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RUFY4 RUN and FYVE domain containing 4 [ Homo sapiens (human) ]

Gene ID: 285180, updated on 3-Apr-2024

Summary

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Official Symbol
RUFY4provided by HGNC
Official Full Name
RUN and FYVE domain containing 4provided by HGNC
Primary source
HGNC:HGNC:24804
See related
Ensembl:ENSG00000188282 AllianceGenome:HGNC:24804
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ZFYVE31
Summary
Enables phosphatidylinositol-3-phosphate binding activity. Involved in autophagosome assembly; cellular response to interleukin-4; and positive regulation of macroautophagy. Located in autophagosome. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in spleen (RPKM 1.0), lymph node (RPKM 0.6) and 16 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
2q35
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (218034934..218090652)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (218519258..218576350)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (218899657..218955307)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene tensin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:218843426-218844314 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17111 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:218859337-218859836 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:218860238-218861016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:218861017-218861794 Neighboring gene TNS1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:218866162-218866662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:218866663-218867163 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17112 Neighboring gene uncharacterized LOC124907982 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12309 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:218890081-218890996 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:218896372-218896928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:218899047-218899580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:218899581-218900113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:218910221-218910722 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:218930441-218930983 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:218933725-218934588 Neighboring gene Sharpr-MPRA regulatory region 3825 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:218940751-218941252 Neighboring gene C-X-C motif chemokine receptor 2 pseudogene 1 Neighboring gene C-X-C motif chemokine receptor 2 Neighboring gene C-X-C motif chemokine receptor 1

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. RUN and FYVE domain-containing protein 4 enhances autophagy and lysosome tethering in response to Interleukin-4. Terawaki S, et al. J Cell Biol, 2015 Sep 28. PMID 26416964, Free PMC Article
  2. An interactome perturbation framework prioritizes damaging missense mutations for developmental disorders. Chen S, et al. Nat Genet, 2018 Jul. PMID 29892012, Free PMC Article
  3. Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains. Haenig C, et al. Cell Rep, 2020 Aug 18. PMID 32814053
  4. A proteome-scale map of the human interactome network. Rolland T, et al. Cell, 2014 Nov 20. PMID 25416956, Free PMC Article
  5. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article

See all (11) citations in PubMed

GeneRIFs: Gene References Into Functions

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

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ46536

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables phosphatidylinositol-3-phosphate binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables phosphatidylinositol-3-phosphate binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in autophagosome assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in autophagosome assembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to interleukin-4 IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of macroautophagy IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of macroautophagy IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in autophagosome IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in autophagosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasmic vesicle IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
RUN and FYVE domain-containing protein 4

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.

mRNA and Protein(s)

  1. NM_198483.4 → NP_940885.2  RUN and FYVE domain-containing protein 4

    See identical proteins and their annotated locations for NP_940885.2

    Status: VALIDATED

    Description
    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.
    Source sequence(s)
    AC124768
    UniProtKB/Swiss-Prot
    Q6ZNE9, Q6ZR96
    UniProtKB/TrEMBL
    C9J235
    Related
    ENSP00000513250.1, ENST00000697321.1
    Conserved Domains (4) summary
    cd15745
    Location:520 → 562
    FYVE_RUFY4; FYVE-related domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins
    cd16269
    Location:477 → 488
    GBP_C; coiled coil [structural motif]
    cl02689
    Location:41 → 163
    RUN; RUN domain
    cl20817
    Location:406 → 503
    GBP_C; Guanylate-binding protein, C-terminal domain

RNA

  1. NR_034176.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) includes alternate exon structure in the 5' region and lacks an internal exon in the central region, compared to variant 1. This variant is represented as non-coding due to the presence of multiple upstream ORFs that are predicted to interfere with translation of the longest ORF; translation of these upstream ORFs would render the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC010136, AC124768, AK128393, AW452848, BX641664
    Related
    ENST00000457754.6

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    218034934..218090652
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047444006.1 → XP_047299962.1  RUN and FYVE domain-containing protein 4 isoform X1

  2. XM_047444008.1 → XP_047299964.1  RUN and FYVE domain-containing protein 4 isoform X2

    Related
    ENSP00000363270.3, ENST00000374155.7

  3. XM_047444011.1 → XP_047299967.1  RUN and FYVE domain-containing protein 4 isoform X6

  4. XM_047444010.1 → XP_047299966.1  RUN and FYVE domain-containing protein 4 isoform X5

  5. XM_047444009.1 → XP_047299965.1  RUN and FYVE domain-containing protein 4 isoform X4

  6. XM_047444012.1 → XP_047299968.1  RUN and FYVE domain-containing protein 4 isoform X7

  7. XM_047444007.1 → XP_047299963.1  RUN and FYVE domain-containing protein 4 isoform X2

  8. XM_017003895.2 → XP_016859384.1  RUN and FYVE domain-containing protein 4 isoform X3

    UniProtKB/TrEMBL
    C9J235
    Conserved Domains (4) summary
    cd15745
    Location:521 → 563
    FYVE_RUFY4; FYVE-related domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins
    cd16269
    Location:478 → 489
    GBP_C; coiled coil [structural motif]
    cl02689
    Location:42 → 164
    RUN; RUN domain
    cl20817
    Location:407 → 504
    GBP_C; Guanylate-binding protein, C-terminal domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    218519258..218576350
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054341521.1 → XP_054197496.1  RUN and FYVE domain-containing protein 4 isoform X5

  2. XM_054341522.1 → XP_054197497.1  RUN and FYVE domain-containing protein 4 isoform X7

  3. XM_054341519.1 → XP_054197494.1  RUN and FYVE domain-containing protein 4 isoform X3

  4. XM_054341518.1 → XP_054197493.1  RUN and FYVE domain-containing protein 4 isoform X3

  5. XM_054341520.1 → XP_054197495.1  RUN and FYVE domain-containing protein 4 isoform X8

    UniProtKB/Swiss-Prot
    Q6ZNE9, Q6ZR96

RNA

  1. XR_008486345.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6ZNE9.2 GenPept UniProtKB/Swiss-Prot:Q6ZNE9

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