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Aliases for YIPF3 Gene

Aliases for YIPF3 Gene

  • Yip1 Domain Family Member 3 2 3 5
  • Natural Killer Cell-Specific Antigen KLIP1 3 4
  • Killer Lineage Protein 1 3 4
  • C6orf109 3 4
  • KLIP1 3 4
  • Chromosome 6 Open Reading Frame 109 2
  • Yip1 Domain Family, Member 3 2
  • YIP1 Family Member 3 4
  • Protein YIPF3 3
  • DJ337H4.3 3
  • FinGER3 3

External Ids for YIPF3 Gene

Previous HGNC Symbols for YIPF3 Gene

  • C6orf109

Previous GeneCards Identifiers for YIPF3 Gene

  • GC06M043588
  • GC06M043197

Summaries for YIPF3 Gene

GeneCards Summary for YIPF3 Gene

YIPF3 (Yip1 Domain Family Member 3) is a Protein Coding gene. Diseases associated with YIPF3 include Frasier Syndrome.

UniProtKB/Swiss-Prot for YIPF3 Gene

  • Involved in the maintenance of the Golgi structure. May play a role in hematopoiesis.

Gene Wiki entry for YIPF3 Gene

Additional gene information for YIPF3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for YIPF3 Gene

Genomics for YIPF3 Gene

GeneHancer (GH) Regulatory Elements for YIPF3 Gene

Promoters and enhancers for YIPF3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06I043515 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 560.7 0.0 -5 3.4 HDGF PKNOX1 SMAD1 FOXA2 ARNT ARID4B NEUROD1 SIN3A DMAP1 ZNF2 YIPF3 POLR1C ABCC10 ZNF318 GTPBP2 UBR2 CUL7 RPS2P29 BICRAL AARS2
GH06I044245 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 32 -730.6 -730557 5 CLOCK DMAP1 YBX1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ZNF548 HSP90AB1 ZNF318 POLH GTPBP2 ABCC10 RPS2P29 POLR1C AARS2 YIPF3 CDC5L
GH06I044216 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 19.7 -706.2 -706177 14.3 CLOCK MLX DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 NFYC SSRP1 SLC29A1 GTPBP2 POLH RPS2P29 ZNF318 ABCC10 YIPF3 MYMX SLC35B2 RPL34P14
GH06I044255 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10 -744.0 -743954 11.9 CLOCK ZFP64 DMAP1 YBX1 IRF4 E2F8 ZNF143 ZNF263 SP3 SSRP1 SLC35B2 ABCC10 RPL34P14 ZNF318 AARS2 NFKBIE RPS2P29 POLH GTPBP2 POLR1C
GH06I043624 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 11.5 -111.0 -111049 7.4 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 ZNF263 SP3 GTPBP2 MAD2L1BP POLH ZNF318 ABCC10 RRP36 RPS2P29 CUL7 BICRAL XPO5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around YIPF3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the YIPF3 gene promoter:

Genomic Locations for YIPF3 Gene

Genomic Locations for YIPF3 Gene
chr6:43,511,827-43,516,990
(GRCh38/hg38)
Size:
5,164 bases
Orientation:
Minus strand
chr6:43,479,565-43,484,728
(GRCh37/hg19)

Genomic View for YIPF3 Gene

Genes around YIPF3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
YIPF3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for YIPF3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for YIPF3 Gene

Proteins for YIPF3 Gene

  • Protein details for YIPF3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9GZM5-YIPF3_HUMAN
    Recommended name:
    Protein YIPF3
    Protein Accession:
    Q9GZM5
    Secondary Accessions:
    • Q5JTD2
    • Q6FI85
    • Q8NI57
    • Q9NWE3
    • Q9Y3U9

    Protein attributes for YIPF3 Gene

    Size:
    350 amino acids
    Molecular mass:
    38248 Da
    Quaternary structure:
    • Interacts with YIPF4 and YIPF5.
    SequenceCaution:
    • Sequence=CAI42626.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

neXtProt entry for YIPF3 Gene

Post-translational modifications for YIPF3 Gene

  • N-glycosylated in the ER (40 kDa form I), then O-glycosylated in the Golgi apparatus (46 kDa form II), the C-terminal lumenal region is later removed in the Golgi apparatus to produce a 36 kDa form III. O-glycosylated with core 1-like and core 2-like glycans. O-glycan heterogeneity at Thr-346: HexNAc (minor), HexHexNAc (major), Hex1HexNAc2 (minor), Hex2HexNAc2 (minor) and dHex1Hex2HexNAc2 (minor).
  • Ubiquitination at posLast=8686, posLast=102102, and posLast=141141
  • Glycosylation at isoforms=333, posLast=334334, isoforms=337, isoforms=339, and posLast=346346

No data available for DME Specific Peptides for YIPF3 Gene

Domains & Families for YIPF3 Gene

Gene Families for YIPF3 Gene

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

Protein Domains for YIPF3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for YIPF3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9GZM5

UniProtKB/Swiss-Prot:

YIPF3_HUMAN :
  • Belongs to the YIP1 family.
Family:
  • Belongs to the YIP1 family.
genes like me logo Genes that share domains with YIPF3: view

Function for YIPF3 Gene

Molecular function for YIPF3 Gene

UniProtKB/Swiss-Prot Function:
Involved in the maintenance of the Golgi structure. May play a role in hematopoiesis.

Phenotypes From GWAS Catalog for YIPF3 Gene

Gene Ontology (GO) - Molecular Function for YIPF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
genes like me logo Genes that share ontologies with YIPF3: view
genes like me logo Genes that share phenotypes with YIPF3: view

Animal Model Products

CRISPR Products

miRNA for YIPF3 Gene

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for YIPF3 Gene

Localization for YIPF3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for YIPF3 Gene

Cell membrane; Multi-pass membrane protein. Cytoplasm. Golgi apparatus, cis-Golgi network membrane; Multi-pass membrane protein. Note=Localization to the cytoplasm or to the cell membrane is developmentally and ontogenetically regulated.

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 YIPF3 gene
Compartment Confidence
plasma membrane 5
golgi apparatus 5
nucleus 2
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (4)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for YIPF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005794 Golgi apparatus IDA --
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with YIPF3: view

Pathways & Interactions for YIPF3 Gene

SuperPathways for YIPF3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for YIPF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030154 cell differentiation IEA --
genes like me logo Genes that share ontologies with YIPF3: view

No data available for Pathways by source and SIGNOR curated interactions for YIPF3 Gene

Drugs & Compounds for YIPF3 Gene

No Compound Related Data Available

Transcripts for YIPF3 Gene

Unigene Clusters for YIPF3 Gene

Yip1 domain family, member 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for YIPF3 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g ^ 2a · 2b · 2c · 2d ^ 3 ^ 4 ^ 5a · 5b · 5c · 5d ^ 6a · 6b · 6c ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b ^
SP1: - - - - - - - -
SP2: - - - -
SP3: - - - - - -
SP4: - - - - - - - - -
SP5: - - - - - -
SP6: - - - - - - -
SP7: - - - - - - - - - -
SP8: - - - - -
SP9: - - - - - -
SP10: -
SP11: - - - -
SP12: - - - -
SP13: - - - - - - -
SP14: - - -
SP15: -

ExUns: 11a · 11b ^ 12
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:

Relevant External Links for YIPF3 Gene

GeneLoc Exon Structure for
YIPF3
ECgene alternative splicing isoforms for
YIPF3

Expression for YIPF3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for YIPF3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for YIPF3 Gene

This gene is overexpressed in Nasal epithelium (25.2), Urine (20.1), and Cerebrospinal fluid (13.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for YIPF3 Gene



NURSA nuclear receptor signaling pathways regulating expression of YIPF3 Gene:

YIPF3

SOURCE GeneReport for Unigene cluster for YIPF3 Gene:

Hs.440950

mRNA Expression by UniProt/SwissProt for YIPF3 Gene:

Q9GZM5-YIPF3_HUMAN
Tissue specificity: Expressed by nucleated hematopoietic cells (at protein level).

Evidence on tissue expression from TISSUES for YIPF3 Gene

  • Lung(4.5)
  • Skin(4.5)
  • Nervous system(4)
  • Pancreas(2.5)
  • Muscle(2.2)
  • Eye(2)
genes like me logo Genes that share expression patterns with YIPF3: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for YIPF3 Gene

Orthologs for YIPF3 Gene

This gene was present in the common ancestor of animals.

Orthologs for YIPF3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia YIPF3 33 34
  • 99.71 (n)
oppossum
(Monodelphis domestica)
Mammalia YIPF3 34
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia YIPF3 33 34
  • 91.87 (n)
cow
(Bos Taurus)
Mammalia YIPF3 33 34
  • 91.64 (n)
rat
(Rattus norvegicus)
Mammalia Yipf3 33
  • 89.48 (n)
mouse
(Mus musculus)
Mammalia Yipf3 33 16 34
  • 89.29 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia YIPF3 34
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves YIPF3 33 34
  • 78.49 (n)
lizard
(Anolis carolinensis)
Reptilia YIPF3 34
  • 81 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.15451 33
zebrafish
(Danio rerio)
Actinopterygii yipf3 34 33
  • 72.77 (n)
OneToOne
wufj97f06 33
worm
(Caenorhabditis elegans)
Secernentea Y53C12A.3 33 34
  • 48.56 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8413 34
  • 49 (a)
OneToOne
Species where no ortholog for YIPF3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for YIPF3 Gene

ENSEMBL:
Gene Tree for YIPF3 (if available)
TreeFam:
Gene Tree for YIPF3 (if available)

Paralogs for YIPF3 Gene

Pseudogenes.org Pseudogenes for YIPF3 Gene

genes like me logo Genes that share paralogs with YIPF3: view

No data available for Paralogs for YIPF3 Gene

Variants for YIPF3 Gene

Sequence variations from dbSNP and Humsavar for YIPF3 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1057519455 pathogenic, Leukodystrophy, hypomyelinating, 11 43,517,324(-) C/T upstream_transcript_variant
rs190872536 uncertain-significance, Treacher Collins Syndrome, Recessive 43,517,089(-) A/G/T upstream_transcript_variant
rs2231756 uncertain-significance, likely-benign, Treacher Collins Syndrome, Recessive, not specified 43,517,106(-) G/A upstream_transcript_variant
rs745593101 uncertain-significance, Treacher Collins Syndrome, Recessive 43,517,177(-) A/G upstream_transcript_variant
rs796052124 pathogenic, Leukodystrophy, hypomyelinating, 11 43,517,331(-) A/T upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for YIPF3 Gene

Variant ID Type Subtype PubMed ID
nsv603000 CNV loss 21841781
nsv818414 CNV gain 17921354
nsv950173 CNV deletion 24416366

Variation tolerance for YIPF3 Gene

Residual Variation Intolerance Score: 18.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.54; 44.26% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for YIPF3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
YIPF3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for YIPF3 Gene

Disorders for YIPF3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for YIPF3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
frasier syndrome
  • fs
- elite association - COSMIC cancer census association via MalaCards
Search YIPF3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for YIPF3

genes like me logo Genes that share disorders with YIPF3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for YIPF3 Gene

Publications for YIPF3 Gene

  1. Functional characterisation of the YIPF protein family in mammalian cells. (PMID: 27999994) Kranjc T … Simpson JC (Histochemistry and cell biology 2017) 3 4 58
  2. Characterization of YIPF3 and YIPF4, cis-Golgi Localizing Yip domain family proteins. (PMID: 21757827) Tanimoto K … Nakamura N (Cell structure and function 2011) 3 4 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. The DNA sequence and analysis of human chromosome 6. (PMID: 14574404) Mungall AJ … Beck S (Nature 2003) 3 4 58

Products for YIPF3 Gene

Sources for YIPF3 Gene

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