LOCUS       NM_001379410            3328 bp    mRNA    linear   ROD 01-JUN-2024
DEFINITION  Mus musculus VPS52 GARP complex subunit (Vps52), transcript variant
            4, mRNA.
ACCESSION   NM_001379410 XM_006524107
VERSION     NM_001379410.1
KEYWORDS    RefSeq.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 3328)
  AUTHORS   Ibuchi,K., Fukaya,M., Shinohara,T., Hara,Y., Shiroshima,T.,
            Sugawara,T. and Sakagami,H.
  TITLE     The Vps52 subunit of the GARP and EARP complexes is a novel
            Arf6-interacting protein that negatively regulates neurite
            outgrowth of hippocampal neurons
  JOURNAL   Brain Res 1745, 146905 (2020)
   PUBMED   32473257
  REMARK    GeneRIF: The Vps52 subunit of the GARP and EARP complexes is a
            novel Arf6-interacting protein that negatively regulates neurite
            outgrowth of hippocampal neurons.
REFERENCE   2  (bases 1 to 3328)
  AUTHORS   Wei,J., Zhang,Y.Y., Luo,J., Wang,J.Q., Zhou,Y.X., Miao,H.H.,
            Shi,X.J., Qu,Y.X., Xu,J., Li,B.L. and Song,B.L.
  TITLE     The GARP Complex Is Involved in Intracellular Cholesterol Transport
            via Targeting NPC2 to Lysosomes
  JOURNAL   Cell Rep 19 (13), 2823-2835 (2017)
   PUBMED   28658628
REFERENCE   3  (bases 1 to 3328)
  AUTHORS   Logunova,N., Korotetskaya,M., Polshakov,V. and Apt,A.
  TITLE     The QTL within the H2 Complex Involved in the Control of
            Tuberculosis Infection in Mice Is the Classical Class II H2-Ab1
            Gene
  JOURNAL   PLoS Genet 11 (11), e1005672 (2015)
   PUBMED   26618355
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3328)
  AUTHORS   Schindler,C., Chen,Y., Pu,J., Guo,X. and Bonifacino,J.S.
  TITLE     EARP is a multisubunit tethering complex involved in endocytic
            recycling
  JOURNAL   Nat Cell Biol 17 (5), 639-650 (2015)
   PUBMED   25799061
REFERENCE   5  (bases 1 to 3328)
  AUTHORS   Sugimoto,M., Kondo,M., Hirose,M., Suzuki,M., Mekada,K., Abe,T.,
            Kiyonari,H., Ogura,A., Takagi,N., Artzt,K. and Abe,K.
  TITLE     Molecular identification of t(w5): Vps52 promotes pluripotential
            cell differentiation through cell-cell interactions
  JOURNAL   Cell Rep 2 (5), 1363-1374 (2012)
   PUBMED   23142660
  REMARK    GeneRIF: The Vps52 was responsible for the tw5 mutation, and
            revealed development-specific functions of this gene, which was
            formerly thought to be solely involved in retrograde endocytic
            transport.
REFERENCE   6  (bases 1 to 3328)
  AUTHORS   Abe,K., Yuzuriha,M., Sugimoto,M., Ko,M.S., Brathwaite,M., Waeltz,P.
            and Nagaraja,R.
  TITLE     Gene content of the 750-kb critical region for mouse embryonic
            ectoderm lethal tcl-w5
  JOURNAL   Mamm Genome 15 (4), 265-276 (2004)
   PUBMED   15112104
REFERENCE   7  (bases 1 to 3328)
  AUTHORS   Allcock,R.J., Martin,A.M. and Price,P.
  TITLE     The mouse as a model for the effects of MHC genes on human disease
  JOURNAL   Immunol Today 21 (7), 328-332 (2000)
   PUBMED   10871872
  REMARK    Review article
REFERENCE   8  (bases 1 to 3328)
  AUTHORS   Walter,L. and Gunther,E.
  TITLE     Identification of a novel highly conserved gene in the centromeric
            part of the major histocompatibility complex
  JOURNAL   Genomics 52 (3), 298-304 (1998)
   PUBMED   9790748
REFERENCE   9  (bases 1 to 3328)
  AUTHORS   Vernet,C., Abe,K. and Artzt,K.
  TITLE     Genetic mapping of 10 microsatellites in the t complex region of
            mouse chromosome 17
  JOURNAL   Mamm Genome 9 (6), 472 (1998)
   PUBMED   9585437
REFERENCE   10 (bases 1 to 3328)
  AUTHORS   Artzt,K., McCormick,P. and Bennett,D.
  TITLE     Gene mapping within the T/t complex of the mouse. I. t-Lethal genes
            are nonallelic
  JOURNAL   Cell 28 (3), 463-470 (1982)
   PUBMED   7074682
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            CR974462.5.
            
            On Apr 2, 2020 this sequence version replaced XM_006524107.2.
            
            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.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR13422598.982158.1,
                                           SRR7345562.137844.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849374, SAMN00849375
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-301               CR974462.5         49054-49354
            302-386             CR974462.5         50102-50186
            387-439             CR974462.5         51021-51073
            440-515             CR974462.5         51189-51264
            516-583             CR974462.5         51462-51529
            584-759             CR974462.5         51773-51948
            760-910             CR974462.5         52397-52547
            911-1011            CR974462.5         53167-53267
            1012-1144           CR974462.5         53359-53491
            1145-1202           CR974462.5         53619-53676
            1203-1336           CR974462.5         54283-54416
            1337-1492           CR974462.5         54785-54940
            1493-1611           CR974462.5         55239-55357
            1612-1750           CR974462.5         55595-55733
            1751-1846           CR974462.5         55898-55993
            1847-1954           CR974462.5         56082-56189
            1955-2020           CR974462.5         56350-56415
            2021-2132           CR974462.5         58453-58564
            2133-2251           CR974462.5         58833-58951
            2252-3328           CR974462.5         59131-60207
FEATURES             Location/Qualifiers
     source          1..3328
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="17"
                     /map="17 17.98 cM"
     gene            1..3328
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /note="VPS52 GARP complex subunit"
                     /db_xref="GeneID:224705"
                     /db_xref="MGI:MGI:1330304"
     exon            1..301
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /inference="alignment:Splign:2.1.0"
     CDS             212..2398
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /note="isoform 4 is encoded by transcript variant 4;
                     vacuolar protein sorting-associated protein 52 homolog;
                     vacuolar protein sorting 52"
                     /codon_start=1
                     /product="vacuolar protein sorting-associated protein 52
                     homolog isoform 4"
                     /protein_id="NP_001366339.1"
                     /db_xref="GeneID:224705"
                     /db_xref="MGI:MGI:1330304"
                     /translation="MAAAATMAAAARELVLRAGASDVEEEEGPLGGGSGLQEPLQLGE
                     LDITSDEFILDEVDVHIQANLEDELVKEALKTGVDLRHYSKQVELELQQIEQKSIRDY
                     IQESENIASLHNQITACDAVLERMEQMLGAFQSDLSSISSEIRTLQEQSGAMNIRLRN
                     RQAVRGKLGELVDGLVVPSALVTAILEAPVTEPRFLEQLQELDAKAAAVREQEAMGTA
                     ACADVRGVLDRLRVKAVTKIREFILQKIYSFRKPMTNYQIPQAALLKYRFFYQFLLGN
                     ERATAKEIRDEYVETLSKIYLSYYRSYVGRLMKVQYEEVAEKDDLMGVEDTAKKGFFS
                     KPSLRSRNTIFTLGTRGTVISPAELEAPILVPHTAQRGEQRYPFEALFRSQHYALLDN
                     SCREYLFICEFFIVSGPAAHDLFHAVMGRTLSMTLKHLESYLADCYDAIAVFLCIHIV
                     LRFRNIAAKRDVPALDRYWEQVLALLWPRFELILEMNVQSVRSTDPQRLGGLDTRPHY
                     VRASKITRRYAEFSSALVSINQTIPNERTLQLLGQLQVEVENFVLRVAAEFSSRKEQL
                     VFLINNYDMMLGVLMERAADDSKEVESFQQLLNARTQEFIEELLSPPFGGLVAFVKEA
                     EALIERGQAERLRGEEARVTQLIRGFGSSWKASVESLSQDVMRSFTNFRNGTSIIQGA
                     LTQLIQLYHRFHRVLSQPQLRALPARAELINIHHLMVELKKHKPNF"
     exon            302..386
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /inference="alignment:Splign:2.1.0"
     exon            387..439
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /inference="alignment:Splign:2.1.0"
     exon            440..515
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /inference="alignment:Splign:2.1.0"
     exon            516..583
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /inference="alignment:Splign:2.1.0"
     exon            584..759
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /inference="alignment:Splign:2.1.0"
     exon            760..910
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /inference="alignment:Splign:2.1.0"
     exon            911..1011
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /inference="alignment:Splign:2.1.0"
     exon            1012..1144
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /inference="alignment:Splign:2.1.0"
     exon            1145..1202
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /inference="alignment:Splign:2.1.0"
     exon            1203..1336
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /inference="alignment:Splign:2.1.0"
     exon            1337..1492
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /inference="alignment:Splign:2.1.0"
     exon            1493..1611
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /inference="alignment:Splign:2.1.0"
     exon            1612..1750
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /inference="alignment:Splign:2.1.0"
     exon            1751..1846
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /inference="alignment:Splign:2.1.0"
     exon            1847..1954
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /inference="alignment:Splign:2.1.0"
     exon            1955..2020
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /inference="alignment:Splign:2.1.0"
     exon            2021..2132
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /inference="alignment:Splign:2.1.0"
     exon            2133..2251
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /inference="alignment:Splign:2.1.0"
     exon            2252..3328
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2763..2768
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /note="hexamer: AATAAT"
     polyA_site      2782
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
                     /note="major polyA site"
     polyA_site      3328
                     /gene="Vps52"
                     /gene_synonym="ARE1; D130068D18; D430041K17Rik; SAC2;
                     Sacm2l; tclw5"
ORIGIN      
        1 agagttgtgt tcgagacgtt caccttcctg tttgcacttg accgaaatga tcaaagccta
       61 accggagagg ctggagccga tcgccttagc tcaaatatct gggacccttt tttgctccat
      121 agaagacatt ccaggacttg tagctttgct tcgggaaacg gactttctga gactgacagc
      181 tgccggaagt cggaagtgaa gctgcggggg aatggcagcc gcagcgacca tggcggccgc
      241 tgcccgggag ctggtgttgc gggctggggc ctcagatgta gaggaggagg agggcccgct
      301 gggggggggt tctggactcc aagaacccct acaacttgga gagttggaca tcacctctga
      361 tgaattcatc ttggatgaag tggatgttca catccaggca aacctggagg atgagttagt
      421 gaaggaagct ctcaaaacgg gtgtggatct tcgacactat tcaaagcagg tggagctgga
      481 gctgcagcag attgagcaga agtcaatccg ggactatatc caagagagtg aaaacatagc
      541 gtctctgcac aatcagatca cggcctgtga cgccgtcctg gagcgcatgg aacagatgct
      601 gggagctttt cagagcgatc tcagctccat cagctctgag atccgaaccc tgcaggagca
      661 gtcgggggcc atgaacatcc gacttcgtaa ccgacaggca gttcggggga aacttgggga
      721 acttgtggat gggctggtgg tgccctctgc tctggtcaca gcaattctgg aagctccagt
      781 gaccgagccc aggttcctgg agcagctaca ggagctggat gccaaggcag ccgcggtgag
      841 agagcaggag gctatgggca ccgctgcctg tgctgacgtc agaggcgtgc tggaccggct
      901 ccgggtcaag gcagtgacga agatccggga gtttattctc cagaagatct actccttcag
      961 aaagcccatg accaactacc agatccccca ggcggccctg ctgaagtaca ggtttttcta
     1021 tcagttcctg ctgggtaatg agcgtgctac agccaaggag atcagggatg agtacgtaga
     1081 gacgctgagc aagatctacc tgtcctacta ccgatcctat gtggggcggc tcatgaaagt
     1141 gcagtacgag gaagttgctg agaaagacga cctaatgggt gttgaagaca cagcaaagaa
     1201 aggcttcttc tcgaagccgt ccctccgaag caggaacacc atctttaccc ttggcactcg
     1261 tggtactgtc atctcaccgg ccgagctgga ggcccccatc ctagtgcccc atactgccca
     1321 acgtggagag cagaggtatc cattcgaagc gctcttccgc agccagcact atgccctcct
     1381 cgacaattct tgccgtgaat atcttttcat ctgtgaattt ttcatcgtgt ctggcccggc
     1441 tgcacatgac ctgttccacg ccgtcatggg ccgcacgctc tccatgacgc tgaaacacct
     1501 ggagtcctac ctggctgact gctacgatgc cattgctgtt tttctctgta tccacattgt
     1561 tctccggttc cgcaacattg cagcgaagag ggacgtccct gccctggaca ggtactggga
     1621 gcaggtgctt gccttgctgt ggcctcggtt tgagctgatc ctggagatga atgtccagag
     1681 tgtccgcagc actgaccccc agcgccttgg gggactggac actcggcccc actatgtaag
     1741 ggcgagcaag atcacacgcc gctatgctga gttctcctct gcacttgtca gcatcaacca
     1801 gacgatcccc aatgaacgca cgctgcagct cctgggacag ctccaggtgg aggtggagaa
     1861 ttttgtcctc cgagtggctg cagagttctc ctccaggaag gagcagcttg tgtttctgat
     1921 caacaactat gacatgatgc tcggggtgct gatggagcgg gctgctgatg acagcaaaga
     1981 ggtggaaagt ttccagcagc tgctcaatgc tcggacacag gagttcattg aggagctgct
     2041 gtctcccccc ttcgggggtc tggtggcatt cgtgaaggag gctgaagcct tgattgagcg
     2101 tgggcaggct gagcggctcc gaggggagga agcccgagtc actcagctga tccgtggctt
     2161 tggtagttcc tggaaggcat cagtggagtc cctgagtcag gatgtaatgc gaagttttac
     2221 caacttccga aatggaacca gcatcatcca gggggcgctg acccagctga tccagctcta
     2281 ccatcgcttc caccgggtgc tgtctcagcc ccagctccgc gcactcccgg ccagggccga
     2341 gctcatcaac atccatcacc tcatggtgga gctgaagaaa cacaagccga acttctgatt
     2401 cagacccccc tcccccgccc ctaagctcct gtgtactctg tgtgtcacac attttcacct
     2461 gggacccctt tcccatccct tttatctcta tggcttccac actcccctct cagcctccat
     2521 tgccaggact ctgcctcaac agagtgcgtt caaggccact ccctgggttt ctgagtgagg
     2581 tgaccttcat ttccagtccg gtcagctcct ctgctgttca ctcacagcct gtgagcttcc
     2641 accgccccag gctctgactg accctcagct cttagggcag agcactgcag gccaccctgt
     2701 agctgatctg tgggctctgc tggaacagtg acatcacctc gtggtgggtc tcactatgtg
     2761 gcaataataa gtactaacag tgctgggacc gtgtcctctc ctttgtccct gggcctctaa
     2821 attctccagc atgtgtttat tgtagaccta gtctgttcct ggtgggcatc aggaagaggg
     2881 tgtgatagta ccccaaggtc tgttgctgct tctggcccag gggtggcata gatgctcagg
     2941 aggggactgt ttgtagctct ccaggagggt ggcacttgtc gcaaggcctg ggaatgtggt
     3001 agctttgggt gctgtcctga gggataccat gggaatagtc cacacagcct ctgagattgt
     3061 gtcagccact aagtggctgt tacagctcct ttgaggatgg agggcctata acacctgcag
     3121 ccatgcatca aggcaggggt ggacctggct ccaaaacaga tcctgtcatt ttcatgtgac
     3181 ccagaccctt cccgctgccc tctgcctcac ctctgtaagg agtttgcaga ctccagagca
     3241 gtggttctca accttcctaa tactgcaacg ctttaacaca gttccttgtg ctgaccccaa
     3301 ccttaaagtt attttcattg ttacttca
//
