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

Gene ID: 80230, updated on 17-Jun-2019

Summary

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
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

Genomic context

See RUFY1 in Genome Data Viewer
Location:
5q35.3
Exon count:
24
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (179550551..179610012)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (178977562..179037027)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene chromosome 5 open reading frame 60 pseudogene Neighboring gene uncharacterized LOC105377762 Neighboring gene peroxiredoxin 2 pseudogene 3 Neighboring gene uncharacterized LOC101928445 Neighboring gene heterogeneous nuclear ribonucleoprotein H1 Neighboring gene Sharpr-MPRA regulatory region 11836 Neighboring gene chromosome 5 open reading frame 60

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

Pathways from BioSystems

  • Endocytosis, organism-specific biosystem (from KEGG)
    Endocytosis, organism-specific biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Endocytosis, conserved biosystem (from KEGG)
    Endocytosis, conserved biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
    Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
  • PI Metabolism, organism-specific biosystem (from REACTOME)
    PI Metabolism, organism-specific biosystemPhosphatidylinositol (PI), a membrane phospholipid, can be reversibly phosphorylated at the 3, 4, and 5 positions of the inositol ring to generate seven phosphoinositides: phosphatidylinositol 3-phos...
  • Phospholipid metabolism, organism-specific biosystem (from REACTOME)
    Phospholipid metabolism, organism-specific biosystemPhospholipids contain a polar head group and two long-chain fatty acyl moieties, one of which is generally unsaturated. The head group is a glycerol or serine phosphate attached to a polar group such...
  • Synthesis of PIPs at the plasma membrane, organism-specific biosystem (from REACTOME)
    Synthesis of PIPs at the plasma membrane, organism-specific biosystemAt the plasma membrane, subsequent phosphorylation of phosphatidylinositol 4-phosphate (PI4P) produces phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) and phosphatidylinositol 3,4,5-trisphosphate (...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ22251

Gene Ontology Provided by GOA

Function Evidence Code Pubs
SH2 domain binding IPI
Inferred from Physical Interaction
more info
PubMed 
SH3 domain binding IPI
Inferred from Physical Interaction
more info
PubMed 
lipid binding IEA
Inferred from Electronic Annotation
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
endocytosis IEA
Inferred from Electronic Annotation
more info
 
phosphatidylinositol biosynthetic process TAS
Traceable Author Statement
more info
 
protein transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of endocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of endocytosis IPI
Inferred from Physical Interaction
more info
PubMed 
small GTPase mediated signal transduction IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 
early endosome membrane TAS
Traceable Author Statement
more info
 
endosome IDA
Inferred from Direct Assay
more info
PubMed 
intracellular membrane-bounded organelle IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
nuclear speck IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
 

General protein information

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)

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
    5001..64466
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001040451.3NP_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/Swiss-Prot
    Q96T51
    UniProtKB/TrEMBL
    A8K7B1
    Related
    ENSP00000390025.2, ENST00000437570.6
    Conserved Domains (3) summary
    cd15758
    Location:526596
    FYVE_RUFY1; FYVE domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins
    pfam02759
    Location:39160
    RUN; RUN domain
    cl25732
    Location:265521
    SMC_N; RecF/RecN/SMC N terminal domain
  2. NM_001040452.3NP_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/Swiss-Prot
    Q96T51
    Related
    ENSP00000377087.2, ENST00000393438.6
    Conserved Domains (3) summary
    cd15758
    Location:526596
    FYVE_RUFY1; FYVE domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins
    pfam02759
    Location:39160
    RUN; RUN domain
    cl25732
    Location:265521
    SMC_N; RecF/RecN/SMC N terminal domain
  3. NM_025158.5NP_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
    Q96T51
    Related
    ENSP00000325594.4, ENST00000319449.9
    Conserved Domains (4) summary
    cd15758
    Location:634704
    FYVE_RUFY1; FYVE domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins
    pfam02759
    Location:147270
    RUN; RUN domain
    pfam13476
    Location:486601
    AAA_23; AAA domain
    pfam13870
    Location:451612
    DUF4201; Domain of unknown function (DUF4201)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    179550551..179610012
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006714921.3XP_006714984.2  RUN and FYVE domain-containing protein 1 isoform X1

    Conserved Domains (4) summary
    cd15758
    Location:612682
    FYVE_RUFY1; FYVE domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins
    pfam02759
    Location:147270
    RUN; RUN domain
    pfam13476
    Location:464579
    AAA_23; AAA domain
    pfam13870
    Location:429590
    DUF4201; Domain of unknown function (DUF4201)
  2. XM_024446220.1XP_024301988.1  RUN and FYVE domain-containing protein 1 isoform X3

    Conserved Domains (2) summary
    cd15758
    Location:364434
    FYVE_RUFY1; FYVE domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins
    cl25732
    Location:103359
    SMC_N; RecF/RecN/SMC N terminal domain
  3. XM_017009891.1XP_016865380.1  RUN and FYVE domain-containing protein 1 isoform X2

  4. XM_017009894.1XP_016865383.1  RUN and FYVE domain-containing protein 1 isoform X5

    Conserved Domains (2) summary
    cd15758
    Location:294364
    FYVE_RUFY1; FYVE domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins
    pfam13476
    Location:194261
    AAA_23; AAA domain
  5. XM_017009895.2XP_016865384.1  RUN and FYVE domain-containing protein 1 isoform X6

    UniProtKB/Swiss-Prot
    Q96T51
    Conserved Domains (2) summary
    cd15758
    Location:236306
    FYVE_RUFY1; FYVE domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins
    pfam13476
    Location:136203
    AAA_23; AAA domain
  6. XM_017009893.2XP_016865382.1  RUN and FYVE domain-containing protein 1 isoform X4

  7. XM_005265993.4XP_005266050.1  RUN and FYVE domain-containing protein 1 isoform X7

    Conserved Domains (2) summary
    cd15758
    Location:391461
    FYVE_RUFY1; FYVE domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins
    pfam13476
    Location:291358
    AAA_23; AAA domain
  8. XM_006714922.3XP_006714985.1  RUN and FYVE domain-containing protein 1 isoform X5

    Conserved Domains (2) summary
    cd15758
    Location:294364
    FYVE_RUFY1; FYVE domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins
    pfam13476
    Location:194261
    AAA_23; AAA domain

RNA

  1. XR_001742278.1 RNA Sequence

  2. XR_245276.3 RNA Sequence

  3. XR_001742279.1 RNA Sequence

  4. XR_245277.3 RNA Sequence

Reference GRCh38.p13 PATCHES

Genomic

  1. NW_016107298.1 Reference GRCh38.p13 PATCHES

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