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

Gene ID: 80230, updated on 7-Apr-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
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Genomic context

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Location:
5q35.3
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (179550554..179610012)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (180103365..180164461)
105.20220307 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 chromosome 5 open reading frame 60

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 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 (53) 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)

Genotypes

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 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 
Process Evidence Code Pubs
involved_in endocytosis IEA
Inferred from Electronic Annotation
more info
  
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
  
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_2023_10

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

  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

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

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

  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

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

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

  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

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

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

  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

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

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

  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

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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