LOCUS       NM_005488               2278 bp    mRNA    linear   PRI 19-SEP-2024
DEFINITION  Homo sapiens target of myb1 membrane trafficking protein (TOM1),
            transcript variant 1, mRNA.
ACCESSION   NM_005488
VERSION     NM_005488.3
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 2278)
  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 2278)
  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 2278)
  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   4  (bases 1 to 2278)
  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   5  (bases 1 to 2278)
  AUTHORS   Fragoza,R., Das,J., Wierbowski,S.D., Liang,J., Tran,T.N., Liang,S.,
            Beltran,J.F., Rivera-Erick,C.A., Ye,K., Wang,T.Y., Yao,L., Mort,M.,
            Stenson,P.D., Cooper,D.N., Wei,X., Keinan,A., Schimenti,J.C.,
            Clark,A.G. and Yu,H.
  TITLE     Extensive disruption of protein interactions by genetic variants
            across the allele frequency spectrum in human populations
  JOURNAL   Nat Commun 10 (1), 4141 (2019)
   PUBMED   31515488
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 2278)
  AUTHORS   Yamakami,M., Yoshimori,T. and Yokosawa,H.
  TITLE     Tom1, a VHS domain-containing protein, interacts with tollip,
            ubiquitin, and clathrin
  JOURNAL   J Biol Chem 278 (52), 52865-52872 (2003)
   PUBMED   14563850
  REMARK    GeneRIF: a Tom1-Tollip complex functions as a factor that links
            polyubiquitinated proteins to clathrin
REFERENCE   7  (bases 1 to 2278)
  AUTHORS   Clark,H.F., Gurney,A.L., Abaya,E., Baker,K., Baldwin,D., Brush,J.,
            Chen,J., Chow,B., Chui,C., Crowley,C., Currell,B., Deuel,B.,
            Dowd,P., Eaton,D., Foster,J., Grimaldi,C., Gu,Q., Hass,P.E.,
            Heldens,S., Huang,A., Kim,H.S., Klimowski,L., Jin,Y., Johnson,S.,
            Lee,J., Lewis,L., Liao,D., Mark,M., Robbie,E., Sanchez,C.,
            Schoenfeld,J., Seshagiri,S., Simmons,L., Singh,J., Smith,V.,
            Stinson,J., Vagts,A., Vandlen,R., Watanabe,C., Wieand,D., Woods,K.,
            Xie,M.H., Yansura,D., Yi,S., Yu,G., Yuan,J., Zhang,M., Zhang,Z.,
            Goddard,A., Wood,W.I., Godowski,P. and Gray,A.
  TITLE     The secreted protein discovery initiative (SPDI), a large-scale
            effort to identify novel human secreted and transmembrane proteins:
            a bioinformatics assessment
  JOURNAL   Genome Res 13 (10), 2265-2270 (2003)
   PUBMED   12975309
  REMARK    Erratum:[Genome Res. 2003 Dec;13(12):2759]
REFERENCE   8  (bases 1 to 2278)
  AUTHORS   Misra,S., Beach,B.M. and Hurley,J.H.
  TITLE     Structure of the VHS domain of human Tom1 (target of myb 1):
            insights into interactions with proteins and membranes
  JOURNAL   Biochemistry 39 (37), 11282-11290 (2000)
   PUBMED   10985773
REFERENCE   9  (bases 1 to 2278)
  AUTHORS   Dunham,I., Shimizu,N., Roe,B.A., Chissoe,S., Hunt,A.R.,
            Collins,J.E., Bruskiewich,R., Beare,D.M., Clamp,M., Smink,L.J.,
            Ainscough,R., Almeida,J.P., Babbage,A., Bagguley,C., Bailey,J.,
            Barlow,K., Bates,K.N., Beasley,O., Bird,C.P., Blakey,S.,
            Bridgeman,A.M., Buck,D., Burgess,J., Burrill,W.D., O'Brien,K.P. et
            al.
  TITLE     The DNA sequence of human chromosome 22
  JOURNAL   Nature 402 (6761), 489-495 (1999)
   PUBMED   10591208
  REMARK    Erratum:[Nature 2000 Apr 20;404(6780):904]
REFERENCE   10 (bases 1 to 2278)
  AUTHORS   Seroussi,E., Kedra,D., Kost-Alimova,M., Sandberg-Nordqvist,A.C.,
            Fransson,I., Jacobs,J.F., Fu,Y., Pan,H.Q., Roe,B.A., Imreh,S. and
            Dumanski,J.P.
  TITLE     TOM1 genes map to human chromosome 22q13.1 and mouse chromosome 8C1
            and encode proteins similar to the endosomal proteins HGS and STAM
  JOURNAL   Genomics 57 (3), 380-388 (1999)
   PUBMED   10329004
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DC297234.1, AJ006973.1 and
            AK097066.1.
            
            On Nov 22, 2018 this sequence version replaced NM_005488.2.
            
            Summary: This gene was identified as a target of the v-myb
            oncogene. The encoded protein shares its N-terminal domain in
            common with proteins associated with vesicular trafficking at the
            endosome. It is recruited to the endosomes by its interaction with
            endofin. Several alternatively spliced transcript variants encoding
            different isoforms have been found for this gene. [provided by
            RefSeq, Oct 2008].
            
            Transcript Variant: This variant (1) represents the most
            predominant transcript and encodes isoform 1.
            
            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 :: SRR1803615.26761.1, AK026576.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000449058.7/ ENSP00000394466.2
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-485               DC297234.1         91-575
            486-2133            AJ006973.1         512-2159
            2134-2278           AK097066.1         1735-1879
FEATURES             Location/Qualifiers
     source          1..2278
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="22"
                     /map="22q12.3"
     gene            1..2278
                     /gene="TOM1"
                     /gene_synonym="IMD85"
                     /note="target of myb1 membrane trafficking protein"
                     /db_xref="GeneID:10043"
                     /db_xref="HGNC:HGNC:11982"
                     /db_xref="MIM:604700"
     exon            1..87
                     /gene="TOM1"
                     /gene_synonym="IMD85"
                     /inference="alignment:Splign:2.1.0"
     CDS             36..1514
                     /gene="TOM1"
                     /gene_synonym="IMD85"
                     /note="isoform 1 is encoded by transcript variant 1;
                     target of myb 1; target of Myb protein 1"
                     /codon_start=1
                     /product="target of Myb1 membrane trafficking protein
                     isoform 1"
                     /protein_id="NP_005479.1"
                     /db_xref="CCDS:CCDS13913.1"
                     /db_xref="GeneID:10043"
                     /db_xref="HGNC:HGNC:11982"
                     /db_xref="MIM:604700"
                     /translation="MDFLLGNPFSSPVGQRIEKATDGSLQSEDWALNMEICDIINETE
                     EGPKDALRAVKKRIVGNKNFHEVMLALTVLETCVKNCGHRFHVLVASQDFVESVLVRT
                     ILPKNNPPTIVHDKVLNLIQSWADAFRSSPDLTGVVTIYEDLRRKGLEFPMTDLDMLS
                     PIHTPQRTVFNSETQSGQDSVGTDSSQQEDSGQHAAPLPAPPILSGDTPIAPTPEQIG
                     KLRSELEMVSGNVRVMSEMLTELVPTQAEPADLELLQELNRTCRAMQQRVLELIPQIA
                     NEQLTEELLIVNDNLNNVFLRHERFERFRTGQTTKAPSEAEPAADLIDMGPDPAATGN
                     LSSQLAGMNLGSSSVRAGLQSLEASGRLEDEFDMFALTRGSSLADQRKEVKYEAPQAT
                     DGLAGALDARQQSTGAIPVTQACLMEDIEQWLSTDVGNDAEEPKGVTSEEFDKFLEER
                     AKAADRLPNLSSPSAEGPPGPPSGPAPRKKTQEKDDDMLFAL"
     exon            88..172
                     /gene="TOM1"
                     /gene_synonym="IMD85"
                     /inference="alignment:Splign:2.1.0"
     exon            173..251
                     /gene="TOM1"
                     /gene_synonym="IMD85"
                     /inference="alignment:Splign:2.1.0"
     exon            252..401
                     /gene="TOM1"
                     /gene_synonym="IMD85"
                     /inference="alignment:Splign:2.1.0"
     exon            402..536
                     /gene="TOM1"
                     /gene_synonym="IMD85"
                     /inference="alignment:Splign:2.1.0"
     exon            537..683
                     /gene="TOM1"
                     /gene_synonym="IMD85"
                     /inference="alignment:Splign:2.1.0"
     exon            684..800
                     /gene="TOM1"
                     /gene_synonym="IMD85"
                     /inference="alignment:Splign:2.1.0"
     exon            801..934
                     /gene="TOM1"
                     /gene_synonym="IMD85"
                     /inference="alignment:Splign:2.1.0"
     exon            935..968
                     /gene="TOM1"
                     /gene_synonym="IMD85"
                     /inference="alignment:Splign:2.1.0"
     exon            969..1062
                     /gene="TOM1"
                     /gene_synonym="IMD85"
                     /inference="alignment:Splign:2.1.0"
     exon            1063..1183
                     /gene="TOM1"
                     /gene_synonym="IMD85"
                     /inference="alignment:Splign:2.1.0"
     exon            1184..1259
                     /gene="TOM1"
                     /gene_synonym="IMD85"
                     /inference="alignment:Splign:2.1.0"
     exon            1260..1319
                     /gene="TOM1"
                     /gene_synonym="IMD85"
                     /inference="alignment:Splign:2.1.0"
     exon            1320..1359
                     /gene="TOM1"
                     /gene_synonym="IMD85"
                     /inference="alignment:Splign:2.1.0"
     exon            1360..2278
                     /gene="TOM1"
                     /gene_synonym="IMD85"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2261..2266
                     /regulatory_class="polyA_signal_sequence"
                     /gene="TOM1"
                     /gene_synonym="IMD85"
                     /note="hexamer: ATTAAA"
     polyA_site      2278
                     /gene="TOM1"
                     /gene_synonym="IMD85"
                     /note="major polyA site"
ORIGIN      
        1 gattcccggg gttggtggca gcggcggtag cagcaatgga ctttctcctg gggaacccgt
       61 tcagctctcc agtgggacag cgcatcgaga aagccacaga tggctccctg cagagcgagg
      121 actgggccct caacatggag atctgcgaca tcatcaacga gacggaggaa ggtcccaaag
      181 atgccctccg agcagtaaag aagagaatcg tggggaataa gaacttccac gaggtgatgc
      241 tggctctcac agtcttagaa acctgtgtca agaactgcgg gcaccgcttc cacgtgctgg
      301 tggccagcca ggacttcgtg gagagtgtgc tggtgaggac catcctgccc aagaacaacc
      361 cacccaccat cgtgcatgac aaagtgctca acctcatcca gtcctgggct gacgcgttcc
      421 gcagctcgcc cgatctgaca ggtgtggtca ccatctatga ggacctgcgg aggaaaggcc
      481 tggagttccc catgactgac ctggacatgc tgtcacccat ccacacaccc cagaggaccg
      541 tgttcaactc agagacacaa tcaggacagg attctgtggg cactgactcc agccagcaag
      601 aggactctgg ccagcatgct gcccctctgc ccgccccgcc catactctcc ggtgacacgc
      661 ccatagcacc aaccccggaa cagattggga agctgcgcag tgagctggag atggtgagtg
      721 ggaacgtgag ggtgatgtcg gagatgctga cggagctggt gcccacccag gccgagcccg
      781 cagacctgga gctgctgcag gagctcaacc gcacgtgccg agccatgcag cagcgggtcc
      841 tggagctcat ccctcagatc gccaatgagc agctgacaga ggagctgctc atcgtcaatg
      901 acaatctcaa caatgtgttc ctgcgccatg aacggtttga acggttccga acaggccaga
      961 ccaccaaggc cccaagtgag gccgagccgg cagctgacct gatcgacatg ggccctgacc
     1021 cagcagccac cggcaacctc tcatcccagc tggcaggaat gaacctgggc tccagcagtg
     1081 tgagagctgg cctgcagtct ctggaggcct ctggtcgact ggaagatgag tttgacatgt
     1141 ttgcgctgac acggggcagc tcactggctg accaacggaa agaggtaaaa tacgaagccc
     1201 cccaagcaac agacggcctg gctggagccc tggacgcccg gcagcagagc actggcgcga
     1261 tcccagtcac ccaggcctgc ctcatggagg acatcgagca gtggctgtcc actgacgtgg
     1321 gtaatgatgc ggaagagcct aagggggtca ccagcgaaga atttgacaaa ttcctggaag
     1381 aacgggccaa agccgcggac cgattgccca acctctccag cccctcagct gaggggcccc
     1441 cgggtccccc atctggccca gcgccccgga agaagaccca ggagaaagat gatgacatgc
     1501 tgtttgcctt atgagtgtgg ggtctggcac cctgcagccc aggtccccac tgctctcaca
     1561 cccttaggct gggacctccc tccctcctct ggtgttaagg ctgctttggg ggtggcttgt
     1621 tacccccttt tcctcctctt tgaagacgga gctgccccag ctgtggctgg gggtgtggag
     1681 gcagtgggat gaactggggg acaggtctgc gctgcagtgg gatctggctg ctctgcctcc
     1741 tttcccaccc cagctgacca tgagactttg ctgagaagtg gaggccccag gacaggctgg
     1801 ctggctggct ggctgcttga cccagtgtga ctctccttca ctgagtgata ccctgctccg
     1861 ggcccatgcc ccaaggagcc cttcagagcc cacactgcca gtcgaggcct ggctggaggc
     1921 tggccacagt ggaaattctg ccgagcctct tgtcccttcc ctgctctgct gcatggggcc
     1981 ccatggcttt ggctggccac tgagggtagg gtgtggaggt gtggaggccc cctgaggagc
     2041 tgcggcggcc caggtacgaa gctgcaactc tgcgcgcagt gggcgagatc tcatcagccc
     2101 caggctgcag gtgaggcttc aggggatgct ggggccccac tgcccctccg ctgccttgcc
     2161 ctccatcctt cctctgttcc ttctggccgg gcaccacagc actggggctc acctcttggt
     2221 tgatcctctt gtactgggag aggtgccttt tgtatcccca attaaaggta gaaaacca
//
