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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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