Human Gene ZFYVE1 (ENST00000556143.6_7) from GENCODE V47lift37
  Description: zinc finger FYVE-type containing 1, transcript variant 1 (from RefSeq NM_021260.4)
Gencode Transcript: ENST00000556143.6_7
Gencode Gene: ENSG00000165861.14_9
Transcript (Including UTRs)
   Position: hg19 chr14:73,436,159-73,493,814 Size: 57,656 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg19 chr14:73,437,590-73,491,216 Size: 53,627 Coding Exon Count: 11 

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Gene AllelesRNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:73,436,159-73,493,814)mRNA (may differ from genome)Protein (777 aa)
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-  Comments and Description Text from UniProtKB
  ID: ZFYV1_HUMAN
DESCRIPTION: RecName: Full=Zinc finger FYVE domain-containing protein 1; AltName: Full=Double FYVE-containing protein 1; AltName: Full=SR3; AltName: Full=Tandem FYVE fingers-1;
SUBUNIT: Binds to phosphatidylinositol 3-phosphate (PtdIns3P) through its FYVE-type zinc finger.
INTERACTION: P62136:PPP1CA; NbExp=2; IntAct=EBI-4401611, EBI-357253;
SUBCELLULAR LOCATION: Golgi apparatus, Golgi stack. Endoplasmic reticulum. Note=Resides predominantly in the cisternal stacks of the Golgi. Colocalizes with TRIM13 on the perinuclear endoplasmic reticulum.
TISSUE SPECIFICITY: Isoform 1 is expressed in all tissues examined, including, brain, placenta, lung, liver, skeletal muscle, pancreas and kidney. Isoform 1 and isoform 2 are highly expressed in heart. Isoform 2 is also detected in the testis.
SIMILARITY: Contains 2 FYVE-type zinc fingers.
SEQUENCE CAUTION: Sequence=AAL55826.1; Type=Frameshift; Positions=480; Sequence=BAB13415.1; Type=Erroneous initiation; Sequence=BAB55085.1; Type=Erroneous termination; Positions=760; Note=Translated as Trp;

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: ZFYVE1
Diseases sorted by gene-association score: mental retardation, x-linked, snyder-robinson type (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 11.14 RPKM in Adrenal Gland
Total median expression: 358.15 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -171.10615-0.278 Picture PostScript Text
3' UTR -505.601431-0.353 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
IPR000306 - Znf_FYVE
IPR017455 - Znf_FYVE-rel
IPR011011 - Znf_FYVE_PHD
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF01363 - FYVE zinc finger

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases
57184 - Growth factor receptor domain
57903 - FYVE/PHD zinc finger

ModBase Predicted Comparative 3D Structure on Q9HBF4
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 DetailsGene Details    
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-  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:0008270 zinc ion binding
GO:0043325 phosphatidylinositol-3,4-bisphosphate binding
GO:0046872 metal ion binding

Biological Process:
GO:0009267 cellular response to starvation
GO:0010923 negative regulation of phosphatase activity
GO:0016236 macroautophagy

Cellular Component:
GO:0000407 pre-autophagosomal structure
GO:0005776 autophagosome
GO:0005783 endoplasmic reticulum
GO:0005794 Golgi apparatus
GO:0005795 Golgi stack
GO:0044233 ER-mitochondrion membrane contact site
GO:0048471 perinuclear region of cytoplasm
GO:0097629 extrinsic component of omegasome membrane
GO:1990462 omegasome
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  AF318319 - Homo sapiens pp10436 mRNA, complete cds.
BC014902 - Homo sapiens, Similar to zinc finger protein, subfamily 2A (FYVE domain containing), 1, clone IMAGE:3919581, mRNA.
BC053520 - Homo sapiens zinc finger, FYVE domain containing 1, mRNA (cDNA clone MGC:51992 IMAGE:5493027), complete cds.
AB046809 - Homo sapiens KIAA1589 mRNA for KIAA1589 protein.
JD336261 - Sequence 317285 from Patent EP1572962.
JD513811 - Sequence 494835 from Patent EP1572962.
JD440675 - Sequence 421699 from Patent EP1572962.
JD500217 - Sequence 481241 from Patent EP1572962.
JD074316 - Sequence 55340 from Patent EP1572962.
DQ581267 - Homo sapiens piRNA piR-49379, complete sequence.
JD354857 - Sequence 335881 from Patent EP1572962.
AJ310569 - Homo sapiens mRNA for phosphoinositide-binding protein, isolate SR3.
JD383173 - Sequence 364197 from Patent EP1572962.
JD206253 - Sequence 187277 from Patent EP1572962.
JD514604 - Sequence 495628 from Patent EP1572962.
JD149903 - Sequence 130927 from Patent EP1572962.
JD539348 - Sequence 520372 from Patent EP1572962.
JD432063 - Sequence 413087 from Patent EP1572962.
JD364427 - Sequence 345451 from Patent EP1572962.
JD232557 - Sequence 213581 from Patent EP1572962.
JD099817 - Sequence 80841 from Patent EP1572962.
JD346252 - Sequence 327276 from Patent EP1572962.
JD150354 - Sequence 131378 from Patent EP1572962.
JD515465 - Sequence 496489 from Patent EP1572962.
JD242456 - Sequence 223480 from Patent EP1572962.
JD358125 - Sequence 339149 from Patent EP1572962.
AF251025 - Homo sapiens double FYVE-containing protein 1 mRNA, complete cds.
AK098542 - Homo sapiens cDNA FLJ25676 fis, clone TST04042, highly similar to Homo sapiens double FYVE-containing protein 1 mRNA.
AF311602 - Homo sapiens tandem FYVE fingers-1 protein mRNA, complete cds.
AB384246 - Synthetic construct DNA, clone: pF1KSDA1589, Homo sapiens ZFYVE1 gene for zinc finger FYVE domain-containing protein 1, complete cds, without stop codon, in Flexi system.
KJ893994 - Synthetic construct Homo sapiens clone ccsbBroadEn_03388 ZFYVE1 gene, encodes complete protein.
AK027399 - Homo sapiens cDNA FLJ14493 fis, clone MAMMA1002972.
CU690974 - Synthetic construct Homo sapiens gateway clone IMAGE:100021519 5' read ZFYVE1 mRNA.
JD511331 - Sequence 492355 from Patent EP1572962.
JD110829 - Sequence 91853 from Patent EP1572962.
JD396331 - Sequence 377355 from Patent EP1572962.
JD497526 - Sequence 478550 from Patent EP1572962.
JD094820 - Sequence 75844 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: DFCP1, ENST00000556143.1, ENST00000556143.2, ENST00000556143.3, ENST00000556143.4, ENST00000556143.5, J3KNL9, KIAA1589, NM_021260, PP10436, Q8WYX7, Q96K57, Q9BXP9, Q9HBF4, Q9HCI3, TAFF1, uc325igf.1, uc325igf.2, ZFYV1_HUMAN, ZNFN2A1
UCSC ID: ENST00000556143.6_7
RefSeq Accession: NM_021260.4
Protein: Q9HBF4 (aka ZFYV1_HUMAN or ZFV1_HUMAN)

-  Gene Model Information
  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.