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RBSN rabenosyn, RAB effector [ Homo sapiens (human) ]

Gene ID: 64145, updated on 17-Jun-2019

Summary

Official Symbol
RBSNprovided by HGNC
Official Full Name
rabenosyn, RAB effectorprovided by HGNC
Primary source
HGNC:HGNC:20759
See related
Ensembl:ENSG00000131381 MIM:609511
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
ZFYVE20; Rabenosyn-5
Summary
This gene encodes a protein that belongs to the FYVE zinc finger family of proteins. The encoded protein interacts with Ras-related proteins that regulate membrane trafficking. A missense mutation in this gene is associated with a defect in the early endocytic pathway. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2014]
Expression
Ubiquitous expression in brain (RPKM 10.8), thyroid (RPKM 6.4) and 25 other tissues See more
Orthologs

Genomic context

See RBSN in Genome Data Viewer
Location:
3p25.1
Exon count:
16
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (15070069..15099163, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (15111580..15140662, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene FGD5 antisense RNA 1 Neighboring gene nuclear receptor subfamily 2 group C member 2 Neighboring gene mitochondrial ribosomal protein S25 Neighboring gene ribosomal protein S24 pseudogene 10 Neighboring gene ribosomal protein S3a pseudogene 53

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

Pathways from BioSystems

  • Endocytosis, organism-specific biosystem (from KEGG)
    Endocytosis, organism-specific biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Endocytosis, conserved biosystem (from KEGG)
    Endocytosis, conserved biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
  • Factors involved in megakaryocyte development and platelet production, organism-specific biosystem (from REACTOME)
    Factors involved in megakaryocyte development and platelet production, organism-specific biosystemMegakaryocytes (MKs) give rise to circulating platelets (thrombocytes) through terminal differentiation of MKs which release cytoplasmic fragments as circulating platelets. As MKs mature they underg...
  • Hemostasis, organism-specific biosystem (from REACTOME)
    Hemostasis, organism-specific biosystemHemostasis is a physiological response that culminates in the arrest of bleeding from an injured vessel. Under normal conditions the vascular endothelium supports vasodilation, inhibits platelet adhe...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Innate Immune System, organism-specific biosystem (from REACTOME)
    Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
  • Toll Like Receptor 9 (TLR9) Cascade, organism-specific biosystem (from REACTOME)
    Toll Like Receptor 9 (TLR9) Cascade, organism-specific biosystemCpG DNA is an unusual Pathogen-Associated Molecular Pattern (PAMP). Cytosine methylation exists in mammalian but not bacterial cells, and most (but not all) CpG in the mammalian genome is methylated....
  • Toll-Like Receptors Cascades, organism-specific biosystem (from REACTOME)
    Toll-Like Receptors Cascades, organism-specific biosystemIn human, ten members of the Toll-like receptor (TLR) family (TLR1-TLR10) have been identified (TLR11 has been found in mouse, but not in human). All TLRs have a similar Toll/IL-1 receptor (TIR) doma...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ34993, MGC126210

Gene Ontology Provided by GOA

Function Evidence Code Pubs
Rab GTPase binding IEA
Inferred from Electronic Annotation
more info
 
nucleic acid binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
zinc ion binding NAS
Non-traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
Golgi to lysosome transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
blood coagulation TAS
Traceable Author Statement
more info
 
early endosome to Golgi transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
endosomal transport NAS
Non-traceable Author Statement
more info
PubMed 
protein transport IEA
Inferred from Electronic Annotation
more info
 
regulation of Golgi organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
cytosol IEA
Inferred from Electronic Annotation
more info
 
early endosome membrane IEA
Inferred from Electronic Annotation
more info
 
endosome NAS
Non-traceable Author Statement
more info
PubMed 
endosome membrane TAS
Traceable Author Statement
more info
 
extracellular exosome HDA PubMed 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
rabenosyn-5
Names
110 kDa protein
FYVE finger-containing Rab5 effector protein rabenosyn-5
RAB effector RBSN
zinc finger, FYVE domain containing 20

NCBI Reference Sequences (RefSeq)

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_041773.1 RefSeqGene

    Range
    5001..34089
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001302378.2NP_001289307.1  rabenosyn-5

    See identical proteins and their annotated locations for NP_001289307.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC090954, AK291288, BX111409
    Consensus CDS
    CCDS2623.1
    UniProtKB/Swiss-Prot
    Q9H1K0
    UniProtKB/TrEMBL
    A0A024R2H4, A8K5H3
    Related
    ENSP00000422551.1, ENST00000476527.6
    Conserved Domains (3) summary
    cd15716
    Location:151262
    FYVE_RBNS5; FYVE domain found in FYVE finger-containing Rab5 effector protein rabenosyn-5 (Rbsn-5) and similar proteins
    pfam11464
    Location:461497
    Rbsn; Rabenosyn Rab binding domain
    pfam16601
    Location:548727
    NPF; Rabosyn-5 repeating NPF sequence-motif
  2. NM_022340.4NP_071735.2  rabenosyn-5

    See identical proteins and their annotated locations for NP_071735.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    AB209673, AC090954, AY009133, BF513881, BX111409, DA320360
    Consensus CDS
    CCDS2623.1
    UniProtKB/Swiss-Prot
    Q9H1K0
    UniProtKB/TrEMBL
    A0A024R2H4
    Related
    ENSP00000253699.3, ENST00000253699.7
    Conserved Domains (3) summary
    cd15716
    Location:151262
    FYVE_RBNS5; FYVE domain found in FYVE finger-containing Rab5 effector protein rabenosyn-5 (Rbsn-5) and similar proteins
    pfam11464
    Location:461497
    Rbsn; Rabenosyn Rab binding domain
    pfam16601
    Location:548727
    NPF; Rabosyn-5 repeating NPF sequence-motif

RNA

  1. NR_126155.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks several exons and its 3' terminal exon extends past a splice site that is used in variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region found in variant 1 and the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    BC032628, DA320360
    Related
    ENST00000449050.5

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    15070069..15099163 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017007026.1XP_016862515.1  rabenosyn-5 isoform X4

  2. XM_017007028.2XP_016862517.1  rabenosyn-5 isoform X5

    Conserved Domains (2) summary
    pfam11464
    Location:219258
    Rbsn; Rabenosyn Rab binding domain
    pfam16601
    Location:309488
    NPF; Rabosyn-5 repeating NPF sequence-motif
  3. XM_017007027.2XP_016862516.1  rabenosyn-5 isoform X5

    Conserved Domains (2) summary
    pfam11464
    Location:219258
    Rbsn; Rabenosyn Rab binding domain
    pfam16601
    Location:309488
    NPF; Rabosyn-5 repeating NPF sequence-motif
  4. XM_017007024.2XP_016862513.1  rabenosyn-5 isoform X3

    Conserved Domains (3) summary
    cd15716
    Location:62173
    FYVE_RBNS5; FYVE domain found in FYVE finger-containing Rab5 effector protein rabenosyn-5 (Rbsn-5) and similar proteins
    pfam11464
    Location:369408
    Rbsn; Rabenosyn Rab binding domain
    pfam16601
    Location:459638
    NPF; Rabosyn-5 repeating NPF sequence-motif
  5. XM_005265385.4XP_005265442.1  rabenosyn-5 isoform X1

    See identical proteins and their annotated locations for XP_005265442.1

    UniProtKB/Swiss-Prot
    Q9H1K0
    UniProtKB/TrEMBL
    A0A024R2H4
    Conserved Domains (3) summary
    cd15716
    Location:151262
    FYVE_RBNS5; FYVE domain found in FYVE finger-containing Rab5 effector protein rabenosyn-5 (Rbsn-5) and similar proteins
    pfam11464
    Location:461497
    Rbsn; Rabenosyn Rab binding domain
    pfam16601
    Location:548727
    NPF; Rabosyn-5 repeating NPF sequence-motif
  6. XM_017007025.2XP_016862514.1  rabenosyn-5 isoform X3

    Conserved Domains (3) summary
    cd15716
    Location:62173
    FYVE_RBNS5; FYVE domain found in FYVE finger-containing Rab5 effector protein rabenosyn-5 (Rbsn-5) and similar proteins
    pfam11464
    Location:369408
    Rbsn; Rabenosyn Rab binding domain
    pfam16601
    Location:459638
    NPF; Rabosyn-5 repeating NPF sequence-motif
  7. XM_005265384.4XP_005265441.1  rabenosyn-5 isoform X1

    See identical proteins and their annotated locations for XP_005265441.1

    UniProtKB/Swiss-Prot
    Q9H1K0
    UniProtKB/TrEMBL
    A0A024R2H4
    Conserved Domains (3) summary
    cd15716
    Location:151262
    FYVE_RBNS5; FYVE domain found in FYVE finger-containing Rab5 effector protein rabenosyn-5 (Rbsn-5) and similar proteins
    pfam11464
    Location:461497
    Rbsn; Rabenosyn Rab binding domain
    pfam16601
    Location:548727
    NPF; Rabosyn-5 repeating NPF sequence-motif
  8. XM_017007023.1XP_016862512.1  rabenosyn-5 isoform X1

    UniProtKB/Swiss-Prot
    Q9H1K0
    UniProtKB/TrEMBL
    A0A024R2H4
    Conserved Domains (3) summary
    cd15716
    Location:151262
    FYVE_RBNS5; FYVE domain found in FYVE finger-containing Rab5 effector protein rabenosyn-5 (Rbsn-5) and similar proteins
    pfam11464
    Location:461497
    Rbsn; Rabenosyn Rab binding domain
    pfam16601
    Location:548727
    NPF; Rabosyn-5 repeating NPF sequence-motif
  9. XM_011534001.2XP_011532303.1  rabenosyn-5 isoform X2

    Conserved Domains (3) summary
    cd15716
    Location:63174
    FYVE_RBNS5; FYVE domain found in FYVE finger-containing Rab5 effector protein rabenosyn-5 (Rbsn-5) and similar proteins
    pfam11464
    Location:370409
    Rbsn; Rabenosyn Rab binding domain
    pfam16601
    Location:460639
    NPF; Rabosyn-5 repeating NPF sequence-motif
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