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    RUFY1 RUN and FYVE domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 80230, updated on 10-Dec-2024

    Summary

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    Official Symbol
    RUFY1provided by HGNC
    Official Full Name
    RUN and FYVE domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:19760
    See related
    Ensembl:ENSG00000176783 MIM:610327; AllianceGenome:HGNC:19760
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RABIP4; ZFYVE12
    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]
    Expression
    Ubiquitous expression in spleen (RPKM 10.3), thyroid (RPKM 9.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RUFY1 in Genome Data Viewer
    Location:
    5q35.3
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (179550554..179610012)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (180103365..180164461)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (178977555..179037013)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene chromosome 5 open reading frame 60-like Neighboring gene uncharacterized LOC128966623 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:178956772-178957378 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:178957379-178957984 Neighboring gene uncharacterized LOC105377762 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:178981435-178981935 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:178982640-178982816 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:178998880-178999380 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:179003374-179004573 Neighboring gene peroxiredoxin 2 pseudogene 3 Neighboring gene RUFY1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:179033750-179034250 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:179034251-179034751 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23752 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23753 Neighboring gene heterogeneous nuclear ribonucleoprotein H1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23754 Neighboring gene Sharpr-MPRA regulatory region 11836 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:179051499-179052283 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:179059505-179060005 Neighboring gene SPATA31 subfamily J member 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Evolutionarily conserved structural and functional roles of the FYVE domain. Hayakawa A, et al. Biochem Soc Symp, 2007. PMID 17233583
    2. Functional cross-talk between Rab14 and Rab4 through a dual effector, RUFY1/Rabip4. Yamamoto H, et al. Mol Biol Cell, 2010 Aug 1. PMID 20534812, Free PMC Article
    3. Early-Onset Alzheimer Disease and Candidate Risk Genes Involved in Endolysosomal Transport. Kunkle BW, et al. JAMA Neurol, 2017 Sep 1. PMID 28738127, Free PMC Article
    4. Rabip4' is an effector of rab5 and rab4 and regulates transport through early endosomes. Fouraux MA, et al. Mol Biol Cell, 2004 Feb. PMID 14617813, Free PMC Article
    5. 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. Yang J, et al. J Biol Chem, 2002 Aug 16. PMID 11877430

    See all (61) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RUFY1 binds Arl8b and mediates endosome-to-TGN CI-M6PR retrieval for cargo sorting to lysosomes.
      Title: RUFY1 binds Arl8b and mediates endosome-to-TGN CI-M6PR retrieval for cargo sorting to lysosomes.
    2. Data suggest that targeting the podocalyxin-like protein (PODXL)/RUN and FYVE domain containing 1 (RUFY1) complex might improve cancer therapy.
      Title: Podocalyxin-like protein promotes gastric cancer progression through interacting with RUN and FYVE domain containing 1 protein.
    3. RUFY1 may be involved in endolysosomal transport-a process known to be important to development of early onset AD.
      Title: Early-Onset Alzheimer Disease and Candidate Risk Genes Involved in Endolysosomal Transport.
    4. Data indicate that RUN and FYVE domain protein Rabip4'(RUFY1) interacts specifically and directly with adaptor protein complex AP-3.
      Title: AP-3 and Rabip4' coordinately regulate spatial distribution of lysosomes.
    5. These findings suggest that Rab14 and Rab4 act sequentially, together with RUFY1.
      Title: Functional cross-talk between Rab14 and Rab4 through a dual effector, RUFY1/Rabip4.
    6. interaction with tyrosine kinase Etk
      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.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association analysis of eating disorder-related symptoms, behaviors, and personality traits.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ22251

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables SH2 domain binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables SH3 domain binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables lipid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-macromolecule adaptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in early endosome to Golgi transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in endocytosis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in endosomal vesicle fusion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of endocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of endocytosis IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    involved_in small GTPase-mediated signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    is_active_in early endosome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in early endosome membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in intracellular membrane-bounded organelle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    RUN and FYVE domain-containing protein 1
    Names
    FYVE-finger protein EIP1
    la-binding protein 1
    rab4-interacting protein
    zinc finger FYVE domain-containing protein 12

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_031967.1 RefSeqGene

      Range
      4994..64452
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001040451.3 → NP_001035541.1  RUN and FYVE domain-containing protein 1 isoform b

      See identical proteins and their annotated locations for NP_001035541.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. Variants 2 and 3 encode the same isoform (b) which has a shorter N-terminus compared to isoform a.
      Source sequence(s)
      AK075021, AK291926, BC032571, BQ014980
      Consensus CDS
      CCDS34312.1
      UniProtKB/TrEMBL
      A8K7B1
      Related
      ENSP00000390025.2, ENST00000437570.6
      Conserved Domains (3) summary
      cd15758
      Location:526 → 596
      FYVE_RUFY1; FYVE domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins
      pfam02759
      Location:39 → 160
      RUN; RUN domain
      cl25732
      Location:265 → 521
      SMC_N; RecF/RecN/SMC N terminal domain

    2. NM_001040452.3 → NP_001035542.1  RUN and FYVE domain-containing protein 1 isoform b

      See identical proteins and their annotated locations for NP_001035542.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. Variants 2 and 3 encode the same isoform (b) which has a shorter N-terminus compared to isoform a.
      Source sequence(s)
      AK025904, BC032571, DA648204
      Consensus CDS
      CCDS34312.1
      UniProtKB/TrEMBL
      A8K7B1
      Related
      ENSP00000377087.2, ENST00000393438.6
      Conserved Domains (3) summary
      cd15758
      Location:526 → 596
      FYVE_RUFY1; FYVE domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins
      pfam02759
      Location:39 → 160
      RUN; RUN domain
      cl25732
      Location:265 → 521
      SMC_N; RecF/RecN/SMC N terminal domain

    3. NM_025158.5 → NP_079434.3  RUN and FYVE domain-containing protein 1 isoform a

      See identical proteins and their annotated locations for NP_079434.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (a, also known as rabip4').
      Source sequence(s)
      AC136604, AF361055, AK075021, BC032571, BQ014980, CB988835
      Consensus CDS
      CCDS4445.2
      UniProtKB/Swiss-Prot
      Q59FF3, Q71S93, Q96T51, Q9H6I3
      UniProtKB/TrEMBL
      A8K7B1
      Related
      ENSP00000325594.4, ENST00000319449.9
      Conserved Domains (4) summary
      cd15758
      Location:634 → 704
      FYVE_RUFY1; FYVE domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins
      pfam02759
      Location:147 → 270
      RUN; RUN domain
      pfam13476
      Location:486 → 601
      AAA_23; AAA domain
      pfam13870
      Location:451 → 612
      DUF4201; Domain of unknown function (DUF4201)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      179550554..179610012
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006714921.4 → XP_006714984.2  RUN and FYVE domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      A8K7B1
      Conserved Domains (4) summary
      cd15758
      Location:612 → 682
      FYVE_RUFY1; FYVE domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins
      pfam02759
      Location:147 → 270
      RUN; RUN domain
      pfam13476
      Location:464 → 579
      AAA_23; AAA domain
      pfam13870
      Location:429 → 590
      DUF4201; Domain of unknown function (DUF4201)

    2. XM_047417780.1 → XP_047273736.1  RUN and FYVE domain-containing protein 1 isoform X7

    3. XM_047417781.1 → XP_047273737.1  RUN and FYVE domain-containing protein 1 isoform X8

    4. XM_047417777.1 → XP_047273733.1  RUN and FYVE domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      A8K7B1

    5. XM_017009891.2 → XP_016865380.1  RUN and FYVE domain-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      A8K7B1

    6. XM_005265993.5 → XP_005266050.1  RUN and FYVE domain-containing protein 1 isoform X4

      Conserved Domains (2) summary
      cd15758
      Location:391 → 461
      FYVE_RUFY1; FYVE domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins
      pfam13476
      Location:291 → 358
      AAA_23; AAA domain

    7. XM_047417779.1 → XP_047273735.1  RUN and FYVE domain-containing protein 1 isoform X6

    8. XM_047417778.1 → XP_047273734.1  RUN and FYVE domain-containing protein 1 isoform X5

    9. XM_047417782.1 → XP_047273738.1  RUN and FYVE domain-containing protein 1 isoform X9

      UniProtKB/TrEMBL
      B3KSL1

    RNA

    1. XR_245276.4 RNA Sequence

    2. XR_245277.4 RNA Sequence

    3. XR_007058642.1 RNA Sequence

    4. XR_007058644.1 RNA Sequence

    5. XR_007058643.1 RNA Sequence

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_016107298.1 Reference GRCh38.p14 PATCHES

      Range
      315196..376273
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054332001.1 → XP_054187976.1  RUN and FYVE domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      A8K7B1

    2. XM_054332002.1 → XP_054187977.1  RUN and FYVE domain-containing protein 1 isoform X10

      UniProtKB/TrEMBL
      A8K7B1

    3. XM_054332009.1 → XP_054187984.1  RUN and FYVE domain-containing protein 1 isoform X7

    4. XM_054332010.1 → XP_054187985.1  RUN and FYVE domain-containing protein 1 isoform X8

    5. XM_054332003.1 → XP_054187978.1  RUN and FYVE domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      A8K7B1

    6. XM_054332004.1 → XP_054187979.1  RUN and FYVE domain-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      A8K7B1

    7. XM_054332005.1 → XP_054187980.1  RUN and FYVE domain-containing protein 1 isoform X11

      UniProtKB/TrEMBL
      A8K7B1

    8. XM_054332006.1 → XP_054187981.1  RUN and FYVE domain-containing protein 1 isoform X4

    9. XM_054332008.1 → XP_054187983.1  RUN and FYVE domain-containing protein 1 isoform X6

    10. XM_054332007.1 → XP_054187982.1  RUN and FYVE domain-containing protein 1 isoform X5

    11. XM_054332011.1 → XP_054187986.1  RUN and FYVE domain-containing protein 1 isoform X9

      UniProtKB/TrEMBL
      B3KSL1

    RNA

    1. XR_008485740.1 RNA Sequence

    2. XR_008485741.1 RNA Sequence

    3. XR_008485742.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      180103365..180164461
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353557.1 → XP_054209532.1  RUN and FYVE domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      A8K7B1

    2. XM_054353558.1 → XP_054209533.1  RUN and FYVE domain-containing protein 1 isoform X12

      UniProtKB/TrEMBL
      A8K7B1

    3. XM_054353565.1 → XP_054209540.1  RUN and FYVE domain-containing protein 1 isoform X7

    4. XM_054353566.1 → XP_054209541.1  RUN and FYVE domain-containing protein 1 isoform X8

    5. XM_054353559.1 → XP_054209534.1  RUN and FYVE domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      A8K7B1

    6. XM_054353560.1 → XP_054209535.1  RUN and FYVE domain-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      A8K7B1

    7. XM_054353562.1 → XP_054209537.1  RUN and FYVE domain-containing protein 1 isoform X14

      UniProtKB/TrEMBL
      A8K7B1

    8. XM_054353561.1 → XP_054209536.1  RUN and FYVE domain-containing protein 1 isoform X13

    9. XM_054353564.1 → XP_054209539.1  RUN and FYVE domain-containing protein 1 isoform X6

    10. XM_054353563.1 → XP_054209538.1  RUN and FYVE domain-containing protein 1 isoform X5

    11. XM_054353567.1 → XP_054209542.1  RUN and FYVE domain-containing protein 1 isoform X9

      UniProtKB/TrEMBL
      B3KSL1

    RNA

    1. XR_008487175.1 RNA Sequence

    2. XR_008487176.1 RNA Sequence

    3. XR_008487177.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96T51.2 GenPept UniProtKB/Swiss-Prot:Q96T51

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