LOCUS       NM_003794               2512 bp    mRNA    linear   PRI 04-OCT-2024
DEFINITION  Homo sapiens sorting nexin 4 (SNX4), transcript variant 1, mRNA.
ACCESSION   NM_003794
VERSION     NM_003794.4
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 2512)
  AUTHORS   Cho,N.H., Cheveralls,K.C., Brunner,A.D., Kim,K., Michaelis,A.C.,
            Raghavan,P., Kobayashi,H., Savy,L., Li,J.Y., Canaj,H., Kim,J.Y.S.,
            Stewart,E.M., Gnann,C., McCarthy,F., Cabrera,J.P., Brunetti,R.M.,
            Chhun,B.B., Dingle,G., Hein,M.Y., Huang,B., Mehta,S.B.,
            Weissman,J.S., Gomez-Sjoberg,R., Itzhak,D.N., Royer,L.A., Mann,M.
            and Leonetti,M.D.
  TITLE     OpenCell: Endogenous tagging for the cartography of human cellular
            organization
  JOURNAL   Science 375 (6585), eabi6983 (2022)
   PUBMED   35271311
REFERENCE   2  (bases 1 to 2512)
  AUTHORS   Huttlin,E.L., Bruckner,R.J., Navarrete-Perea,J., Cannon,J.R.,
            Baltier,K., Gebreab,F., Gygi,M.P., Thornock,A., Zarraga,G., Tam,S.,
            Szpyt,J., Gassaway,B.M., Panov,A., Parzen,H., Fu,S., Golbazi,A.,
            Maenpaa,E., Stricker,K., Guha Thakurta,S., Zhang,T., Rad,R.,
            Pan,J., Nusinow,D.P., Paulo,J.A., Schweppe,D.K., Vaites,L.P.,
            Harper,J.W. and Gygi,S.P.
  TITLE     Dual proteome-scale networks reveal cell-specific remodeling of the
            human interactome
  JOURNAL   Cell 184 (11), 3022-3040 (2021)
   PUBMED   33961781
REFERENCE   3  (bases 1 to 2512)
  AUTHORS   Ravussin,A., Brech,A., Tooze,S.A. and Stenmark,H.
  TITLE     The phosphatidylinositol 3-phosphate-binding protein SNX4 controls
            ATG9A recycling and autophagy
  JOURNAL   J Cell Sci 134 (3) (2021)
   PUBMED   33468622
  REMARK    GeneRIF: The phosphatidylinositol 3-phosphate-binding protein SNX4
            controls ATG9A recycling and autophagy.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2512)
  AUTHORS   Anton,Z., Betin,V.M.S., Simonetti,B., Traer,C.J., Attar,N.,
            Cullen,P.J. and Lane,J.D.
  TITLE     A heterodimeric SNX4--SNX7 SNX-BAR autophagy complex coordinates
            ATG9A trafficking for efficient autophagosome assembly
  JOURNAL   J Cell Sci 133 (14) (2020)
   PUBMED   32513819
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2512)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   6  (bases 1 to 2512)
  AUTHORS   Leprince,C., Le Scolan,E., Meunier,B., Fraisier,V., Brandon,N., De
            Gunzburg,J. and Camonis,J.
  TITLE     Sorting nexin 4 and amphiphysin 2, a new partnership between
            endocytosis and intracellular trafficking
  JOURNAL   J Cell Sci 116 (Pt 10), 1937-1948 (2003)
   PUBMED   12668730
  REMARK    GeneRIF: Sorting nexin 4 and amphiphysin 2 have roles in
            endocytosis and intracellular trafficking
REFERENCE   7  (bases 1 to 2512)
  AUTHORS   Parks,W.T., Frank,D.B., Huff,C., Renfrew Haft,C., Martin,J.,
            Meng,X., de Caestecker,M.P., McNally,J.G., Reddi,A., Taylor,S.I.,
            Roberts,A.B., Wang,T. and Lechleider,R.J.
  TITLE     Sorting nexin 6, a novel SNX, interacts with the transforming
            growth factor-beta family of receptor serine-threonine kinases
  JOURNAL   J Biol Chem 276 (22), 19332-19339 (2001)
   PUBMED   11279102
REFERENCE   8  (bases 1 to 2512)
  AUTHORS   Wurthner,J.U., Frank,D.B., Felici,A., Green,H.M., Cao,Z.,
            Schneider,M.D., McNally,J.G., Lechleider,R.J. and Roberts,A.B.
  TITLE     Transforming growth factor-beta receptor-associated protein 1 is a
            Smad4 chaperone
  JOURNAL   J Biol Chem 276 (22), 19495-19502 (2001)
   PUBMED   11278302
REFERENCE   9  (bases 1 to 2512)
  AUTHORS   Haft,C.R., de la Luz Sierra,M., Barr,V.A., Haft,D.H. and
            Taylor,S.I.
  TITLE     Identification of a family of sorting nexin molecules and
            characterization of their association with receptors
  JOURNAL   Mol Cell Biol 18 (12), 7278-7287 (1998)
   PUBMED   9819414
REFERENCE   10 (bases 1 to 2512)
  AUTHORS   Perlman,S.
  TITLE     Hereditary Ataxia Overview
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301317
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DA289870.1, AK001835.1 and
            AI187416.1.
            
            On Nov 23, 2018 this sequence version replaced NM_003794.3.
            
            Summary: This gene encodes a member of the sorting nexin family.
            Members of this family contain a phox (PX) domain, which is a
            phosphoinositide binding domain, and are involved in intracellular
            trafficking. This protein associated with the long isoform of the
            leptin receptor and with receptor tyrosine kinases for
            platelet-derived growth factor, insulin, and epidermal growth
            factor in cell cultures, but its function is unknown. This protein
            may form oligomeric complexes with family members. Two transcript
            variants, one protein coding and the other non-protein coding, have
            been found for this gene. [provided by RefSeq, Nov 2012].
            
            Transcript Variant: This variant (1) represents the longer
            transcript and is the protein-coding variant.
            
            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 :: SRR3476690.876872.1,
                                           SRR1660807.172311.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000251775.9/ ENSP00000251775.4
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-26                DA289870.1         13-38
            27-2511             AK001835.1         1-2485
            2512-2512           AI187416.1         11-11               c
FEATURES             Location/Qualifiers
     source          1..2512
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="3"
                     /map="3q21.2"
     gene            1..2512
                     /gene="SNX4"
                     /gene_synonym="ATG24B"
                     /note="sorting nexin 4"
                     /db_xref="GeneID:8723"
                     /db_xref="HGNC:HGNC:11175"
                     /db_xref="MIM:605931"
     exon            1..171
                     /gene="SNX4"
                     /gene_synonym="ATG24B"
                     /inference="alignment:Splign:2.1.0"
     CDS             31..1383
                     /gene="SNX4"
                     /gene_synonym="ATG24B"
                     /codon_start=1
                     /product="sorting nexin-4"
                     /protein_id="NP_003785.1"
                     /db_xref="CCDS:CCDS3032.1"
                     /db_xref="GeneID:8723"
                     /db_xref="HGNC:HGNC:11175"
                     /db_xref="MIM:605931"
                     /translation="MEQAPPDPERQLQPAPLEPLGSPDAGLGAAVGKEAEGAGEESSG
                     VDTMTHNNFWLKKIEISVSEAEKRTGRNAMNMQETYTAYLIETRSVEHTDGQSVLTDS
                     LWRRYSEFELLRSYLLVYYPHIVVPPLPEKRAEFVWHKLSADNMDPDFVERRRIGLEN
                     FLLRIASHPILCRDKIFYLFLTQEGNWKETVNETGFQLKADSRLKALNATFRVKNPDK
                     RFTDLKHYSDELQSVISHLLRVRARVADRLYGVYKVHGNYGRVFSEWSAIEKEMGDGL
                     QSAGHHMDVYASSIDDILEDEEHYADQLKEYLFYAEALRAVCRKHELMQYDLEMAAQD
                     LASKKQQCEELVTGTVRTFSLKGMTTKLFGQETPEQREARIKVLEEQINEGEQQLKSK
                     NLEGREFVKNAWADIERFKEQKNRDLKEALISYAVMQISMCKKGIQVWTNAKECFSKM
                     "
     exon            172..293
                     /gene="SNX4"
                     /gene_synonym="ATG24B"
                     /inference="alignment:Splign:2.1.0"
     exon            294..429
                     /gene="SNX4"
                     /gene_synonym="ATG24B"
                     /inference="alignment:Splign:2.1.0"
     exon            430..579
                     /gene="SNX4"
                     /gene_synonym="ATG24B"
                     /inference="alignment:Splign:2.1.0"
     exon            580..627
                     /gene="SNX4"
                     /gene_synonym="ATG24B"
                     /inference="alignment:Splign:2.1.0"
     exon            628..683
                     /gene="SNX4"
                     /gene_synonym="ATG24B"
                     /inference="alignment:Splign:2.1.0"
     exon            684..756
                     /gene="SNX4"
                     /gene_synonym="ATG24B"
                     /inference="alignment:Splign:2.1.0"
     exon            757..818
                     /gene="SNX4"
                     /gene_synonym="ATG24B"
                     /inference="alignment:Splign:2.1.0"
     exon            819..884
                     /gene="SNX4"
                     /gene_synonym="ATG24B"
                     /inference="alignment:Splign:2.1.0"
     exon            885..974
                     /gene="SNX4"
                     /gene_synonym="ATG24B"
                     /inference="alignment:Splign:2.1.0"
     exon            975..1074
                     /gene="SNX4"
                     /gene_synonym="ATG24B"
                     /inference="alignment:Splign:2.1.0"
     exon            1075..1220
                     /gene="SNX4"
                     /gene_synonym="ATG24B"
                     /inference="alignment:Splign:2.1.0"
     exon            1221..1335
                     /gene="SNX4"
                     /gene_synonym="ATG24B"
                     /inference="alignment:Splign:2.1.0"
     exon            1336..2512
                     /gene="SNX4"
                     /gene_synonym="ATG24B"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2487..2492
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SNX4"
                     /gene_synonym="ATG24B"
                     /note="hexamer: AATAAA"
     polyA_site      2512
                     /gene="SNX4"
                     /gene_synonym="ATG24B"
                     /note="major polyA site"
ORIGIN      
        1 gcactgggtt cgccgcgccg aactgcagcc atggagcagg cacctccgga ccccgagcgg
       61 cagctccagc cggcgccctt ggagccgctg ggctccccag acgctgggct gggggctgcg
      121 gtcggcaagg aagcggaggg ggccggagaa gagagctctg gggtcgacac gatgacacac
      181 aataattttt ggttgaagaa gatagaaatc agtgtttcag aagcagaaaa acgaactgga
      241 agaaatgcca tgaacatgca agaaacatat actgcttacc tcattgaaac aaggtcagtt
      301 gaacataccg atggtcagag tgtcctaaca gactcactat ggcggcgata tagtgaattt
      361 gagttgttga gaagctacct tttagtttac tatccacata ttgttgtgcc acctctgcca
      421 gaaaaacggg cagaatttgt ttggcataaa ctctctgctg acaacatgga tccagatttt
      481 gtggagaggc gacggattgg tttagaaaac tttctcttga ggattgcttc acatcccatc
      541 ctttgtagag acaaaatctt ctatctgttt ttaacacagg aaggtaactg gaaggagact
      601 gtgaatgaaa ctgggtttca gctgaaggca gactccaggt taaaagcgct taatgcaaca
      661 ttcagagtga aaaacccaga caagagattt actgacctta agcactatag tgatgaactg
      721 cagtctgtca tctcacatct tcttcgagtc agagctagag tagcagatcg actctatggt
      781 gtatataaag tacatgggaa ttatggtcga gttttcagtg aatggagtgc catagaaaaa
      841 gaaatgggtg atggactgca gagtgctggt catcatatgg atgtgtatgc atcttctatt
      901 gatgatattt tggaagatga agaacattat gcagatcagt taaaagagta tcttttttat
      961 gcagaagcat tgcgggctgt gtgcaggaaa catgaactta tgcagtatga cttggagatg
     1021 gctgctcagg acttagcatc caagaagcag cagtgtgagg aactggtaac tgggactgtg
     1081 agaacattct ctttgaaggg aatgactacc aagctctttg gtcaagaaac tccagagcag
     1141 agagaagcca gaataaaggt gctagaagaa caaataaatg aaggagaaca acagctaaag
     1201 tctaaaaatc tggaaggcag agaatttgtg aaaaacgcat gggctgatat tgaacgcttc
     1261 aaagaacaaa agaaccgaga cttaaaggag gccctcataa gctatgcagt catgcagatc
     1321 agtatgtgca aaaagggaat tcaagtttgg accaatgcta aggaatgctt tagcaagatg
     1381 taatcctgtg aattgaattt ctcttcaatc aaagtgcccc aaaacagaag cacaagtaaa
     1441 taaaagaaat ttaagtcact acctagtata cataaacata tacaataagt taaataaatt
     1501 cagctttctt taacttaatt gtggtcgtgt taatgtagca caaaaaatat attttaatga
     1561 agattaaata ttataatttg aggttttggg gactggtgct gattccaaaa agttaattta
     1621 ataatatata ccaacagatt gtttgtcacg cttctgaacc aatgactgaa tgtcaagatg
     1681 ttcgttaatt tctagatgtt tgtttcaaga ccagctgttt cagatctatt aatgtaggga
     1741 atttttccct aagattgaat tcctatattt acttggtaag atccactaat ctgttatagg
     1801 gagttgtttt ctcttgcctt atagttgagc tatttggttt gacaaagctc agcagaaact
     1861 tgatgtgaaa aatctacgat tttcttctac attcattgat gccccttgta atgtttgcat
     1921 acactagaaa atgccttcaa tttgtgtttt accagaattt tgatactggt cagaaatttt
     1981 atactgccaa caaagaagac tcaacttctc agatctataa tgggatacat tgtcatcctc
     2041 tagcaactcc tatatagaaa gttttaactg aatatgttac atataagaat taaattcttc
     2101 tcaaataatt cttaacctca gtaatgagcc taaatttact ctgcttggct ctctacacat
     2161 ggcatttcag ggtataagat gtagcatttc aatgtgtaag atatatgtac taaacatatg
     2221 tgttgctatc ttcatcatta acatccttct tttctattgc ttggctgtaa tttttgtaaa
     2281 gataaattat attgtttttt tgtatgtgtg tttgtagtat atgttcagaa ggcaagcatc
     2341 ttcattttgc tagctttgca gaatcttaaa atgtgtactc gttatttcta atgatgtaaa
     2401 aaaaaatccc tagtcctgtt tagcatttga cttttttata tgttttaaat gttgctggat
     2461 ttttgtgctg tttgccaaac ttatacaata aataaatgaa atattgtgct ga
//
