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

Gene ID: 22902, updated on 8-Jul-2018
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; Vega:OTTHUMG00000129910
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
See RUFY3 in Genome Data Viewer
Location:
4q13.3
Exon count:
24
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 4 NC_000004.12 (70704204..70808622)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (71570647..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

  • 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 Jun 15 11:32:44 2016
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • KIAA0871

Gene Ontology Provided by GOA

Function Evidence Code Pubs
phosphatidylinositol binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
actin filament organization ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of axonogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of axon extension ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of cell migration IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of intracellular protein transport ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of axonogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of establishment of cell polarity ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
axon IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
axon ISS
Inferred from Sequence or Structural Similarity
more info
 
cell junction IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
dendrite IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
dendrite ISS
Inferred from Sequence or Structural Similarity
more info
 
endomembrane system IEA
Inferred from Electronic Annotation
more info
 
filopodium ISS
Inferred from Sequence or Structural Similarity
more info
 
growth cone ISS
Inferred from Sequence or Structural Similarity
more info
 
invadopodium IDA
Inferred from Direct Assay
more info
PubMed 
lamellipodium ISS
Inferred from Sequence or Structural Similarity
more info
 
membrane IEA
Inferred from Electronic Annotation
more info
 
neuronal cell body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
perikaryon ISS
Inferred from Sequence or Structural Similarity
more info
 
Preferred Names
protein RUFY3
Names
rap2 interacting protein x
single axon-regulated protein
single axon-related 1

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
    22157..108937
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001037442.3NP_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, DA484908, DC299541
    Consensus CDS
    CCDS34001.1
    UniProtKB/Swiss-Prot
    Q7L099
    Related
    ENSP00000370394.3, OTTHUMP00000160359, ENST00000381006.7, OTTHUMT00000252162
    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_001130709.1NP_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)
    AF112221, AK000911, BM920380, DA015234, DB482497, DB483639
    Consensus CDS
    CCDS47068.1
    UniProtKB/Swiss-Prot
    Q7L099
    Related
    ENSP00000399771.2, OTTHUMP00000219126, ENST00000417478.6, OTTHUMT00000362591
    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_001291993.1NP_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, OTTHUMP00000219124, ENST00000502653.5, OTTHUMT00000362589
    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_001291994.1NP_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)
    AB020678, AK296501, BC051716, BC053837, DA248021, DA484908
    UniProtKB/Swiss-Prot
    Q7L099
    UniProtKB/TrEMBL
    B4DKC2
    Conserved Domains (1) summary
    pfam02759
    Location:121244
    RUN; RUN domain
  5. NM_001345840.1NP_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)
    AB020678, BC051716, DA285699, DA293149, DA346780, DB482497, DC322301
    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_014961.4NP_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)
    AB020678, AK294421, AK296501, BC051716, BC053837, DA248021, DA484908
    Consensus CDS
    CCDS3547.1
    UniProtKB/Swiss-Prot
    Q7L099
    UniProtKB/TrEMBL
    A0A024RDD7, B4DG59, B4DKC2
    Related
    ENSP00000226328.4, OTTHUMP00000160358, ENST00000226328.8, OTTHUMT00000252161
    Conserved Domains (2) summary
    pfam02759
    Location:103224
    RUN; RUN domain
    cl25732
    Location:258464
    SMC_N; RecF/RecN/SMC N terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p12 Primary Assembly

    Range
    70704204..70808622
    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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