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

    Gene ID: 285180, updated on 2-Nov-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 MIM:620994; 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, Nov 2024]
    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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    See RUFY4 in Genome Data Viewer
    Location:
    2q35
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (218034934..218090652)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (218519258..218576350)
    RS_2024_09 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 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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    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)

    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_2024_08

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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