Human Gene ZFYVE16 (uc003kgq.4)
  Description: Homo sapiens zinc finger, FYVE domain containing 16 (ZFYVE16), transcript variant 1, mRNA.
RefSeq Summary (NM_014733): 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].
Transcript (Including UTRs)
   Position: hg19 chr5:79,703,838-79,775,498 Size: 71,661 Total Exon Count: 18 Strand: +
Coding Region
   Position: hg19 chr5:79,729,967-79,773,196 Size: 43,230 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:79,703,838-79,775,498)mRNA (may differ from genome)Protein (1539 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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neXtProtOMIMPubMedReactomeTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ZFY16_HUMAN
DESCRIPTION: RecName: Full=Zinc finger FYVE domain-containing protein 16; AltName: Full=Endofin; AltName: Full=Endosome-associated FYVE domain protein;
FUNCTION: May be involved in regulating membrane trafficking in the endosomal pathway. Overexpression induces endosome aggregation. Required to target TOM1 to endosomes.
SUBUNIT: Interacts with the C-terminus of TOM1. Does not interact with TOM1L1 or TOM1L2.
INTERACTION: O60784:TOM1; NbExp=5; IntAct=EBI-298055, EBI-74634;
SUBCELLULAR LOCATION: Cytoplasm. Early endosome membrane; Peripheral membrane protein. Note=Localized to early endosomes. Membrane-associated, probably via its association with phosphatidylinositol 3-phosphate (PI3P).
TISSUE SPECIFICITY: Widely expressed. Highly expressed in kidney, placenta and lung. Expressed at intermediate level in heart, brain, skeletal muscle, spleen and liver. Weakly expressed in colon, thymus and peripheral blood lymphocytes.
DOMAIN: The FYVE-type zinc finger is necessary and sufficient for its localization into early endosomes and mediates the association with PI3P.
SIMILARITY: Contains 1 FYVE-type zinc finger.
SEQUENCE CAUTION: Sequence=BAA20764.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ZFYVE16
CDC HuGE Published Literature: ZFYVE16
Positive Disease Associations: Body Weights and Measures
Related Studies:
  1. Body Weights and Measures
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 15.35 RPKM in Brain - Spinal cord (cervical c-1)
Total median expression: 346.94 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -76.40174-0.439 Picture PostScript Text
3' UTR -517.422302-0.225 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR022557 - DUF3480
IPR000306 - Znf_FYVE
IPR017455 - Znf_FYVE-rel
IPR011011 - Znf_FYVE_PHD
IPR017165 - Znf_FYVE_SARA/endofin
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF01363 - FYVE zinc finger
PF11979 - Domain of unknown function (DUF3480)

SCOP Domains:
57903 - FYVE/PHD zinc finger

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3T7L - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q7Z3T8
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0005545 1-phosphatidylinositol binding
GO:0005547 phosphatidylinositol-3,4,5-trisphosphate binding
GO:0008565 protein transporter activity
GO:0046872 metal ion binding

Biological Process:
GO:0006622 protein targeting to lysosome
GO:0007165 signal transduction
GO:0016050 vesicle organization
GO:0016197 endosomal transport
GO:0030100 regulation of endocytosis
GO:0030509 BMP signaling pathway

Cellular Component:
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005769 early endosome
GO:0005829 cytosol
GO:0016020 membrane
GO:0031901 early endosome membrane
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  LP895515 - Sequence 379 from Patent EP3253886.
BC032227 - Homo sapiens zinc finger, FYVE domain containing 16, mRNA (cDNA clone IMAGE:5204515), with apparent retained intron.
BX537424 - Homo sapiens mRNA; cDNA DKFZp686K236 (from clone DKFZp686K236); complete cds.
CR933621 - Homo sapiens mRNA; cDNA DKFZp686E13162 (from clone DKFZp686E13162).
AB002303 - Homo sapiens mRNA for KIAA0305 gene.
BC030808 - Homo sapiens zinc finger, FYVE domain containing 16, mRNA (cDNA clone MGC:22300 IMAGE:4701661), complete cds.
JD404787 - Sequence 385811 from Patent EP1572962.
CU689306 - Synthetic construct Homo sapiens gateway clone IMAGE:100020577 5' read ZFYVE16 mRNA.
CU689018 - Synthetic construct Homo sapiens gateway clone IMAGE:100021997 5' read ZFYVE16 mRNA.
KJ904632 - Synthetic construct Homo sapiens clone ccsbBroadEn_14026 ZFYVE16 gene, encodes complete protein.
AB384456 - Synthetic construct DNA, clone: pF1KA0305, Homo sapiens ZFYVE16 gene for zinc finger FYVE domain-containing protein 16, complete cds, without stop codon, in Flexi system.
AF434817 - Homo sapiens endofin mRNA, complete cds.
AL833087 - Homo sapiens mRNA; cDNA DKFZp451M1519 (from clone DKFZp451M1519).
AK127003 - Homo sapiens cDNA FLJ45058 fis, clone BRAWH3023172, highly similar to Zinc finger FYVE domain-containing protein 16.
BX649172 - Homo sapiens mRNA; cDNA DKFZp686G0694 (from clone DKFZp686G0694).
AK090896 - Homo sapiens cDNA FLJ33577 fis, clone BRAMY2011480.
JD541378 - Sequence 522402 from Patent EP1572962.
JD166948 - Sequence 147972 from Patent EP1572962.
JD053194 - Sequence 34218 from Patent EP1572962.
JD312610 - Sequence 293634 from Patent EP1572962.
JD276926 - Sequence 257950 from Patent EP1572962.
JD299049 - Sequence 280073 from Patent EP1572962.
JD539543 - Sequence 520567 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04144 - Endocytosis
hsa04350 - TGF-beta signaling pathway

Reactome (by CSHL, EBI, and GO)

Protein Q7Z3T8 (Reactome details) participates in the following event(s):

R-HSA-201648 An anchoring protein, Endofin, recruits R-Smad1/5/8
R-HSA-201453 Phospho-R-Smad1/5/8 dissociates from the receptor complex
R-HSA-201476 Activated type I receptor phosphorylates R-Smad1/5/8 directly
R-HSA-201451 Signaling by BMP
R-HSA-9006936 Signaling by TGF-beta family members
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: KIAA0305, NM_014733, NP_055548, O15023, Q5H9U2, Q7LAU7, Q7Z3T8, Q86T69, Q8N5L3, Q8NEK3, ZFY16_HUMAN
UCSC ID: uc003kgq.4
RefSeq Accession: NM_014733
Protein: Q7Z3T8 (aka ZFY16_HUMAN or ZY16_HUMAN)
CCDS: CCDS4050.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014733.3
exon count: 18CDS single in 3' UTR: no RNA size: 7096
ORF size: 4620CDS single in intron: no Alignment % ID: 99.96
txCdsPredict score: 9437.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.