LOCUS       NM_025158               2636 bp    mRNA    linear   PRI 11-FEB-2025
DEFINITION  Homo sapiens RUN and FYVE domain containing 1 (RUFY1), transcript
            variant 1, mRNA.
ACCESSION   NM_025158
VERSION     NM_025158.5
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 2636)
  AUTHORS   Rawat,S., Chatterjee,D., Marwaha,R., Charak,G., Kumar,G., Shaw,S.,
            Khatter,D., Sharma,S., de Heus,C., Liv,N., Klumperman,J., Tuli,A.
            and Sharma,M.
  TITLE     RUFY1 binds Arl8b and mediates endosome-to-TGN CI-M6PR retrieval
            for cargo sorting to lysosomes
  JOURNAL   J Cell Biol 222 (1) (2023)
   PUBMED   36282215
  REMARK    GeneRIF: RUFY1 binds Arl8b and mediates endosome-to-TGN CI-M6PR
            retrieval for cargo sorting to lysosomes.
REFERENCE   2  (bases 1 to 2636)
  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   3  (bases 1 to 2636)
  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   4  (bases 1 to 2636)
  AUTHORS   Zhi,Q., Chen,H., Liu,F., Han,Y., Wan,D., Xu,Z., Kuang,Y. and
            Zhou,J.
  TITLE     Podocalyxin-like protein promotes gastric cancer progression
            through interacting with RUN and FYVE domain containing 1 protein
  JOURNAL   Cancer Sci 110 (1), 118-134 (2019)
   PUBMED   30407695
  REMARK    GeneRIF: Data suggest that targeting the podocalyxin-like protein
            (PODXL)/RUN and FYVE domain containing 1 (RUFY1) complex might
            improve cancer therapy.
            Erratum:[Cancer Sci. 2019 Apr;110(4):1504. doi: 10.1111/cas.13994..
            PMID: 30945404]
REFERENCE   5  (bases 1 to 2636)
  AUTHORS   Boraska,V., Davis,O.S., Cherkas,L.F., Helder,S.G., Harris,J.,
            Krug,I., Liao,T.P., Treasure,J., Ntalla,I., Karhunen,L.,
            Keski-Rahkonen,A., Christakopoulou,D., Raevuori,A., Shin,S.Y.,
            Dedoussis,G.V., Kaprio,J., Soranzo,N., Spector,T.D., Collier,D.A.
            and Zeggini,E.
  TITLE     Genome-wide association analysis of eating disorder-related
            symptoms, behaviors, and personality traits
  JOURNAL   Am J Med Genet B Neuropsychiatr Genet 159B (7), 803-811 (2012)
   PUBMED   22911880
REFERENCE   6  (bases 1 to 2636)
  AUTHORS   Wang,J., Huo,K., Ma,L., Tang,L., Li,D., Huang,X., Yuan,Y., Li,C.,
            Wang,W., Guan,W., Chen,H., Jin,C., Wei,J., Zhang,W., Yang,Y.,
            Liu,Q., Zhou,Y., Zhang,C., Wu,Z., Xu,W., Zhang,Y., Liu,T., Yu,D.,
            Zhang,Y., Chen,L., Zhu,D., Zhong,X., Kang,L., Gan,X., Yu,X., Ma,Q.,
            Yan,J., Zhou,L., Liu,Z., Zhu,Y., Zhou,T., He,F. and Yang,X.
  TITLE     Toward an understanding of the protein interaction network of the
            human liver
  JOURNAL   Mol Syst Biol 7, 536 (2011)
   PUBMED   21988832
  REMARK    Erratum:[Mol Syst Biol. 2017 Dec 18;13(12):965. doi:
            10.15252/msb.20178107.. PMID: 29254952]
            Publication Status: Online-Only
REFERENCE   7  (bases 1 to 2636)
  AUTHORS   Yamamoto,H., Koga,H., Katoh,Y., Takahashi,S., Nakayama,K. and
            Shin,H.W.
  TITLE     Functional cross-talk between Rab14 and Rab4 through a dual
            effector, RUFY1/Rabip4
  JOURNAL   Mol Biol Cell 21 (15), 2746-2755 (2010)
   PUBMED   20534812
  REMARK    GeneRIF: These findings suggest that Rab14 and Rab4 act
            sequentially, together with RUFY1.
REFERENCE   8  (bases 1 to 2636)
  AUTHORS   Hayakawa,A., Hayes,S., Leonard,D., Lambright,D. and Corvera,S.
  TITLE     Evolutionarily conserved structural and functional roles of the
            FYVE domain
  JOURNAL   Biochem Soc Symp (74), 95-105 (2007)
   PUBMED   17233583
  REMARK    Review article
REFERENCE   9  (bases 1 to 2636)
  AUTHORS   Fouraux,M.A., Deneka,M., Ivan,V., van der Heijden,A.,
            Raymackers,J., van Suylekom,D., van Venrooij,W.J., van der
            Sluijs,P. and Pruijn,G.J.
  TITLE     Rabip4' is an effector of rab5 and rab4 and regulates transport
            through early endosomes
  JOURNAL   Mol Biol Cell 15 (2), 611-624 (2004)
   PUBMED   14617813
REFERENCE   10 (bases 1 to 2636)
  AUTHORS   Yang,J., Kim,O., Wu,J. and Qiu,Y.
  TITLE     Interaction between tyrosine kinase Etk and a RUN domain- and FYVE
            domain-containing protein RUFY1. A possible role of ETK in
            regulation of vesicle trafficking
  JOURNAL   J Biol Chem 277 (33), 30219-30226 (2002)
   PUBMED   11877430
  REMARK    GeneRIF: interaction with tyrosine kinase Etk
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC136604.2, CB988835.1,
            AF361055.2, BC032571.1, AK075021.1 and BQ014980.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 22, 2018 this sequence version replaced NM_025158.4.
            
            Summary: This gene encodes a protein that contains a RUN domain and
            a FYVE-type zinc finger domain. The encoded protein binds to
            phosphatidylinositol-3-phosphate (PI3P) and plays a role in early
            endosomal trafficking, tethering and fusion through interactions
            with small GTPases including Rab4, Rab5 and Rab14. Alternatively
            spliced transcript variants encoding multiple isoforms have been
            observed for this gene. [provided by RefSeq, Dec 2011].
            
            Transcript Variant: This variant (1) encodes the longer isoform (a,
            also known as rabip4').
            
            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 :: AF312367.1, SRR1803617.262538.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000319449.9/ ENSP00000325594.4
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-7                 AC136604.2         131797-131803       c
            8-280               CB988835.1         28-300
            281-1404            AF361055.2         247-1370
            1405-1557           BC032571.1         1142-1294
            1558-2381           AK075021.1         1465-2288
            2382-2636           BQ014980.1         32-286              c
FEATURES             Location/Qualifiers
     source          1..2636
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q35.3"
     gene            1..2636
                     /gene="RUFY1"
                     /gene_synonym="RABIP4; ZFYVE12"
                     /note="RUN and FYVE domain containing 1"
                     /db_xref="GeneID:80230"
                     /db_xref="HGNC:HGNC:19760"
                     /db_xref="MIM:610327"
     exon            1..326
                     /gene="RUFY1"
                     /gene_synonym="RABIP4; ZFYVE12"
                     /inference="alignment:Splign:2.1.0"
     CDS             17..2143
                     /gene="RUFY1"
                     /gene_synonym="RABIP4; ZFYVE12"
                     /note="isoform a is encoded by transcript variant 1;
                     la-binding protein 1; FYVE-finger protein EIP1;
                     rab4-interacting protein; zinc finger FYVE
                     domain-containing protein 12"
                     /codon_start=1
                     /product="RUN and FYVE domain-containing protein 1 isoform
                     a"
                     /protein_id="NP_079434.3"
                     /db_xref="CCDS:CCDS4445.2"
                     /db_xref="GeneID:80230"
                     /db_xref="HGNC:HGNC:19760"
                     /db_xref="MIM:610327"
                     /translation="MADREGGCAAGRGRELEPELEPGPGPGSALEPGEEFEIVDRSQL
                     PGPGDLRSATRPRAAEGWSAPILTLARRATGNLSASCGSALRAAAGLGGGDSGDGTAR
                     AASKCQMMEERANLMHMMKLSIKVLLQSALSLGRSLDADHAPLQQFFVVMEHCLKHGL
                     KVKKSFIGQNKSFFGPLELVEKLCPEASDIATSVRNLPELKTAVGRGRAWLYLALMQK
                     KLADYLKVLIDNKHLLSEFYEPEALMMEEEGMVIVGLLVGLNVLDANLCLKGEDLDSQ
                     VGVIDFSLYLKDVQDLDGGKEHERITDVLDQKNYVEELNRHLSCTVGDLQTKIDGLEK
                     TNSKLQEELSAATDRICSLQEEQQQLREQNELIRERSEKSVEITKQDTKVELETYKQT
                     RQGLDEMYSDVWKQLKEEKKVRLELEKELELQIGMKTEMEIAMKLLEKDTHEKQDTLV
                     ALRQQLEEVKAINLQMFHKAQNAESSLQQKNEAITSFEGKTNQVMSSMKQMEERLQHS
                     ERARQGAEERSHKLQQELGGRIGALQLQLSQLHEQCSSLEKELKSEKEQRQALQRELQ
                     HEKDTSSLLRMELQQVEGLKKELRELQDEKAELQKICEEQEQALQEMGLHLSQSKLKM
                     EDIKEVNQALKGHAWLKDDEATHCRQCEKEFSISRRKHHCRNCGHIFCNTCSSNELAL
                     PSYPKPVRVCDSCHTLLLQRCSSTAS"
     exon            327..500
                     /gene="RUFY1"
                     /gene_synonym="RABIP4; ZFYVE12"
                     /inference="alignment:Splign:2.1.0"
     exon            501..618
                     /gene="RUFY1"
                     /gene_synonym="RABIP4; ZFYVE12"
                     /inference="alignment:Splign:2.1.0"
     exon            619..720
                     /gene="RUFY1"
                     /gene_synonym="RABIP4; ZFYVE12"
                     /inference="alignment:Splign:2.1.0"
     exon            721..844
                     /gene="RUFY1"
                     /gene_synonym="RABIP4; ZFYVE12"
                     /inference="alignment:Splign:2.1.0"
     exon            845..906
                     /gene="RUFY1"
                     /gene_synonym="RABIP4; ZFYVE12"
                     /inference="alignment:Splign:2.1.0"
     exon            907..972
                     /gene="RUFY1"
                     /gene_synonym="RABIP4; ZFYVE12"
                     /inference="alignment:Splign:2.1.0"
     exon            973..1042
                     /gene="RUFY1"
                     /gene_synonym="RABIP4; ZFYVE12"
                     /inference="alignment:Splign:2.1.0"
     exon            1043..1144
                     /gene="RUFY1"
                     /gene_synonym="RABIP4; ZFYVE12"
                     /inference="alignment:Splign:2.1.0"
     exon            1145..1261
                     /gene="RUFY1"
                     /gene_synonym="RABIP4; ZFYVE12"
                     /inference="alignment:Splign:2.1.0"
     exon            1262..1429
                     /gene="RUFY1"
                     /gene_synonym="RABIP4; ZFYVE12"
                     /inference="alignment:Splign:2.1.0"
     exon            1430..1527
                     /gene="RUFY1"
                     /gene_synonym="RABIP4; ZFYVE12"
                     /inference="alignment:Splign:2.1.0"
     exon            1528..1647
                     /gene="RUFY1"
                     /gene_synonym="RABIP4; ZFYVE12"
                     /inference="alignment:Splign:2.1.0"
     exon            1648..1777
                     /gene="RUFY1"
                     /gene_synonym="RABIP4; ZFYVE12"
                     /inference="alignment:Splign:2.1.0"
     exon            1778..1872
                     /gene="RUFY1"
                     /gene_synonym="RABIP4; ZFYVE12"
                     /inference="alignment:Splign:2.1.0"
     exon            1873..1921
                     /gene="RUFY1"
                     /gene_synonym="RABIP4; ZFYVE12"
                     /inference="alignment:Splign:2.1.0"
     exon            1922..1999
                     /gene="RUFY1"
                     /gene_synonym="RABIP4; ZFYVE12"
                     /inference="alignment:Splign:2.1.0"
     exon            2000..2636
                     /gene="RUFY1"
                     /gene_synonym="RABIP4; ZFYVE12"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2616..2621
                     /regulatory_class="polyA_signal_sequence"
                     /gene="RUFY1"
                     /gene_synonym="RABIP4; ZFYVE12"
                     /note="hexamer: AATAAA"
     polyA_site      2636
                     /gene="RUFY1"
                     /gene_synonym="RABIP4; ZFYVE12"
                     /note="major polyA site"
ORIGIN      
        1 acatgacacg gccaagatgg ccgaccggga aggcggctgc gctgctgggc gggggcggga
       61 gctggagccg gagctggagc cggggccggg gcccgggtca gcgcttgagc cgggagaaga
      121 gtttgagatc gtggaccgaa gccagctgcc cggcccaggc gacctgcgga gcgcaacgag
      181 gccgcgggcg gccgagggct ggtcggcgcc catcctgacc ctggcacgca gggccaccgg
      241 gaacctgtcg gcgagctgcg ggagcgcgct gcgcgcggcc gcggggctgg gcggcgggga
      301 cagcggggac ggcacggcgc gcgcagcttc taagtgccag atgatggagg agcgtgccaa
      361 cctgatgcac atgatgaaac tcagcatcaa ggtgttgctc cagtcggctc tgagcctggg
      421 ccgcagcctg gatgcggacc atgccccctt gcagcagttc tttgtagtga tggagcactg
      481 cctcaaacat gggctgaaag ttaagaagag ttttattggc caaaataaat cattctttgg
      541 tcctttggag ctggtggaga aactttgtcc agaagcatca gatatagcga ctagtgtcag
      601 aaatcttcca gaattaaaga cagctgtggg aagaggccga gcgtggcttt atcttgcact
      661 catgcaaaag aaactggcag attatctgaa agtgcttata gacaataaac atctcttaag
      721 cgagttctat gagcctgagg ctttaatgat ggaggaagaa gggatggtga ttgttggtct
      781 gctggtggga ctcaatgttc tcgatgccaa tctctgcttg aaaggagaag acttggattc
      841 tcaggttgga gtaatagatt tttccctcta ccttaaggat gtgcaggatc ttgatggtgg
      901 caaggagcat gaaagaatta ctgatgtcct tgatcaaaaa aattatgtgg aagaacttaa
      961 ccggcacttg agctgcacag ttggggatct tcaaaccaag atagatggct tggaaaagac
     1021 taactcaaag cttcaagaag agctttcagc tgcaacagac cgaatttgct cacttcaaga
     1081 agaacagcag cagttaagag aacaaaatga attaattcga gaaagaagtg aaaagagtgt
     1141 agagataaca aaacaggata ccaaagttga gctggagact tacaagcaaa ctcggcaagg
     1201 tctggatgaa atgtacagtg atgtgtggaa gcagctaaaa gaggagaaga aagtccggtt
     1261 ggaactggaa aaagaactgg agttacaaat tggaatgaaa accgaaatgg aaattgcaat
     1321 gaagttactg gaaaaggaca cccacgagaa gcaggacaca ctagttgccc tccgccagca
     1381 gctggaagaa gtcaaagcga ttaatttaca gatgtttcac aaagctcaga atgcagagag
     1441 cagtttgcag cagaagaatg aagccatcac atcctttgaa ggaaaaacca accaagttat
     1501 gtccagcatg aaacaaatgg aagaaaggtt gcagcactcg gagcgggcga ggcagggggc
     1561 tgaggagcgg agccacaagc tgcagcagga gctgggcggg aggatcggcg ccctgcagct
     1621 gcagctctcc cagctgcacg agcaatgctc aagcctggag aaagaattga aatcagaaaa
     1681 agagcaaaga caggctcttc agcgcgaatt acagcacgag aaagacactt cctctctact
     1741 caggatggag ctgcaacaag tggaaggact gaaaaaggag ttgcgggagc ttcaggacga
     1801 gaaggcagag ctgcagaaga tctgcgagga gcaggaacaa gccctccagg aaatgggcct
     1861 gcacctcagc cagtccaagc tgaagatgga agatataaaa gaagtgaacc aggcactgaa
     1921 gggccacgcc tggctgaaag atgacgaagc gacacactgt aggcagtgtg agaaggagtt
     1981 ctccatttcc cggagaaagc accactgccg gaactgtggc cacatcttct gcaacacctg
     2041 ctccagcaac gagctggccc tgccctccta ccccaagccg gtgcgagtgt gcgacagctg
     2101 ccacaccctg ctcctgcagc gctgctcctc cacggcctcc tgaacgtccg tcctcaggag
     2161 cacagcctca cggacagtgc caaaccctgt gggtctccag gggcttggga aatgtgttct
     2221 ttcccaagag tatcaaagga aagaatcaaa tttcttgccc ggtcactggc actccagaag
     2281 acagcgtgcc ggaaccggca gctctcacct ttctgtgact tgttcggaat taactcctct
     2341 ggatggaaac ttccatctta cttggttaca tcacggctct ggttcagata caacttcatg
     2401 attttgctac tatcattttt cacttttcaa agaatttaac ctattttaca gcagttcagt
     2461 tctgctagtg agtagttttc ctctcctacc ttccttctaa aaacctgatt catgcacagc
     2521 gtttgacaca catggagtct gccagtgtgc cttctctgct tcagacaaga gatctgccat
     2581 ttcatgccct tgtgactacc tatcattggc cctgcaataa aatcatttat ttttca
//
