LOCUS       NM_021249               3438 bp    mRNA    linear   PRI 19-SEP-2024
DEFINITION  Homo sapiens sorting nexin 6 (SNX6), transcript variant 1, mRNA.
ACCESSION   NM_021249
VERSION     NM_021249.5
KEYWORDS    RefSeq.
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 3438)
  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 3438)
  AUTHORS   Ghosh,C., Xing,Y., Li,S., Hoyle,R.G., Sun,M., Li,J. and Sun,Y.
  TITLE     Sorting nexin 6 interacts with Cullin3 and regulates programmed
            death ligand 1 expression
  JOURNAL   FEBS Lett 595 (20), 2558-2569 (2021)
   PUBMED   34510437
  REMARK    GeneRIF: Sorting nexin 6 interacts with Cullin3 and regulates
            programmed death ligand 1 expression.
REFERENCE   3  (bases 1 to 3438)
  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   4  (bases 1 to 3438)
  AUTHORS   Haenig,C., Atias,N., Taylor,A.K., Mazza,A., Schaefer,M.H., Russ,J.,
            Riechers,S.P., Jain,S., Coughlin,M., Fontaine,J.F., Freibaum,B.D.,
            Brusendorf,L., Zenkner,M., Porras,P., Stroedicke,M., Schnoegl,S.,
            Arnsburg,K., Boeddrich,A., Pigazzini,L., Heutink,P., Taylor,J.P.,
            Kirstein,J., Andrade-Navarro,M.A., Sharan,R. and Wanker,E.E.
  TITLE     Interactome Mapping Provides a Network of Neurodegenerative Disease
            Proteins and Uncovers Widespread Protein Aggregation in Affected
            Brains
  JOURNAL   Cell Rep 32 (7), 108050 (2020)
   PUBMED   32814053
REFERENCE   5  (bases 1 to 3438)
  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 3438)
  AUTHORS   Camargo,L.M., Collura,V., Rain,J.C., Mizuguchi,K., Hermjakob,H.,
            Kerrien,S., Bonnert,T.P., Whiting,P.J. and Brandon,N.J.
  TITLE     Disrupted in Schizophrenia 1 Interactome: evidence for the close
            connectivity of risk genes and a potential synaptic basis for
            schizophrenia
  JOURNAL   Mol Psychiatry 12 (1), 74-86 (2007)
   PUBMED   17043677
REFERENCE   7  (bases 1 to 3438)
  AUTHORS   Ishibashi,Y., Maita,H., Yano,M., Koike,N., Tamai,K., Ariga,H. and
            Iguchi-Ariga,S.M.
  TITLE     Pim-1 translocates sorting nexin 6/TRAF4-associated factor 2 from
            cytoplasm to nucleus
  JOURNAL   FEBS Lett 506 (1), 33-38 (2001)
   PUBMED   11591366
REFERENCE   8  (bases 1 to 3438)
  AUTHORS   Teasdale,R.D., Loci,D., Houghton,F., Karlsson,L. and Gleeson,P.A.
  TITLE     A large family of endosome-localized proteins related to sorting
            nexin 1
  JOURNAL   Biochem J 358 (Pt 1), 7-16 (2001)
   PUBMED   11485546
REFERENCE   9  (bases 1 to 3438)
  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   10 (bases 1 to 3438)
  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
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DB021488.1, AL445883.3,
            BC001798.1, BI870378.1, AF121856.2, AK124315.1 and AI446034.1.
            
            On Oct 10, 2018 this sequence version replaced NM_021249.4.
            
            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 associates with the long isoform of the
            leptin receptor, the transforming growth factor-beta family of
            receptor serine-threonine kinases, and with receptor tyrosine
            kinases for platelet-derived growth factor, insulin, and epidermal
            growth factor. This protein may form oligomeric complexes with
            family member proteins through interactions of both the PX domain
            and the coiled coil regions of the molecules. Translocation of this
            protein from the cytoplasm to the nucleus occurs after binding to
            proviral integration site 1 protein. This gene results in two
            transcripts encoding two distinct isoforms. [provided by RefSeq,
            Jul 2008].
            
            Transcript Variant: This variant (1) retains an intron in the 5'
            UTR and represents the longest transcript. The resulting isoform
            (a) has a shorter N-terminus compared to isoform b.
            
            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 :: SRR1803611.110079.1,
                                           SRR1660805.54258.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-38                DB021488.1         36-73
            39-39               AL445883.3         140546-140546
            40-844              BC001798.1         1-805
            845-1442            BI870378.1         82-679
            1443-1624           BC001798.1         1404-1585
            1625-2122           AF121856.2         1450-1947
            2123-3119           AK124315.1         1275-2271
            3120-3438           AI446034.1         9-327               c
FEATURES             Location/Qualifiers
     source          1..3438
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="14"
                     /map="14q13.1"
     gene            1..3438
                     /gene="SNX6"
                     /gene_synonym="MSTP010; TFAF2"
                     /note="sorting nexin 6"
                     /db_xref="GeneID:58533"
                     /db_xref="HGNC:HGNC:14970"
                     /db_xref="MIM:606098"
     exon            1..242
                     /gene="SNX6"
                     /gene_synonym="MSTP010; TFAF2"
                     /inference="alignment:Splign:2.1.0"
     exon            243..347
                     /gene="SNX6"
                     /gene_synonym="MSTP010; TFAF2"
                     /inference="alignment:Splign:2.1.0"
     exon            348..458
                     /gene="SNX6"
                     /gene_synonym="MSTP010; TFAF2"
                     /inference="alignment:Splign:2.1.0"
     exon            459..580
                     /gene="SNX6"
                     /gene_synonym="MSTP010; TFAF2"
                     /inference="alignment:Splign:2.1.0"
     CDS             537..1409
                     /gene="SNX6"
                     /gene_synonym="MSTP010; TFAF2"
                     /note="isoform a is encoded by transcript variant 1; tumor
                     necrosis factor receptor-associated factor
                     4(TRAF4)-associated factor 2; TRAF4-associated factor 2"
                     /codon_start=1
                     /product="sorting nexin-6 isoform a"
                     /protein_id="NP_067072.3"
                     /db_xref="CCDS:CCDS9648.1"
                     /db_xref="GeneID:58533"
                     /db_xref="HGNC:HGNC:14970"
                     /db_xref="MIM:606098"
                     /translation="MTKEEFTKMKQELEAEYLAIFKKTVAMHEVFLCRVAAHPILRRD
                     LNFHVFLEYNQDLSVRGKNKKEKLEDFFKNMVKSADGVIVSGVKDVDDFFEHERTFLL
                     EYHNRVKDASAKSDRMTRSHKSAADDYNRIGSSLYALGTQDSTDICKFFLKVSELFDK
                     TRKIEARVSADEDLKLSDLLKYYLRESQAAKDLLYRRSRSLVDYENANKALDKARAKN
                     KDVLQAETSQQLCCQKFEKISESAKQELIDFKTRRVAAFRKNLVELAELELKHAKGNL
                     QLLQNCLAVLNGDT"
     exon            581..704
                     /gene="SNX6"
                     /gene_synonym="MSTP010; TFAF2"
                     /inference="alignment:Splign:2.1.0"
     exon            705..800
                     /gene="SNX6"
                     /gene_synonym="MSTP010; TFAF2"
                     /inference="alignment:Splign:2.1.0"
     exon            801..906
                     /gene="SNX6"
                     /gene_synonym="MSTP010; TFAF2"
                     /inference="alignment:Splign:2.1.0"
     exon            907..982
                     /gene="SNX6"
                     /gene_synonym="MSTP010; TFAF2"
                     /inference="alignment:Splign:2.1.0"
     exon            983..1022
                     /gene="SNX6"
                     /gene_synonym="MSTP010; TFAF2"
                     /inference="alignment:Splign:2.1.0"
     exon            1023..1109
                     /gene="SNX6"
                     /gene_synonym="MSTP010; TFAF2"
                     /inference="alignment:Splign:2.1.0"
     exon            1110..1269
                     /gene="SNX6"
                     /gene_synonym="MSTP010; TFAF2"
                     /inference="alignment:Splign:2.1.0"
     exon            1270..1355
                     /gene="SNX6"
                     /gene_synonym="MSTP010; TFAF2"
                     /inference="alignment:Splign:2.1.0"
     exon            1356..3438
                     /gene="SNX6"
                     /gene_synonym="MSTP010; TFAF2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2027..2032
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SNX6"
                     /gene_synonym="MSTP010; TFAF2"
                     /note="hexamer: AATAAA"
     polyA_site      2047
                     /gene="SNX6"
                     /gene_synonym="MSTP010; TFAF2"
                     /note="major polyA site"
     regulatory      2101..2106
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SNX6"
                     /gene_synonym="MSTP010; TFAF2"
                     /note="hexamer: AATAAA"
     polyA_site      2128
                     /gene="SNX6"
                     /gene_synonym="MSTP010; TFAF2"
     regulatory      3095..3100
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SNX6"
                     /gene_synonym="MSTP010; TFAF2"
                     /note="hexamer: AATAAA"
     polyA_site      3130
                     /gene="SNX6"
                     /gene_synonym="MSTP010; TFAF2"
     regulatory      3418..3423
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SNX6"
                     /gene_synonym="MSTP010; TFAF2"
                     /note="hexamer: AATGAA"
     polyA_site      3438
                     /gene="SNX6"
                     /gene_synonym="MSTP010; TFAF2"
ORIGIN      
        1 gcgcctgcgc cggccctcgc ctcggagcag ccatgatggt gggtgttctc cgcggcgccg
       61 agtcccggga gcgcggtggg ggcagcgggc gcggggcggg cgcggggacc gcgccagcct
      121 gtcactaatg tctccctttg tgtctccccc atctcatcct tttccccggc gcgccgtgcc
      181 cgccgacccc acaggaaggc ctggacgacg gcccggactt cctctcagaa gaggaccgcg
      241 gacttaaagc aataaatgta gatcttcaaa gtgatgctgc tctgcaggtg gacatttctg
      301 atgctcttag tgagcgggat aaagtaaaat tcactgttca cacaaagagt tcattgccaa
      361 attttaaaca aaacgagttt tcagttgttc ggcaacatga ggaatttatc tggcttcatg
      421 attcctttgt tgaaaatgaa gactatgcag gttatatcat tccaccagca ccaccaagac
      481 ctgattttga tgcttcaagg gaaaaactac agaagcttgg tgaaggagaa gggtcaatga
      541 cgaaggaaga attcacaaag atgaaacagg aactggaagc tgaatatttg gcaatattca
      601 agaagacagt tgcgatgcat gaagtgttcc tgtgtcgtgt ggcagcacat cctattttga
      661 gaagagattt aaatttccat gtcttcttgg aatataatca agatttgagt gtgcgaggaa
      721 aaaataaaaa agagaaactt gaagacttct ttaaaaacat ggttaaatca gcagatggag
      781 taatcgtttc aggagtaaag gatgtagatg atttctttga gcacgaacga acatttcttt
      841 tggagtatca taaccgagtt aaggatgcat ctgctaaatc tgatagaatg acaagatccc
      901 acaaaagtgc tgcagatgat tacaatagaa ttggttcttc attatatgct ttaggaactc
      961 aggattctac agatatatgc aagttttttc tcaaagtttc agaactgttc gataaaacaa
     1021 gaaaaataga agcacgagtg tctgctgatg aagacctcaa actttctgat cttttaaaat
     1081 attacttaag agaatctcaa gctgctaagg atctcctgta tcgaaggtct aggtcactag
     1141 tggattatga aaatgctaat aaagcactgg ataaagcaag agcaaaaaat aaagatgttc
     1201 tacaggccga aacttcccaa caattatgtt gtcagaaatt tgaaaaaata tctgagtctg
     1261 caaaacaaga acttatagat tttaagacaa gaagagttgc tgcattcaga aaaaatttag
     1321 tggaactggc agagttagaa ctgaagcatg caaagggtaa tctacagttg ctgcagaact
     1381 gcctggcagt gttaaatgga gacacataag ccacactccg ccttcctgtt aaaaagggct
     1441 gccttccttc aaattttatt tttgttttct taatgatgtt aagcatttat gctcactgga
     1501 aacaaacaaa aagcagctga aaaagtgcat caactcctct ttttctgaga aacatggagc
     1561 agcgcacgcc caggcgatgc cagtctgtgt gccgtgatgc cgcactgtgt tccccatgac
     1621 agtggtccat catcgtgcac tcgtcatact cagaagtcca aagttcattc ttctttaaag
     1681 tagcctctat aactctgttt attttataaa tagtattcct tatggctgcc actcttattt
     1741 acctttaaat aatttctgaa atttaacctt ttcagaatgc attgttgaaa caagataaag
     1801 attgcctttt ttgaattttt taaattttgt ttttaaaagc atataccacc ttagttcatt
     1861 catgtatcct ggtaaagcat cttaatcaga cttattttta attactgaat atttcttaga
     1921 cgttttggga cagattttat gtaatcttta taagtatgat ttctgaagaa aagcaaatgc
     1981 attagtatgt ttgccttaaa cttgtagact aaaccaagta ttgtaaaata aacagcgata
     2041 acagtgatag tttttaactc tatggtcatt gtatcactct ggaaaatgtg gagtagctgt
     2101 aataaatcta ctcctgtatt atgctttaca gtgcaggtct tagtttttct tttttctcat
     2161 ttcttttgaa atggcatctc gaacaaagtc caccaatccc tttacaaaag aatgaactgc
     2221 tcctctgtgt gtacttcata gaaggtggaa tcggacagag gcaggttagt gacagttatt
     2281 cctgaaatac aggagcagag tacagtctgt tgtggtttcc cggattccgc gcctagctca
     2341 gccaattaag catgagacat aggccattga gccacttagt agttatgcga gtggatagat
     2401 tggtatgtag agggaaagag gtctgctgta aagaacaaca cttgtttgtc tgtggggaaa
     2461 gaaaagcaga atacttgaga tgaaagttgg catacaaata ggatactatc gccagtagtt
     2521 atattacaaa cattatcggc ctttctagtg tgaatgaaca ttagacacat tattgtcatt
     2581 cctagtttaa agttaaggtt gcgtggttgg atttttccac tatctttttc taatttttct
     2641 accatttgga gaccgtaggc atttgggcct gtcacccctt ggatgggttc ctagtttgtt
     2701 tacattttcc tgaaccctcc tgagcgcccg ttcttggtct aatccccagt cgtgatgatt
     2761 ccacacttcc tcagccgcat gttgtcttgc ctcattcatg agctggtcag cgtttcgtct
     2821 ctttaactga catgttcccc agtgctgttt gaactgttga gtttccgttg ctggctgagt
     2881 gcgttttgtc cttcacgtaa ccttcgctgg taaaaataag cccatgtgat gtccaccagt
     2941 ggatgaatgc tggaccgaga gccctagctt ctggatccag gtctaggccc ttcatctgct
     3001 gctctgtggc ccagggcagg tttgcttgac ctctgcctca gttctcgact ctaaaggaca
     3061 tactgaccta cctcacaggg gtgttgtgag gattaataaa tgttggtact ctgctttgga
     3121 aatgtgaaaa tgctgtgtaa atgttaagaa atactaagta tagggccaga agctatacag
     3181 tgtttcactt aaccgtttgc cattctgtat ttaccaaggt ggtcttttct ggggaaggaa
     3241 gtagagtgga aggtgcatcc cttggcccct ggtttacatt attagggtgc ttattgtagg
     3301 aatgcactct aaaaagtggg cgtagaatga aagcagccgt ccagtggtcc tcccttttct
     3361 gtagtttcac ttttcttgct tcaagttaca gcagtcacct gaaatctgaa aatactaaat
     3421 gaaaaactcc agaaacaa
//
