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    RUFY2 RUN and FYVE domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 55680, updated on 3-Apr-2024

    Summary

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    Official Symbol
    RUFY2provided by HGNC
    Official Full Name
    RUN and FYVE domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:19761
    See related
    Ensembl:ENSG00000204130 MIM:610328; AllianceGenome:HGNC:19761
    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
    RABIP4R; ZFYVE13
    Summary
    Enables SH3 domain binding activity. Predicted to be involved in regulation of endocytosis. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in brain (RPKM 7.8), endometrium (RPKM 4.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    10q21.3
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (68341112..68407277, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (69210323..69276503, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (70100869..70167034, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene keratin 19 pseudogene 4 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16457 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16478 Neighboring gene MPRA-validated peak989 silencer Neighboring gene MPRA-validated peak990 silencer Neighboring gene phenazine biosynthesis like protein domain containing Neighboring gene MPRA-validated peak991 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3460 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16557 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3461 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3462 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:70091533-70092347 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:70092348-70093161 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16564 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16571 Neighboring gene heterogeneous nuclear ribonucleoprotein H3 Neighboring gene MPRA-validated peak992 silencer Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16583 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16593 Neighboring gene MPRA-validated peak994 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:70166191-70166692 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:70166693-70167192 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16635 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16643 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16656 Neighboring gene Neanderthal introgressed variant-containing enhancers experimental_16661/16662 and experimental_16666/16667 Neighboring gene ribosomal protein L26 pseudogene 29 Neighboring gene DNA replication helicase/nuclease 2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16674 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16683 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16686/16687 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_16694 Neighboring gene RNA, 5S ribosomal pseudogene 319

    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. Interaction between tyrosine kinase Etk and a RUN domain- and FYVE domain-containing protein RUFY1. A possible role of ETK in regulation of vesicle trafficking. Yang J, et al. J Biol Chem, 2002 Aug 16. PMID 11877430
    2. Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. Nagase T, et al. DNA Res, 2000 Apr 28. PMID 10819331
    3. TRIM37 Mediates Chemoresistance and Maintenance of Stemness in Pancreatic Cancer Cells via Ubiquitination of PTEN and Activation of the AKT-GSK-3β-β-Catenin Signaling Pathway. Chen S, et al. Front Oncol, 2020. PMID 33194618, Free PMC Article
    4. RUFY1 binds Arl8b and mediates endosome-to-TGN CI-M6PR retrieval for cargo sorting to lysosomes. Rawat S, et al. J Cell Biol, 2023 Jan 2. PMID 36282215, Free PMC Article
    5. The DNA sequence and comparative analysis of human chromosome 10. Deloukas P, et al. Nature, 2004 May 27. PMID 15164054

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Observational study of gene-disease association. (HuGE Navigator)
      Title: A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease.
    Submit: New GeneRIF Correction

    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

    • FLJ10063, KIAA1537

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables SH3 domain binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in regulation of endocytosis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    RUN and FYVE domain-containing protein 2
    Names
    Run- and FYVE-domain containing protein
    antigen MU-RMS-40.17
    rab4-interacting protein related

    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_001042417.2 → NP_001035882.1  RUN and FYVE domain-containing protein 2 isoform b

      See identical proteins and their annotated locations for NP_001035882.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate first exon, lacks an alternate in-frame exon, and contains an alternate last exon in place of the last several exons compared to variant 1. The resulting isoform (b) has shorter and distinct N- and C-termini and lacks an alternate internal segment compared to isoform a.
      Source sequence(s)
      BC041092, BM150360
      Consensus CDS
      CCDS44414.1
      UniProtKB/TrEMBL
      Q5GIA6
      Related
      ENSP00000382151.2, ENST00000399200.7
      Conserved Domains (2) summary
      COG1196
      Location:176 → 380
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cl02689
      Location:45 → 132
      RUN; RUN domain

    2. NM_001278225.2 → NP_001265154.1  RUN and FYVE domain-containing protein 2 isoform c

      See identical proteins and their annotated locations for NP_001265154.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate first exon, lacks an alternate in-frame exon, and contains an alternate last exon in place of the last several exons compared to variant 1. The resulting isoform (c) has shorter and distinct N- and C-termini and lacks an alternate internal segment compared to isoform a.
      Source sequence(s)
      AK294211, BC041092
      Consensus CDS
      CCDS60544.1
      UniProtKB/TrEMBL
      Q5GIA6
      Related
      ENSP00000404986.2, ENST00000454950.6
      Conserved Domains (2) summary
      COG1196
      Location:172 → 356
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam02759
      Location:1 → 108
      RUN; RUN domain

    3. NM_001330103.2 → NP_001317032.1  RUN and FYVE domain-containing protein 2 isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) uses an alternate 5'-terminal exon, resulting in a different 5' UTR and use of an alternate start codon compared to variant 1. It encodes isoform d, which has a distinct N-terminus and is shorter than isoform d.
      Source sequence(s)
      AC016395, AF411980, AL136233, AY528716, BM998747
      Consensus CDS
      CCDS81470.1
      UniProtKB/Swiss-Prot
      B3KXB2, B4DFR0, Q5TC48, Q8IW33, Q8WXA3, Q96P51, Q9P1Z1
      UniProtKB/TrEMBL
      H0YD93
      Related
      ENSP00000473462.1, ENST00000602465.6
      Conserved Domains (3) summary
      COG1196
      Location:230 → 536
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cd15759
      Location:534 → 604
      FYVE_RUFY2; FYVE domain found in RUN and FYVE domain-containing protein 2 (RUFY2) and similar proteins
      pfam02759
      Location:45 → 166
      RUN; RUN domain

    4. NM_017987.5 → NP_060457.4  RUN and FYVE domain-containing protein 2 isoform a

      See identical proteins and their annotated locations for NP_060457.4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AC016395, AK127019, AL136233, BG681628, BQ006812
      Consensus CDS
      CCDS41534.1
      UniProtKB/TrEMBL
      H0YD93
      Related
      ENSP00000373420.2, ENST00000388768.6
      Conserved Domains (3) summary
      COG1196
      Location:245 → 571
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cd15759
      Location:569 → 639
      FYVE_RUFY2; FYVE domain found in RUN and FYVE domain-containing protein 2 (RUFY2) and similar proteins
      pfam02759
      Location:80 → 201
      RUN; RUN domain

    RNA

    1. NR_103475.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' and 3' ends compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AB040970, AC016395, AK127019, AL136233
      Related
      ENST00000466493.5

    2. NR_103476.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' and 3' ends compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC016395, AF461266, BM150360, DA858392

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      68341112..68407277 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047425448.1 → XP_047281404.1  RUN and FYVE domain-containing protein 2 isoform X9

    2. XM_005269957.6 → XP_005270014.1  RUN and FYVE domain-containing protein 2 isoform X5

      See identical proteins and their annotated locations for XP_005270014.1

      UniProtKB/TrEMBL
      H0YD93
      Conserved Domains (3) summary
      COG1196
      Location:196 → 502
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cd15759
      Location:500 → 570
      FYVE_RUFY2; FYVE domain found in RUN and FYVE domain-containing protein 2 (RUFY2) and similar proteins
      cl02689
      Location:45 → 132
      RUN; RUN domain

    3. XM_047425446.1 → XP_047281402.1  RUN and FYVE domain-containing protein 2 isoform X7

    4. XM_047425445.1 → XP_047281401.1  RUN and FYVE domain-containing protein 2 isoform X6

    5. XM_005269953.5 → XP_005270010.1  RUN and FYVE domain-containing protein 2 isoform X1

      See identical proteins and their annotated locations for XP_005270010.1

      UniProtKB/TrEMBL
      H0YD93
      Conserved Domains (3) summary
      COG1196
      Location:231 → 537
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cd15759
      Location:535 → 605
      FYVE_RUFY2; FYVE domain found in RUN and FYVE domain-containing protein 2 (RUFY2) and similar proteins
      cl02689
      Location:80 → 167
      RUN; RUN domain

    6. XM_005269956.5 → XP_005270013.1  RUN and FYVE domain-containing protein 2 isoform X4

      UniProtKB/TrEMBL
      H0YD93
      Conserved Domains (6) summary
      cd15759
      Location:513 → 583
      FYVE_RUFY2; FYVE domain found in RUN and FYVE domain-containing protein 2 (RUFY2) and similar proteins
      pfam02759
      Location:80 → 203
      RUN; RUN domain
      pfam06156
      Location:258 → 335
      DUF972; Protein of unknown function (DUF972)
      pfam09728
      Location:233 → 514
      Taxilin; Myosin-like coiled-coil protein
      pfam16505
      Location:329 → 408
      Emaravirus_P4; P4 movement protein of Emaravirus, and the 30K superfamily
      cl19219
      Location:355 → 484
      DUF342; Protein of unknown function (DUF342)

    7. XM_047425444.1 → XP_047281400.1  RUN and FYVE domain-containing protein 2 isoform X2

      UniProtKB/Swiss-Prot
      B3KXB2, B4DFR0, Q5TC48, Q8IW33, Q8WXA3, Q96P51, Q9P1Z1

    8. XM_047425447.1 → XP_047281403.1  RUN and FYVE domain-containing protein 2 isoform X8

    9. XM_011539942.3 → XP_011538244.1  RUN and FYVE domain-containing protein 2 isoform X2

      See identical proteins and their annotated locations for XP_011538244.1

      UniProtKB/Swiss-Prot
      B3KXB2, B4DFR0, Q5TC48, Q8IW33, Q8WXA3, Q96P51, Q9P1Z1
      UniProtKB/TrEMBL
      H0YD93
      Conserved Domains (3) summary
      COG1196
      Location:230 → 536
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cd15759
      Location:534 → 604
      FYVE_RUFY2; FYVE domain found in RUN and FYVE domain-containing protein 2 (RUFY2) and similar proteins
      pfam02759
      Location:45 → 166
      RUN; RUN domain

    10. XM_005269955.5 → XP_005270012.1  RUN and FYVE domain-containing protein 2 isoform X3

      See identical proteins and their annotated locations for XP_005270012.1

      UniProtKB/TrEMBL
      H0YD93
      Conserved Domains (3) summary
      COG1196
      Location:214 → 520
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cd15759
      Location:518 → 588
      FYVE_RUFY2; FYVE domain found in RUN and FYVE domain-containing protein 2 (RUFY2) and similar proteins
      pfam02759
      Location:29 → 150
      RUN; RUN domain

    11. XM_047425456.1 → XP_047281412.1  RUN and FYVE domain-containing protein 2 isoform X17

    12. XM_047425455.1 → XP_047281411.1  RUN and FYVE domain-containing protein 2 isoform X16

    13. XM_047425450.1 → XP_047281406.1  RUN and FYVE domain-containing protein 2 isoform X11

    14. XM_047425457.1 → XP_047281413.1  RUN and FYVE domain-containing protein 2 isoform X18

    15. XM_047425452.1 → XP_047281408.1  RUN and FYVE domain-containing protein 2 isoform X13

    16. XM_047425451.1 → XP_047281407.1  RUN and FYVE domain-containing protein 2 isoform X12

    17. XM_047425454.1 → XP_047281410.1  RUN and FYVE domain-containing protein 2 isoform X15

    18. XM_047425449.1 → XP_047281405.1  RUN and FYVE domain-containing protein 2 isoform X10

    19. XM_047425453.1 → XP_047281409.1  RUN and FYVE domain-containing protein 2 isoform X14

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      69210323..69276503 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054366258.1 → XP_054222233.1  RUN and FYVE domain-containing protein 2 isoform X9

    2. XM_054366254.1 → XP_054222229.1  RUN and FYVE domain-containing protein 2 isoform X5

    3. XM_054366256.1 → XP_054222231.1  RUN and FYVE domain-containing protein 2 isoform X7

    4. XM_054366255.1 → XP_054222230.1  RUN and FYVE domain-containing protein 2 isoform X6

    5. XM_054366250.1 → XP_054222225.1  RUN and FYVE domain-containing protein 2 isoform X1

    6. XM_054366253.1 → XP_054222228.1  RUN and FYVE domain-containing protein 2 isoform X4

    7. XM_054366251.1 → XP_054222226.1  RUN and FYVE domain-containing protein 2 isoform X2

      UniProtKB/Swiss-Prot
      B3KXB2, B4DFR0, Q5TC48, Q8IW33, Q8WXA3, Q96P51, Q9P1Z1

    8. XM_054366257.1 → XP_054222232.1  RUN and FYVE domain-containing protein 2 isoform X8

    9. XM_054366252.1 → XP_054222227.1  RUN and FYVE domain-containing protein 2 isoform X3

    10. XM_054366266.1 → XP_054222241.1  RUN and FYVE domain-containing protein 2 isoform X17

    11. XM_054366265.1 → XP_054222240.1  RUN and FYVE domain-containing protein 2 isoform X16

    12. XM_054366260.1 → XP_054222235.1  RUN and FYVE domain-containing protein 2 isoform X11

    13. XM_054366267.1 → XP_054222242.1  RUN and FYVE domain-containing protein 2 isoform X18

    14. XM_054366262.1 → XP_054222237.1  RUN and FYVE domain-containing protein 2 isoform X13

    15. XM_054366261.1 → XP_054222236.1  RUN and FYVE domain-containing protein 2 isoform X12

    16. XM_054366264.1 → XP_054222239.1  RUN and FYVE domain-containing protein 2 isoform X15

    17. XM_054366259.1 → XP_054222234.1  RUN and FYVE domain-containing protein 2 isoform X10

    18. XM_054366263.1 → XP_054222238.1  RUN and FYVE domain-containing protein 2 isoform X14

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WXA3.3 GenPept UniProtKB/Swiss-Prot:Q8WXA3

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