LOCUS       NM_198483               2526 bp    mRNA    linear   PRI 26-OCT-2024
DEFINITION  Homo sapiens RUN and FYVE domain containing 4 (RUFY4), transcript
            variant 1, mRNA.
ACCESSION   NM_198483 XM_209499
VERSION     NM_198483.4
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 2526)
  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   2  (bases 1 to 2526)
  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   3  (bases 1 to 2526)
  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   4  (bases 1 to 2526)
  AUTHORS   Chen,S., Fragoza,R., Klei,L., Liu,Y., Wang,J., Roeder,K., Devlin,B.
            and Yu,H.
  TITLE     An interactome perturbation framework prioritizes damaging missense
            mutations for developmental disorders
  JOURNAL   Nat Genet 50 (7), 1032-1040 (2018)
   PUBMED   29892012
REFERENCE   5  (bases 1 to 2526)
  AUTHORS   Terawaki,S., Camosseto,V., Prete,F., Wenger,T., Papadopoulos,A.,
            Rondeau,C., Combes,A., Rodriguez Rodrigues,C., Vu Manh,T.P.,
            Fallet,M., English,L., Santamaria,R., Soares,A.R., Weil,T.,
            Hammad,H., Desjardins,M., Gorvel,J.P., Santos,M.A., Gatti,E. and
            Pierre,P.
  TITLE     RUN and FYVE domain-containing protein 4 enhances autophagy and
            lysosome tethering in response to Interleukin-4
  JOURNAL   J Cell Biol 210 (7), 1133-1152 (2015)
   PUBMED   26416964
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC124768.4.
            
            On Oct 14, 2020 this sequence version replaced NM_198483.3.
            
            Transcript Variant: This variant (1) represents the shorter
            transcript but encodes the supported protein. The exon combination
            of this variant lacks full-length support in human; it is predicted
            based on alignments of partial human transcripts and homologous
            transcripts from mouse GeneID:435626.
            
            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.
            
            ##Evidence-Data-START##
            Transcript exon combination :: SRR18074968.3429666.1,
                                           SRR7346977.2097001.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2149876, SAMEA2153031
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000697321.1/ ENSP00000513250.1
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-96                AC124768.4         4853-4948
            97-174              AC124768.4         5081-5158
            175-326             AC124768.4         6100-6251
            327-433             AC124768.4         6353-6459
            434-559             AC124768.4         7974-8099
            560-666             AC124768.4         8379-8485
            667-810             AC124768.4         8843-8986
            811-880             AC124768.4         9416-9485
            881-1528            AC124768.4         10693-11340
            1529-1635           AC124768.4         12027-12133
            1636-1782           AC124768.4         18710-18856
            1783-1893           AC124768.4         24852-24962
            1894-2526           AC124768.4         25552-26184
FEATURES             Location/Qualifiers
     source          1..2526
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
                     /map="2q35"
     gene            1..2526
                     /gene="RUFY4"
                     /gene_synonym="ZFYVE31"
                     /note="RUN and FYVE domain containing 4"
                     /db_xref="GeneID:285180"
                     /db_xref="HGNC:HGNC:24804"
                     /db_xref="MIM:620994"
     exon            1..96
                     /gene="RUFY4"
                     /gene_synonym="ZFYVE31"
                     /inference="alignment:Splign:2.1.0"
     exon            97..174
                     /gene="RUFY4"
                     /gene_synonym="ZFYVE31"
                     /inference="alignment:Splign:2.1.0"
     exon            175..326
                     /gene="RUFY4"
                     /gene_synonym="ZFYVE31"
                     /inference="alignment:Splign:2.1.0"
     CDS             281..1996
                     /gene="RUFY4"
                     /gene_synonym="ZFYVE31"
                     /codon_start=1
                     /product="RUN and FYVE domain-containing protein 4"
                     /protein_id="NP_940885.2"
                     /db_xref="GeneID:285180"
                     /db_xref="HGNC:HGNC:24804"
                     /db_xref="MIM:620994"
                     /translation="MAEEGAILKVTKDLRAAVSAILQGYGDGQGPVTDTSAELHRLCG
                     CLELLLQFDQKEQKSFLGPRKDYWDFLCTALRRQRGNMEPIHFVRSQDKLKTPLGKGR
                     AFIRFCLARGQLAEALQLCLLNSELTREWYGPRSPLLCPERQEDILDSLYALNGVAFE
                     LDLQQPDLDGAWPMFSESRCSSSTQTQGRRPRKNKDAPKKIPAAYGGPENVQIEDSHT
                     SQAICLQDAPSGQQLAGLPRSQQQRHLPFFLEKKGESSRKHRYPQSMWEPEGKELQLD
                     QEERAPWIEIFLGNSTPSTQGQGKGAMGTQKEVIGMEAEVTGVLLVAEGQRTTEGTHK
                     KEAEWSHVQRLLMPSPRGAVEGAVSGSRQGSGGSSILGEPWVLQGHATKEDSTVENPQ
                     VQTEVTLVARREEQAEVSLQDEIKSLRLGLRKAEEQAQRQEQLLREQEGELQALREQL
                     SRCQEERAELQAQLEQKQQEAERRDAMYQEELGGQRDLVQAMKRRVLELIQEKDRLWQ
                     RLQHLSSMAPECCVACSKIFGRFSRRYPCRLCGGLLCHACSMDYKKRDRCCPPCAQGR
                     EAQVT"
     exon            327..433
                     /gene="RUFY4"
                     /gene_synonym="ZFYVE31"
                     /inference="alignment:Splign:2.1.0"
     exon            434..559
                     /gene="RUFY4"
                     /gene_synonym="ZFYVE31"
                     /inference="alignment:Splign:2.1.0"
     exon            560..666
                     /gene="RUFY4"
                     /gene_synonym="ZFYVE31"
                     /inference="alignment:Splign:2.1.0"
     exon            667..810
                     /gene="RUFY4"
                     /gene_synonym="ZFYVE31"
                     /inference="alignment:Splign:2.1.0"
     exon            811..880
                     /gene="RUFY4"
                     /gene_synonym="ZFYVE31"
                     /inference="alignment:Splign:2.1.0"
     exon            881..1528
                     /gene="RUFY4"
                     /gene_synonym="ZFYVE31"
                     /inference="alignment:Splign:2.1.0"
     exon            1529..1635
                     /gene="RUFY4"
                     /gene_synonym="ZFYVE31"
                     /inference="alignment:Splign:2.1.0"
     exon            1636..1782
                     /gene="RUFY4"
                     /gene_synonym="ZFYVE31"
                     /inference="alignment:Splign:2.1.0"
     exon            1783..1893
                     /gene="RUFY4"
                     /gene_synonym="ZFYVE31"
                     /inference="alignment:Splign:2.1.0"
     exon            1894..2526
                     /gene="RUFY4"
                     /gene_synonym="ZFYVE31"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2504..2509
                     /regulatory_class="polyA_signal_sequence"
                     /gene="RUFY4"
                     /gene_synonym="ZFYVE31"
                     /note="hexamer: GATAAA"
     polyA_site      2526
                     /gene="RUFY4"
                     /gene_synonym="ZFYVE31"
                     /note="major polyA site"
ORIGIN      
        1 gtaaatcctg ggactgctgt gcaaggcaga gtcactaggg acggactctg gcagcagagc
       61 tgcgctctcg tgccccagcc agccaggctc tcctgggatc tgggctggaa ggggctgccg
      121 agaccatcag tccaatcttt ggtctacagg ttgggaaact gaggctcaag gaaggctctg
      181 cgtcctgctt tgtgtaagga gagagctggg cagtgaggcc gaaagtcctt cctgagctca
      241 cagtccaagt tgcaaggaat cacatcattt ccaagtaccc atggcagaag agggagccat
      301 cctcaaggtc accaaagacc taagagctgc cgtctctgcc atcctccagg gctatgggga
      361 tgggcagggg ccagtgacgg acaccagtgc cgagctgcac agactctgtg gctgcctgga
      421 gctgctgctg cagtttgacc agaaagagca gaagagcttc ctggggcctc ggaaggatta
      481 ctgggacttt ctctgcactg ccctacgacg gcagcgggga aacatggagc caatccactt
      541 tgtccgttcc caggacaagt tgaagacccc tctggggaaa ggccgtgcct tcatccgctt
      601 ctgcctggcc cgtgggcagc tggctgaggc cctgcagctt tgcctcctga actcagagct
      661 caccagggaa tggtatggac cccggagccc tctgctctgc ccagaacgcc aagaagacat
      721 cctggactct ctctatgctc tcaatggggt ggccttcgag ttggacctcc agcagccaga
      781 cctggatgga gcctggccca tgttctcaga gtcacgctgc tccagttcca cccaaaccca
      841 gggaaggaga cccagaaaaa acaaagatgc cccaaagaag atcccagccg catatggagg
      901 gcctgaaaat gtccagattg aggactcaca caccagtcaa gccatctgtc tgcaagatgc
      961 acccagtgga cagcagctgg cagggcttcc caggtcccag caacaaaggc atcttccttt
     1021 ctttttggaa aagaaggggg aaagttccag gaaacatagg tacccccaga gcatgtggga
     1081 gccagaaggg aaggagcttc agctagacca ggaggaaaga gccccatgga ttgagatctt
     1141 cctggggaac tcaacaccca gcacccaggg acaggggaag ggggctatgg gcactcagaa
     1201 ggaggtgata gggatggagg ctgaggtcac aggggttctg ctggttgcag agggtcagag
     1261 aacaacagag gggactcaca aaaaggaagc agagtggagt cacgtccaga ggctgctgat
     1321 gcccagcccc agaggggctg tagagggagc agtatcaggg agcaggcagg ggtcgggggg
     1381 ctctagcatc ctgggggagc cctgggtcct tcagggacac gcaacaaagg aagactctac
     1441 cgtggagaat ccacaagtgc aaacagaagt gacccttgtg gccagaaggg aggagcaagc
     1501 cgaggtgtcc ctgcaggacg agatcaagag cctcagactt gggctccgga aggctgagga
     1561 gcaggcccag cgccaggagc agctgctgag ggagcaggag ggggagctgc aggcacttcg
     1621 ggagcagctc agcaggtgtc aggaagagag agccgagctg caggcacagc tggagcagaa
     1681 gcaacaggag gctgagagga gggatgccat gtaccaggag gagcttggag ggcagcggga
     1741 cttggtccag gccatgaaga ggcgggtgtt ggaactgatc caagagaagg accgcctgtg
     1801 gcagaggctc cagcatctct cttccatggc tcccgagtgc tgtgtggcct gtagcaagat
     1861 ctttggccga ttttctcggc ggtatccatg caggctctgt ggaggcctgc tctgccatgc
     1921 ttgctccatg gattacaaga agagagaccg ctgctgccca ccctgcgccc agggaagaga
     1981 agcccaggtc acctgaccaa gaccaagacc agcccatgac tggcctccca cctgcctgcc
     2041 catcccactc aatccactcc ctgcccgtag ctcttcccag ccctcttgtt tgtccagtcc
     2101 tcattctaga cactgaagat ctaaggcacc agcacttctg tgggcagagt agggtgtggg
     2161 gagtggttcc agccctgcaa ctaccacaac gagccaggtg actttggcga agctctcagt
     2221 gctcagggct tcttctctaa tgttaagagt tgggccccat cctctctaaa gtccctctgg
     2281 gctcagcaaa tccatgactg tggataagac cccagcagcc ctgacatttc tcctccacac
     2341 tccccactca cccagcagcg gtgcccacct ttcctgattc acgagaagtg aagcctgcac
     2401 tatcttggac tctccagcag cttcctgtct ggagtcagct tcagggatct gtgtttgtgt
     2461 tgctgtgttt ctttttatgt ttattgaagt actactgaca tatgataaac atcacagagt
     2521 gtacaa
//
