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Aliases for ZFYVE28 Gene

Aliases for ZFYVE28 Gene

  • Zinc Finger FYVE-Type Containing 28 2 3 5
  • Zinc Finger FYVE Domain-Containing Protein 28 3 4
  • Zinc Finger, FYVE Domain Containing 28 2 3
  • HLst2 3 4
  • LST2 3 4
  • Lateral Signaling Target Protein 2 Homolog 3
  • KIAA1643 4
  • LYST2 3

External Ids for ZFYVE28 Gene

Previous GeneCards Identifiers for ZFYVE28 Gene

  • GC04M002233
  • GC04M002238

Summaries for ZFYVE28 Gene

GeneCards Summary for ZFYVE28 Gene

ZFYVE28 (Zinc Finger FYVE-Type Containing 28) is a Protein Coding gene. Among its related pathways are Internalization of ErbB1. GO annotations related to this gene include phosphatidylinositol-3-phosphate binding. An important paralog of this gene is ZFYVE16.

UniProtKB/Swiss-Prot for ZFYVE28 Gene

  • Negative regulator of epidermal growth factor receptor (EGFR) signaling. Acts by promoting EGFR degradation in endosomes when not monoubiquitinated.

Additional gene information for ZFYVE28 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZFYVE28 Gene

Genomics for ZFYVE28 Gene

Regulatory Elements for ZFYVE28 Gene

Enhancers for ZFYVE28 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH04H002411 2 FANTOM5 Ensembl ENCODE dbSUPER 34.9 +5.6 5636 4 PKNOX1 ATF1 ARID4B SIN3A FEZF1 ETS1 ZNF766 GLIS2 ZNF143 FOS ZFYVE28 HAUS3 RNF4 MXD4 SH3BP2 CFAP99 HTT TNIP2 GC04M002409
GH04H002361 1.2 FANTOM5 ENCODE 43.4 +55.2 55240 4 HDAC1 TBP FOXA2 PKNOX1 ATF1 RB1 RAD21 YY1 EGR1 CREM ZFYVE28 ENSG00000251148 MXD4 CFAP99 LOC105374353 RNF4 HAUS3 POLN NELFA C4orf48
GH04H002401 1.6 FANTOM5 Ensembl ENCODE dbSUPER 26.2 +16.3 16290 1 HDAC1 PKNOX1 SIN3A EGR1 KLF7 ATF7 EGR2 SP3 SP5 NR2F2 ZFYVE28 RNF4 LOC105374353 ENSG00000251148 MXD4 POLN HAUS3 NELFA C4orf48 GC04P002406
GH04H002393 1.3 Ensembl ENCODE dbSUPER 27.6 +24.9 24866 0 HDAC1 ATF1 SAP130 ETV1 RELA CTBP1 CBX5 ELK1 FOXK2 POLR2A ZFYVE28 ENSG00000251148 MXD4 POLN HAUS3 RNF4 LOC105374353 C4orf48 NELFA PIR44270
GH04H002290 1.5 FANTOM5 Ensembl ENCODE dbSUPER 18.9 +127.5 127500 2 PKNOX1 RFX1 NR2F1 BHLHE40 MAX IKZF1 IKZF2 SPI1 HAUS3 ZFYVE28 RNF4 CFAP99 TNIP2 ENSG00000251148 GC04P002288
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around ZFYVE28 on UCSC Golden Path with GeneCards custom track

Promoters for ZFYVE28 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000164955 590 2201 ATF1 ARID4B SIN3A ZNF2 YY1 ETS1 ZNF766 GLIS2 ELK1 ZNF207

Genomic Location for ZFYVE28 Gene

Chromosome:
4
Start:
2,267,524 bp from pter
End:
2,418,690 bp from pter
Size:
151,167 bases
Orientation:
Minus strand

Genomic View for ZFYVE28 Gene

Genes around ZFYVE28 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZFYVE28 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZFYVE28 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZFYVE28 Gene

Proteins for ZFYVE28 Gene

  • Protein details for ZFYVE28 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HCC9-LST2_HUMAN
    Recommended name:
    Lateral signaling target protein 2 homolog
    Protein Accession:
    Q9HCC9
    Secondary Accessions:
    • B2RP83
    • B3KX50
    • B7Z1Q7
    • B7Z2G9
    • B7Z2M2
    • B7ZB19
    • E9PB54
    • E9PB64
    • E9PG77
    • Q7Z6J3

    Protein attributes for ZFYVE28 Gene

    Size:
    887 amino acids
    Molecular mass:
    96490 Da
    Quaternary structure:
    • Interacts with TRIM3.
    SequenceCaution:
    • Sequence=AAH53664.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB13469.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for ZFYVE28 Gene

neXtProt entry for ZFYVE28 Gene

Post-translational modifications for ZFYVE28 Gene

  • Monoubiquitination at Lys-87 prevents binding to phosphatidylinositol 3-phosphate (PI3P) and localization to early endosome membranes.
  • Ubiquitination at Lys87
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for ZFYVE28 Gene

Domains & Families for ZFYVE28 Gene

Gene Families for ZFYVE28 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for ZFYVE28 Gene

Suggested Antigen Peptide Sequences for ZFYVE28 Gene

Graphical View of Domain Structure for InterPro Entry

Q9HCC9

UniProtKB/Swiss-Prot:

LST2_HUMAN :
  • The FYVE-type zinc finger mediates the interaction with phosphatidylinositol 3-phosphate (PI3P) and localization to early endosome membranes when not monoubiquitinated at Lys-87.
  • Belongs to the lst-2 family.
Domain:
  • The FYVE-type zinc finger mediates the interaction with phosphatidylinositol 3-phosphate (PI3P) and localization to early endosome membranes when not monoubiquitinated at Lys-87.
Family:
  • Belongs to the lst-2 family.
genes like me logo Genes that share domains with ZFYVE28: view

Function for ZFYVE28 Gene

Molecular function for ZFYVE28 Gene

UniProtKB/Swiss-Prot Function:
Negative regulator of epidermal growth factor receptor (EGFR) signaling. Acts by promoting EGFR degradation in endosomes when not monoubiquitinated.

Phenotypes From GWAS Catalog for ZFYVE28 Gene

Gene Ontology (GO) - Molecular Function for ZFYVE28 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 19460345
GO:0032266 phosphatidylinositol-3-phosphate binding IDA 19460345
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with ZFYVE28: view
genes like me logo Genes that share phenotypes with ZFYVE28: view

Animal Models for ZFYVE28 Gene

MGI Knock Outs for ZFYVE28:

Animal Model Products

CRISPR Products

miRNA for ZFYVE28 Gene

miRTarBase miRNAs that target ZFYVE28

Clone Products

  • Applied Biological Materials Clones for ZFYVE28
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ZFYVE28 Gene

Localization for ZFYVE28 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZFYVE28 Gene

Cytoplasm, cytosol. Early endosome membrane. Note=Localizes to early endosome membrane in absence of Lys-87 monoubiquitination. Localizes to cytosol when monoubiquitinated.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ZFYVE28 gene
Compartment Confidence
cytosol 5
endosome 5
plasma membrane 2
nucleus 2
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleus (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ZFYVE28 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005768 endosome IEA --
GO:0005829 cytosol IDA,IEA 19460345
GO:0016020 membrane IEA --
GO:0031901 early endosome membrane IDA,IEA 19460345
genes like me logo Genes that share ontologies with ZFYVE28: view

Pathways & Interactions for ZFYVE28 Gene

SuperPathways for ZFYVE28 Gene

SuperPathway Contained pathways
1 Internalization of ErbB1
genes like me logo Genes that share pathways with ZFYVE28: view

Pathways by source for ZFYVE28 Gene

1 BioSystems pathway for ZFYVE28 Gene

Gene Ontology (GO) - Biological Process for ZFYVE28 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007175 negative regulation of epidermal growth factor-activated receptor activity IMP 19460345
GO:0042059 negative regulation of epidermal growth factor receptor signaling pathway IMP 19460345
genes like me logo Genes that share ontologies with ZFYVE28: view

No data available for SIGNOR curated interactions for ZFYVE28 Gene

Drugs & Compounds for ZFYVE28 Gene

No Compound Related Data Available

Transcripts for ZFYVE28 Gene

Unigene Clusters for ZFYVE28 Gene

Zinc finger, FYVE domain containing 28:
Representative Sequences:

CRISPR Products

Clone Products

  • Applied Biological Materials Clones for ZFYVE28
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for ZFYVE28 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19a ·
SP1: - - - - - - - - - - -
SP2:
SP3: - - - - - - - -
SP4: - - - - -
SP5: - - - - - - - - -
SP6: - - -
SP7:
SP8:
SP9:

ExUns: 19b ^ 20a · 20b ^ 21
SP1: -
SP2: -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for ZFYVE28 Gene

GeneLoc Exon Structure for
ZFYVE28
ECgene alternative splicing isoforms for
ZFYVE28

Expression for ZFYVE28 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ZFYVE28 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for ZFYVE28 Gene

This gene is overexpressed in Brain - Cerebellum (x6.7) and Brain - Cerebellar Hemisphere (x5.9).

Protein differential expression in normal tissues from HIPED for ZFYVE28 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for ZFYVE28 Gene



Protein tissue co-expression partners for ZFYVE28 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ZFYVE28 Gene:

ZFYVE28

SOURCE GeneReport for Unigene cluster for ZFYVE28 Gene:

Hs.292056

Evidence on tissue expression from TISSUES for ZFYVE28 Gene

  • Nervous system(4.4)
  • Pancreas(4.1)
genes like me logo Genes that share expression patterns with ZFYVE28: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ZFYVE28 Gene

Orthologs for ZFYVE28 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for ZFYVE28 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ZFYVE28 33 34
  • 97.66 (n)
mouse
(Mus musculus)
Mammalia Zfyve28 33 16 34
  • 82.73 (n)
cow
(Bos Taurus)
Mammalia ZFYVE28 33 34
  • 82.66 (n)
rat
(Rattus norvegicus)
Mammalia Zfyve28 33
  • 82.24 (n)
dog
(Canis familiaris)
Mammalia ZFYVE28 33 34
  • 81.25 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia ZFYVE28 34
  • 75 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia ZFYVE28 34
  • 71 (a)
OneToOne
chicken
(Gallus gallus)
Aves ZFYVE28 33 34
  • 66.67 (n)
lizard
(Anolis carolinensis)
Reptilia ZFYVE28 34
  • 55 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia zfyve28 33
  • 68.22 (n)
zebrafish
(Danio rerio)
Actinopterygii zfyve28 33 34
  • 66.3 (n)
idibd1374 33
fruit fly
(Drosophila melanogaster)
Insecta CG6051 34
  • 32 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea lst-2 34
  • 41 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes FAB1 34
  • 5 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4065 34
  • 10 (a)
OneToMany
Species where no ortholog for ZFYVE28 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for ZFYVE28 Gene

ENSEMBL:
Gene Tree for ZFYVE28 (if available)
TreeFam:
Gene Tree for ZFYVE28 (if available)

Paralogs for ZFYVE28 Gene

Paralogs for ZFYVE28 Gene

(1) SIMAP similar genes for ZFYVE28 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with ZFYVE28: view

Variants for ZFYVE28 Gene

Sequence variations from dbSNP and Humsavar for ZFYVE28 Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type
rs1000006441 -- 2,382,921(+) AAAGC(A/G)GAAAC intron-variant
rs1000011008 -- 2,419,669(+) GCCAG(C/G)TGCTC intron-variant, upstream-variant-2KB
rs1000011773 -- 2,301,358(+) GGCAC(A/C)GTGCT intron-variant
rs1000057054 -- 2,397,931(+) GAGAA(A/G)CTAGG intron-variant
rs1000058735 -- 2,388,642(+) GAGCT(C/T)AGGAG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for ZFYVE28 Gene

Variant ID Type Subtype PubMed ID
dgv118e180 CNV deletion 20482838
dgv2709n106 CNV tandem duplication 24896259
dgv2710n106 CNV deletion 24896259
dgv312n21 CNV loss 19592680
dgv805e201 CNV deletion 23290073
dgv8917n54 CNV gain+loss 21841781
dgv8918n54 CNV loss 21841781
dgv8919n54 CNV loss 21841781
esv1496535 CNV deletion 17803354
esv1676935 CNV deletion 17803354
esv2058080 CNV deletion 18987734
esv2490640 CNV insertion 19546169
esv25676 CNV loss 19812545
esv2573577 CNV insertion 19546169
esv2581020 CNV deletion 19546169
esv2669640 CNV deletion 23128226
esv27184 CNV loss 19812545
esv2726835 CNV deletion 23290073
esv2726836 CNV deletion 23290073
esv2726837 CNV deletion 23290073
esv2726838 CNV deletion 23290073
esv2726839 CNV deletion 23290073
esv2726842 CNV deletion 23290073
esv2726844 CNV deletion 23290073
esv2726845 CNV deletion 23290073
esv2831347 CNV deletion 24192839
esv2861791 CNV duplication 24192839
esv3046134 CNV deletion 24192839
esv32578 CNV loss 17666407
esv3354048 CNV duplication 20981092
esv33985 CNV gain+loss 17666407
esv3444124 CNV duplication 20981092
esv3563255 CNV deletion 23714750
esv3563256 CNV deletion 23714750
esv3575671 CNV gain 25503493
esv4159 CNV loss 18987735
esv6725 CNV loss 19470904
nsv1009347 CNV gain 25217958
nsv1013194 CNV gain 25217958
nsv1072350 CNV deletion 25765185
nsv1074670 CNV deletion 25765185
nsv1114480 CNV deletion 24896259
nsv1141809 CNV insertion 24896259
nsv1143074 CNV tandem duplication 24896259
nsv1148780 CNV deletion 26484159
nsv1153819 CNV deletion 26484159
nsv291825 CNV deletion 16902084
nsv4200 CNV insertion 18451855
nsv508990 CNV insertion 20534489
nsv513117 CNV loss 21212237
nsv518472 CNV loss 19592680
nsv524965 CNV loss 19592680
nsv527189 CNV loss 19592680
nsv593401 CNV loss 21841781
nsv593402 CNV loss 21841781
nsv593403 CNV loss 21841781
nsv593404 CNV loss 21841781
nsv593405 CNV gain 21841781
nsv593409 CNV gain+loss 21841781
nsv593410 CNV loss 21841781
nsv593413 CNV gain 21841781
nsv593418 CNV loss 21841781
nsv593419 CNV loss 21841781
nsv821601 CNV deletion 20802225
nsv829838 CNV loss 17160897
nsv954400 CNV deletion 24416366

Variation tolerance for ZFYVE28 Gene

Residual Variation Intolerance Score: 92% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.85; 67.28% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for ZFYVE28 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ZFYVE28

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZFYVE28 Gene

Disorders for ZFYVE28 Gene

Relevant External Links for ZFYVE28

Genetic Association Database (GAD)
ZFYVE28
Human Genome Epidemiology (HuGE) Navigator
ZFYVE28
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
ZFYVE28

No disorders were found for ZFYVE28 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ZFYVE28 Gene

Publications for ZFYVE28 Gene

  1. Prediction of the coding sequences of unidentified human genes. XVIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10997877) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3 4 60
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 45 60
  3. Monoubiquitinylation regulates endosomal localization of Lst2, a negative regulator of EGF receptor signaling. (PMID: 19460345) Mosesson Y … Yarden Y (Developmental cell 2009) 3 4 60
  4. Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects. (PMID: 24324551) Deng X … REDSII Chagas Study Group from the NHLBI Retrovirus Epidemiology Donor Study-II Component International (PloS one 2013) 3 60
  5. Toward a comprehensive characterization of a human cancer cell phosphoproteome. (PMID: 23186163) Zhou H … Mohammed S (Journal of proteome research 2013) 4 60

Products for ZFYVE28 Gene

Sources for ZFYVE28 Gene

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