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ZFYVE16 zinc finger FYVE-type containing 16 [ Homo sapiens (human) ]

Gene ID: 9765, updated on 15-Jun-2019

Summary

Official Symbol
ZFYVE16provided by HGNC
Official Full Name
zinc finger FYVE-type containing 16provided by HGNC
Primary source
HGNC:HGNC:20756
See related
Ensembl:ENSG00000039319 MIM:608880
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
PPP1R69
Summary
This gene encodes an endosomal protein that belongs to the FYVE zinc finger family of proteins. The encoded protein is thought to regulate membrane trafficking in the endosome. This protein functions as a scaffold protein in the transforming growth factor-beta signaling pathway and is involved in positive and negative feedback regulation of the bone morphogenetic protein signaling pathway. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]
Expression
Ubiquitous expression in brain (RPKM 10.1), endometrium (RPKM 9.9) and 25 other tissues See more
Orthologs

Genomic context

See ZFYVE16 in Genome Data Viewer
Location:
5q14.1
Exon count:
24
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 5 NC_000005.10 (80407615..80483379)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (79703386..79775498)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 12 Neighboring gene RNA, U6 small nuclear 211, pseudogene Neighboring gene family with sequence similarity 151 member B Neighboring gene ribosomal protein S27a pseudogene 9 Neighboring gene ribosomal protein L7 pseudogene 24

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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • BMP receptor signaling, organism-specific biosystem (from Pathway Interaction Database)
    BMP receptor signaling, organism-specific biosystem
    BMP receptor signaling
  • 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...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by BMP, organism-specific biosystem (from REACTOME)
    Signaling by BMP, organism-specific biosystemBone morphogenetic proteins (BMPs) have many biological activities in various tissues, including bone, cartilage, blood vessels, heart, kidney, neurons, liver and lung. They are members of the Transf...
  • TGF-beta Signaling Pathway, organism-specific biosystem (from WikiPathways)
    TGF-beta Signaling Pathway, organism-specific biosystemThe signal transduction mechanisms underlying the pathophysiological activities of transforming growth factor-? (TGF-?) have been extensively studied since its discovery nearly 30 years ago. TGF-? li...
  • TGF-beta receptor signaling, organism-specific biosystem (from Pathway Interaction Database)
    TGF-beta receptor signaling, organism-specific biosystem
    TGF-beta receptor signaling
  • TGF-beta signaling pathway, organism-specific biosystem (from KEGG)
    TGF-beta signaling pathway, organism-specific biosystemThe transforming growth factor-beta (TGF-beta) family members, which include TGF-betas, activins and bone morphogenetic proteins (BMPs), are structurally related secreted cytokines found in species r...
  • TGF-beta signaling pathway, conserved biosystem (from KEGG)
    TGF-beta signaling pathway, conserved biosystemThe transforming growth factor-beta (TGF-beta) family members, which include TGF-betas, activins and bone morphogenetic proteins (BMPs), are structurally related secreted cytokines found in species r...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0305, DKFZp686E13162

Gene Ontology Provided by GOA

Function Evidence Code Pubs
1-phosphatidylinositol binding IDA
Inferred from Direct Assay
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
phosphatidylinositol-3,4,5-trisphosphate binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
BMP signaling pathway TAS
Traceable Author Statement
more info
 
endosomal transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endosomal transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein targeting to lysosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein targeting to lysosome IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of endocytosis TAS
Traceable Author Statement
more info
PubMed 
signal transduction NAS
Non-traceable Author Statement
more info
PubMed 
vesicle organization NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
cytosol IDA
Inferred from Direct Assay
more info
 
early endosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
early endosome IDA
Inferred from Direct Assay
more info
PubMed 
early endosome membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
early endosome membrane TAS
Traceable Author Statement
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
zinc finger FYVE domain-containing protein 16
Names
endosome-associated FYVE-domain protein
protein phosphatase 1, regulatory subunit 69
zinc finger, FYVE domain containing 16

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.

mRNA and Protein(s)

  1. NM_001105251.4NP_001098721.2  zinc finger FYVE domain-containing protein 16 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 5 encode the same protein (isoform a).
    Source sequence(s)
    AC008771
    Consensus CDS
    CCDS4050.1
    Related
    ENSP00000423663.1, ENST00000510158.5
  2. NM_001284236.3NP_001271165.2  zinc finger FYVE domain-containing protein 16 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 ,3 and 5 encode the same protein (isoform a).
    Source sequence(s)
    AC008771
    Consensus CDS
    CCDS4050.1
    Related
    ENSP00000426848.1, ENST00000505560.5
    Conserved Domains (2) summary
    cd15729
    Location:738804
    FYVE_endofin; FYVE domain found in endofin and similar proteins
    pfam11979
    Location:11671515
    DUF3480; Domain of unknown function (DUF3480)
  3. NM_001284237.2NP_001271166.2  zinc finger FYVE domain-containing protein 16 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks several exons in the 3' coding region and contains a 3' terminal exon that extends past a splice site that is used in variant 1 resulting in an early stop codon, and a different 3' UTR, compared to variant 1. The encoded protein (isoform b) has a distinct C-terminus and is shorter than isoform a.
    Source sequence(s)
    AC008771
  4. NM_001349434.2NP_001336363.2  zinc finger FYVE domain-containing protein 16 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 5 encode the same protein (isoform a).
    Source sequence(s)
    AC008771
    Consensus CDS
    CCDS4050.1
  5. NM_014733.6NP_055548.4  zinc finger FYVE domain-containing protein 16 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (a). Variants 1, 2, 3 and 5 encode the same protein (isoform a).
    Source sequence(s)
    AC008771
    Consensus CDS
    CCDS4050.1
    Related
    ENSP00000337159.5, ENST00000338008.9

RNA

  1. NR_146172.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) contains three alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB002303, AC008771, AL833087, BC063868, CB854699, DA216169
  2. NR_146173.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) contains two alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB002303, AC008771, AL833087, BC063868, CB854699, DA216169, DA216340
  3. NR_146174.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) contains two alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AB002303, AC008771, AL833087, BC063868, CB854699, DA216169

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_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    80407615..80483379
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005248632.4XP_005248689.1  zinc finger FYVE domain-containing protein 16 isoform X1

    See identical proteins and their annotated locations for XP_005248689.1

    UniProtKB/Swiss-Prot
    Q7Z3T8
    Conserved Domains (2) summary
    cd15729
    Location:738804
    FYVE_endofin; FYVE domain found in endofin and similar proteins
    pfam11979
    Location:11671515
    DUF3480; Domain of unknown function (DUF3480)
  2. XM_017010092.2XP_016865581.1  zinc finger FYVE domain-containing protein 16 isoform X1

    UniProtKB/Swiss-Prot
    Q7Z3T8
    Conserved Domains (2) summary
    cd15729
    Location:738804
    FYVE_endofin; FYVE domain found in endofin and similar proteins
    pfam11979
    Location:11671515
    DUF3480; Domain of unknown function (DUF3480)
  3. XM_017010091.1XP_016865580.1  zinc finger FYVE domain-containing protein 16 isoform X1

    UniProtKB/Swiss-Prot
    Q7Z3T8
    Conserved Domains (2) summary
    cd15729
    Location:738804
    FYVE_endofin; FYVE domain found in endofin and similar proteins
    pfam11979
    Location:11671515
    DUF3480; Domain of unknown function (DUF3480)
  4. XM_024446270.1XP_024302038.1  zinc finger FYVE domain-containing protein 16 isoform X1

    Conserved Domains (2) summary
    cd15729
    Location:738804
    FYVE_endofin; FYVE domain found in endofin and similar proteins
    pfam11979
    Location:11671515
    DUF3480; Domain of unknown function (DUF3480)
  5. XM_024446273.1XP_024302041.1  zinc finger FYVE domain-containing protein 16 isoform X2

    Conserved Domains (1) summary
    pfam11979
    Location:355703
    DUF3480; Domain of unknown function (DUF3480)
  6. XM_024446271.1XP_024302039.1  zinc finger FYVE domain-containing protein 16 isoform X2

    Conserved Domains (1) summary
    pfam11979
    Location:355703
    DUF3480; Domain of unknown function (DUF3480)
  7. XM_024446272.1XP_024302040.1  zinc finger FYVE domain-containing protein 16 isoform X2

    Conserved Domains (1) summary
    pfam11979
    Location:355703
    DUF3480; Domain of unknown function (DUF3480)
  8. XM_017010096.1XP_016865585.1  zinc finger FYVE domain-containing protein 16 isoform X3

RNA

  1. XR_001742375.1 RNA Sequence

  2. XR_001742377.2 RNA Sequence

  3. XR_001742376.2 RNA Sequence

  4. XR_001742380.2 RNA Sequence

  5. XR_001742373.1 RNA Sequence

  6. XR_001742382.2 RNA Sequence

  7. XR_001742379.2 RNA Sequence

  8. XR_001742384.1 RNA Sequence

  9. XR_001742381.1 RNA Sequence

  10. XR_002956199.1 RNA Sequence

  11. XR_001742378.2 RNA Sequence

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