                     /gene_synonym="Lin-10; Lin10; RGD621098"
                     /inference="alignment:Splign:2.1.0"
     exon            1379..2055
                     /gene="Phaf1"
                     /gene_synonym="Lin-10; Lin10; RGD621098"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 cggggctgct gcccgggagg tgaagggagg ttaagtgtgt tgttgtgtta gtgctgccgt
       61 cgccgcccgg gacggagctg agagccggac gtccgcaggc tgacgagagc ggccagtcag
      121 cagctgcgtg ctctcctcag gccgggtcct gtctgcgctg ccgcagggag gccgcccggc
      181 ccagcgaacc gaaccaatgc tggacctgga ggtggtgcct gaacgctctc tggggaacga
      241 gcaatgggaa ttcacactgg gaatgcctct ggctcaggca gtagccattc ttcagaagca
      301 ctgtcgcatc atcaaaaatg tccaggttct ctacagtgag cagtctcctc taagccatga
      361 cctcatcctt aacctgactc aagacgggat caagctactg tttgatgctt tcaatcagag
      421 acttaaggtg attgaagttt atgacttaac aaaagtaaag ttaaagtatt gtggagtgca
      481 ttttaactct caggccatcg ctcctaccat tgagcaaatt gaccagtctt ttggtgcaac
      541 ccatccagga gtgtacaact ctgctgagca gctcttccac ctcaacttca gaggactgtc
      601 tttctctttt cagttagact catggacgga ggctcccaag tatgagccca attttgccca
      661 tggtctagct tctcttcaga taccccatgg agcaactgta aaacgaatgt acatctatag
      721 tggaaacagc ctccaggata ccaaggctcc tatgatgccc ctgagctgtt tcctggggaa
      781 tgtatatgct gaaagtgtag acgttcttcg agacggaact ggaccctcag ggttgcgact
      841 tcgcttgctc gctgcaggtt gtggacccgg agtattggca gatgccaaaa tgagagtatt
      901 tgagcgtgcg gtgtattttg gtgattcttg ccaagatgtt cttagcatgc ttggctctcc
      961 acacaaagtc ttctataaat ctgaagacaa gatgaaaatt cactctcctt cccctcataa
     1021 acaagttcca tccaagtgca atgactactt ttttaactat ttcactcttg gagtggacat
     1081 cctgtttgat gcaaatacac acaaagtgaa gaagtttgtc ctgcatacca attaccctgg
     1141 gcattataat tttaacattt accaccgctg tgagttcaag atcccactag ccataaagaa
     1201 agaaaatgca ggtggtcaaa ccgaaatatg cacaacctac agcaagtggg acagcatcca
     1261 ggagcttctg ggccatcctg tggaaaagcc ggttgtcttg cacagatcct catccccaaa
     1321 taacaccaac ccatttggct ctacattctg ctttggtctt cagcggatga tctttgaggt
     1381 catgcagaac aaccacattg cctcagtgac cctgtatggc ccccctaggc ctggtgccca
     1441 cctgagaaca gcagagctgc cctaaggact tcactgtttt ccctctgtcc atggaactgt
     1501 gcatcacatc cagctcagtg ggtctctgtg ccaccaccct gtgtgttttc ttgggcacct
     1561 tggcagtgtt gaagggctgt gggactttgg gtttggaagg ctgagttttc tgccttggga
     1621 cagaggaccc agctgtccaa agcctgctgt cgccatgaga gaacacagtc tgcaaagaga
     1681 agcacaaact ttgagcctgg atgagggctc tcttattaac atgtaataaa ggacacgcca
     1741 gccctgtcct gcacatgagg aagacggggc tctttctcta tctaaggacc tgtacctagg
     1801 agagaacagg gtcctgcttt tggcccgaca ttgccatgtg ctcaccttaa ggtgagcaga
     1861 gcagatgtat agcatgtcag tagtacttgg ttgcaatatt tgcactacat ccactttagt
     1921 tacttgatga gctggctgtg gctggtgtgg cccactgccc tttcctgttt cttctgtgtg
     1981 agtgctcctt gccatgccca ggtggcatac ccaagtggtt gaaatacagt tttctcccag
     2041 gtatgtacca ggcct
//
