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    RUFY3 RUN and FYVE domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 22902, updated on 5-Dec-2021

    Summary

    Official Symbol
    RUFY3provided by HGNC
    Official Full Name
    RUN and FYVE domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:30285
    See related
    Ensembl:ENSG00000018189 MIM:611194
    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
    RIPX; SINGAR1; ZFYVE30
    Summary
    This gene encodes a RPIP8, UNC-14, and NESCA domain-containing protein that is required for maintenance of neuronal polarity. In addition, it has been implicated in mediation of gastric cancer cell migration and invasion via interaction with P21-activated kinase-1, which promotes its expression. The encoded protein localizes to F-actin-enriched invadopodia to induce formation of protrusions, thereby facilitating cell migration. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]
    Expression
    Ubiquitous expression in brain (RPKM 27.2), testis (RPKM 10.8) and 24 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See RUFY3 in Genome Data Viewer
    Location:
    4q13.3
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    109.20211119 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (70704204..70808619)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (71570456..71674336)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 520, pseudogene Neighboring gene RNA, U6 small nuclear 784, pseudogene Neighboring gene G-rich RNA sequence binding factor 1 Neighboring gene RNA, U6 small nuclear 891, pseudogene

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • KIAA0871

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in actin filament organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of axonogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of axon extension ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of intracellular protein transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of axonogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in regulation of establishment of cell polarity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    is_active_in axon IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in axon ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cell junction IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    is_active_in dendrite IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in dendrite ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in endomembrane system IEA
    Inferred from Electronic Annotation
    more info
     
    located_in filopodium ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in growth cone ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in lamellipodium ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in neuronal cell body IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in perikaryon ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    protein RUFY3
    Names
    rap2 interacting protein x
    single axon-regulated protein
    single axon-related 1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_051554.1 RefSeqGene

      Range
      22279..108934
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001037442.4NP_001032519.1  protein RUFY3 isoform 1

      See identical proteins and their annotated locations for NP_001032519.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AA435606, AC009570, AC021989, AK302637, BC053837, DA248021, DC299541
      Consensus CDS
      CCDS34001.1
      UniProtKB/Swiss-Prot
      Q7L099
      Related
      ENSP00000370394.3, ENST00000381006.8
      Conserved Domains (2) summary
      cd15744
      Location:561608
      FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins
      pfam02759
      Location:103226
      RUN; RUN domain
    2. NM_001130709.2NP_001124181.1  protein RUFY3 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) has multiple differences in the 5' and 3' coding regions and the 5' and 3' UTRs, compared to variant 1. The encoded protein (isoform 3) has a distinct N-terminus and a shorter C-terminus, compared to isoform 1.
      Source sequence(s)
      AC009570, AF112221, AK000911, BM920380, DA015234, DB482497, DB483639
      Consensus CDS
      CCDS47068.1
      UniProtKB/Swiss-Prot
      Q7L099
      Related
      ENSP00000399771.2, ENST00000417478.6
      Conserved Domains (5) summary
      pfam01442
      Location:334506
      Apolipoprotein; Apolipoprotein A1/A4/E domain
      pfam02759
      Location:163286
      RUN; RUN domain
      pfam05038
      Location:2164
      Cytochrom_B558a; Cytochrome Cytochrome b558 alpha-subunit
      pfam10212
      Location:333382
      TTKRSYEDQ; Predicted coiled-coil domain-containing protein
      cl23720
      Location:400506
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
    3. NM_001291993.2NP_001278922.1  protein RUFY3 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has an alternate 5' exon structure and initiates translation at an alternate start codon, compared to variant 1. It encodes isoform 4, which is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AA435606, AC009570, AC021989, AK302637, BC053837, DA285699, DC299541
      Consensus CDS
      CCDS75138.1
      UniProtKB/Swiss-Prot
      Q7L099
      Related
      ENSP00000425400.1, ENST00000502653.5
      Conserved Domains (2) summary
      cd15744
      Location:508555
      FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins
      pfam02759
      Location:50173
      RUN; RUN domain
    4. NM_001291994.2NP_001278923.1  protein RUFY3 isoform 5

      See identical proteins and their annotated locations for NP_001278923.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks an alternate in-frame exon in the 5' coding region and has an alternate 3' exon structure, compared to variant 1. It encodes isoform 5, which is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC009570
      UniProtKB/Swiss-Prot
      Q7L099
      UniProtKB/TrEMBL
      B4DKC2
      Conserved Domains (2) summary
      COG1196
      Location:276482
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam02759
      Location:121242
      RUN; RUN domain
    5. NM_001345840.2NP_001332769.1  protein RUFY3 isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) represents use of an alternate promoter, uses an alternate start codon, and has an alternate 3' exon structure compared to variant 1. It encodes isoform 6, which is shorter than and has distinct N- and C-termini compared to isoform 1.
      Source sequence(s)
      AC009570
      UniProtKB/Swiss-Prot
      Q7L099
      Conserved Domains (2) summary
      pfam02759
      Location:50171
      RUN; RUN domain
      cl25732
      Location:203411
      SMC_N; RecF/RecN/SMC N terminal domain
    6. NM_014961.5NP_055776.1  protein RUFY3 isoform 2

      See identical proteins and their annotated locations for NP_055776.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has multiple differences in the 3' coding region and 3' UTR, compared to variant 1. It encodes isoform 2, which has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC009570
      Consensus CDS
      CCDS3547.1
      UniProtKB/Swiss-Prot
      Q7L099
      UniProtKB/TrEMBL
      A0A024RDD7, B4DG59, B4DKC2
      Related
      ENSP00000226328.4, ENST00000226328.8
      Conserved Domains (2) summary
      COG1196
      Location:258464
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam02759
      Location:103224
      RUN; RUN domain

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

      Range
      70704204..70808619
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011531750.2XP_011530052.1  protein RUFY3 isoform X1

      Conserved Domains (5) summary
      cd15744
      Location:621668
      FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins
      pfam01442
      Location:334507
      Apolipoprotein; Apolipoprotein A1/A4/E domain
      pfam02759
      Location:163286
      RUN; RUN domain
      pfam05038
      Location:2164
      Cytochrom_B558a; Cytochrome Cytochrome b558 alpha-subunit
      pfam15960
      Location:402558
      DUF4763; Domain of unknown function (DUF4763)
    2. XM_011531751.3XP_011530053.1  protein RUFY3 isoform X2

      Conserved Domains (5) summary
      cd15744
      Location:611645
      FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins
      pfam01442
      Location:334507
      Apolipoprotein; Apolipoprotein A1/A4/E domain
      pfam02759
      Location:163286
      RUN; RUN domain
      pfam05038
      Location:2164
      Cytochrom_B558a; Cytochrome Cytochrome b558 alpha-subunit
      pfam15960
      Location:402558
      DUF4763; Domain of unknown function (DUF4763)
    3. XM_011531752.3XP_011530054.1  protein RUFY3 isoform X4

      Conserved Domains (4) summary
      pfam01442
      Location:334507
      Apolipoprotein; Apolipoprotein A1/A4/E domain
      pfam02759
      Location:163286
      RUN; RUN domain
      pfam05038
      Location:2164
      Cytochrom_B558a; Cytochrome Cytochrome b558 alpha-subunit
      pfam15960
      Location:402558
      DUF4763; Domain of unknown function (DUF4763)
    4. XM_011531754.3XP_011530056.1  protein RUFY3 isoform X7

      Conserved Domains (5) summary
      pfam01442
      Location:334507
      Apolipoprotein; Apolipoprotein A1/A4/E domain
      pfam02759
      Location:163286
      RUN; RUN domain
      pfam05038
      Location:2164
      Cytochrom_B558a; Cytochrome Cytochrome b558 alpha-subunit
      pfam10212
      Location:333382
      TTKRSYEDQ; Predicted coiled-coil domain-containing protein
      pfam15960
      Location:402558
      DUF4763; Domain of unknown function (DUF4763)
    5. XM_011531753.3XP_011530055.1  protein RUFY3 isoform X5

      Conserved Domains (4) summary
      pfam01442
      Location:334507
      Apolipoprotein; Apolipoprotein A1/A4/E domain
      pfam02759
      Location:163286
      RUN; RUN domain
      pfam05038
      Location:2164
      Cytochrom_B558a; Cytochrome Cytochrome b558 alpha-subunit
      pfam15960
      Location:402558
      DUF4763; Domain of unknown function (DUF4763)
    6. XM_011531756.3XP_011530058.1  protein RUFY3 isoform X10

      Conserved Domains (5) summary
      pfam01442
      Location:334507
      Apolipoprotein; Apolipoprotein A1/A4/E domain
      pfam02759
      Location:163286
      RUN; RUN domain
      pfam05038
      Location:2164
      Cytochrom_B558a; Cytochrome Cytochrome b558 alpha-subunit
      pfam10212
      Location:333382
      TTKRSYEDQ; Predicted coiled-coil domain-containing protein
      cl23720
      Location:400506
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
    7. XM_017007890.2XP_016863379.1  protein RUFY3 isoform X6

    8. XM_011531755.3XP_011530057.1  protein RUFY3 isoform X9

      Conserved Domains (5) summary
      pfam01442
      Location:334506
      Apolipoprotein; Apolipoprotein A1/A4/E domain
      pfam02759
      Location:163286
      RUN; RUN domain
      pfam05038
      Location:2164
      Cytochrom_B558a; Cytochrome Cytochrome b558 alpha-subunit
      pfam10212
      Location:333382
      TTKRSYEDQ; Predicted coiled-coil domain-containing protein
      cl23720
      Location:400528
      RILP-like; Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2)
    9. XM_005265656.3XP_005265713.1  protein RUFY3 isoform X3

      Conserved Domains (2) summary
      cd15744
      Location:579626
      FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins
      pfam02759
      Location:121244
      RUN; RUN domain
    10. XM_024453936.1XP_024309704.1  protein RUFY3 isoform X11

      Conserved Domains (2) summary
      pfam02759
      Location:103224
      RUN; RUN domain
      pfam09731
      Location:274445
      Mitofilin; Mitochondrial inner membrane protein
    11. XM_005265658.2XP_005265715.1  protein RUFY3 isoform X8

      Conserved Domains (2) summary
      cd15744
      Location:497544
      FYVE_RUFY3; FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins
      pfam02759
      Location:39162
      RUN; RUN domain
    12. XM_017007892.2XP_016863381.1  protein RUFY3 isoform X12

    RNA

    1. XR_938712.3 RNA Sequence

    2. XR_001741173.2 RNA Sequence

    3. XR_938710.3 RNA Sequence

    4. XR_938713.3 RNA Sequence

    5. XR_938714.3 RNA Sequence

    6. XR_938708.3 RNA Sequence

    7. XR_938711.3 RNA Sequence

    8. XR_001741174.2 RNA Sequence

    9. XR_938709.3 RNA Sequence

    10. XR_002959720.1 RNA Sequence

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