Aliases for YIPF1 Gene

Aliases for YIPF1 Gene

  • Yip1 Domain Family Member 1 2 3 5
  • YIP1 Family Member 1 3 4
  • Protein YIPF1 3 4
  • DJ167A19.1 2 3
  • FinGER1 2 3
  • Yip1 Domain Family, Member 1 2
  • YIPF1 5

External Ids for YIPF1 Gene

Previous GeneCards Identifiers for YIPF1 Gene

  • GC01M054030
  • GC01M054317
  • GC01M052433

Summaries for YIPF1 Gene

GeneCards Summary for YIPF1 Gene

YIPF1 (Yip1 Domain Family Member 1) is a Protein Coding gene. Diseases associated with YIPF1 include De Quervain Disease and Synostoses, Tarsal, Carpal, And Digital. Gene Ontology (GO) annotations related to this gene include RNA binding and ribonuclease activity. An important paralog of this gene is YIPF2.

Gene Wiki entry for YIPF1 Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for YIPF1 Gene

Genomics for YIPF1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for YIPF1 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
GH01J053889 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 255.8 0.0 -3 2.4 SP1 ZNF207 MYC NCOR1 ZNF600 ZNF580 ZMYM3 POLR2A CHD4 ZBTB10 DIO1 YIPF1 HSALNG0003720 lnc-HSPB11-3 MAGOH SSBP3-AS1 ENSG00000279049 LRRC42 HSPB11 CYB5RL
GH01J053942 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 250.2 -55.6 -55612 5.6 SP1 ZNF207 MYC IKZF1 ZNF600 ZNF580 ZNF592 POLR2A ZNF223 ZNF10 HSPB11 LRRC42 lnc-YIPF1-2 YIPF1 SSBP3-AS1 MAGOH NDC1 CYB5RL PARS2 TTC4
GH01J053895 Promoter 0.7 Ensembl 255.6 -1.9 -1903 0.6 NCOR1 ZFP91 RAD51 HDAC2 MTA2 TRIM24 USF1 SMARCA4 YIPF1 DIO1 HSALNG0003720 lnc-HSPB11-3 lnc-HSPB11-1 LRRC42
GH01J053891 Enhancer 0.6 ENCODE 250.7 -1.4 -1405 0.2 NCOR1 TAL1 STAT5A HDAC2 ZEB2 TCF12 MTA2 TEAD4 DPF2 ARID1B DIO1 HSALNG0003720 YIPF1 lnc-HSPB11-3
GH01J053835 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 6.1 +52.7 52665 4.1 BCLAF1 SP1 ZNF207 ZNF600 MYC IKZF1 SIX5 ZNF580 ZNF592 KLF9 NDC1 lnc-YIPF1-1 MAGOH SSBP3-AS1 HSPB11 LRRC42 ECHDC2 ENSG00000256407 CYB5RL PODN
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around YIPF1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for YIPF1

Top Transcription factor binding sites by QIAGEN in the YIPF1 gene promoter:
  • AML1a
  • AREB6
  • E4BP4
  • GR
  • GR-alpha
  • GR-beta
  • Pax-5
  • Sp1

Genomic Locations for YIPF1 Gene

Latest Assembly
chr1:53,851,719-53,889,798
(GRCh38/hg38)
Size:
38,080 bases
Orientation:
Minus strand

Previous Assembly
chr1:54,317,406-54,355,470
(GRCh37/hg19 by Entrez Gene)
Size:
38,065 bases
Orientation:
Minus strand

chr1:54,317,392-54,356,407
(GRCh37/hg19 by Ensembl)
Size:
39,016 bases
Orientation:
Minus strand

Genomic View for YIPF1 Gene

Genes around YIPF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
YIPF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for YIPF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for YIPF1 Gene

Proteins for YIPF1 Gene

  • Protein details for YIPF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y548-YIPF1_HUMAN
    Recommended name:
    Protein YIPF1
    Protein Accession:
    Q9Y548
    Secondary Accessions:
    • B2RCM7
    • D3DQ40
    • Q9NWJ1

    Protein attributes for YIPF1 Gene

    Size:
    306 amino acids
    Molecular mass:
    34277 Da
    Quaternary structure:
    • Interacts with YIPF6; this interaction may stabilize YIPF1. May also form a ternary complex with YIPF2 and YIPF6.
    SequenceCaution:
    • Sequence=AAH09674.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};

    Alternative splice isoforms for YIPF1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for YIPF1 Gene

Post-translational modifications for YIPF1 Gene

  • Glycosylation at Asn297
  • Ubiquitination at Lys63 and Lys107
  • Modification sites at PhosphoSitePlus

Other Protein References for YIPF1 Gene

No data available for DME Specific Peptides for YIPF1 Gene

Domains & Families for YIPF1 Gene

Gene Families for YIPF1 Gene

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

Protein Domains for YIPF1 Gene

Suggested Antigen Peptide Sequences for YIPF1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ54858, highly similar to Protein YIPF1 (B7Z6F5_HUMAN)
  • YIP1 family member 1 (YIPF1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9Y548

UniProtKB/Swiss-Prot:

YIPF1_HUMAN :
  • Belongs to the YIP1 family.
Family:
  • Belongs to the YIP1 family.
genes like me logo Genes that share domains with YIPF1: view

Function for YIPF1 Gene

Phenotypes From GWAS Catalog for YIPF1 Gene

Gene Ontology (GO) - Molecular Function for YIPF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
GO:0017137 Rab GTPase binding IEA --
GO:0031267 small GTPase binding IBA --
genes like me logo Genes that share ontologies with YIPF1: view
genes like me logo Genes that share phenotypes with YIPF1: view

Animal Models for YIPF1 Gene

MGI Knock Outs for YIPF1:
  • Yipf1 Yipf1<tm1a(EUCOMM)Wtsi>

miRNA for YIPF1 Gene

miRTarBase miRNAs that target YIPF1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for YIPF1

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for YIPF1 Gene

Localization for YIPF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for YIPF1 Gene

Golgi apparatus, cis-Golgi network membrane. Multi-pass membrane protein. Golgi apparatus, trans-Golgi network membrane. Late endosome membrane. Note=Mainly localizes within medial-/trans-Golgi and trans-Golgi network (TGN), while less so within cis-Golgi. {ECO:0000269 PubMed:27999994, ECO:0000269 PubMed:28286305}.

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 YIPF1 gene
Compartment Confidence
golgi apparatus 5
plasma membrane 3
nucleus 3
endosome 3
extracellular 2
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 2
cytosol 2
lysosome 2
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (3)
  • Plasma membrane (2)
  • Nucleoplasm (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for YIPF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000138 Golgi trans cisterna IDA 28286305
GO:0005654 nucleoplasm IDA --
GO:0005768 endosome IEA --
GO:0005794 Golgi apparatus IBA,IDA --
GO:0005797 Golgi medial cisterna IDA 28286305
genes like me logo Genes that share ontologies with YIPF1: view

Pathways & Interactions for YIPF1 Gene

PathCards logo

SuperPathways for YIPF1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for YIPF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016192 vesicle-mediated transport IEA --
genes like me logo Genes that share ontologies with YIPF1: view

No data available for Pathways by source and SIGNOR curated interactions for YIPF1 Gene

Drugs & Compounds for YIPF1 Gene

No Compound Related Data Available

Transcripts for YIPF1 Gene

mRNA/cDNA for YIPF1 Gene

1 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for YIPF1

Alternative Splicing Database (ASD) splice patterns (SP) for YIPF1 Gene

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

Relevant External Links for YIPF1 Gene

GeneLoc Exon Structure for
YIPF1

Expression for YIPF1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for YIPF1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for YIPF1 Gene

This gene is overexpressed in Whole Blood (x6.8).

Protein differential expression in normal tissues from HIPED for YIPF1 Gene

This gene is overexpressed in Pancreas (47.4) and Placenta (21.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for YIPF1 Gene



Protein tissue co-expression partners for YIPF1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for YIPF1

SOURCE GeneReport for Unigene cluster for YIPF1 Gene:

Hs.11923

Evidence on tissue expression from TISSUES for YIPF1 Gene

  • Nervous system(4.6)
  • Lung(4.3)
  • Pancreas(4.3)
  • Muscle(3)
  • Liver(2.4)
  • Heart(2.3)
  • Blood(2.2)
  • Thyroid gland(2.2)
  • Skin(2.1)
  • Kidney(2.1)
genes like me logo Genes that share expression patterns with YIPF1: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for YIPF1 Gene

Orthologs for YIPF1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for YIPF1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia YIPF1 29 30
  • 99.78 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia YIPF1 29 30
  • 92.13 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia YIPF1 29
  • 90.96 (n)
Rat
(Rattus norvegicus)
Mammalia Yipf1 29
  • 84.2 (n)
Mouse
(Mus musculus)
Mammalia Yipf1 29 16 30
  • 83.77 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia YIPF1 30
  • 81 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia YIPF1 30
  • 80 (a)
OneToOne
Chicken
(Gallus gallus)
Aves YIPF1 29 30
  • 75.61 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia YIPF1 30
  • 78 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia yipf1 29
  • 67.01 (n)
Zebrafish
(Danio rerio)
Actinopterygii yipf1 29 30
  • 61.99 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG4645 29 30
  • 50.55 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006951 29
  • 48.19 (n)
Worm
(Caenorhabditis elegans)
Secernentea Y25C1A.7 29 30
  • 51.47 (n)
OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YIP5 32
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT5G27490 29
  • 47.59 (n)
Rice
(Oryza sativa)
Liliopsida Os01g0610500 29
  • 47.4 (n)
Bread mold
(Neurospora crassa)
Ascomycetes NCU05276 29
  • 44.74 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC227.06 29
  • 44.25 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 41 (a)
OneToMany
Species where no ortholog for YIPF1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • 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 Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for YIPF1 Gene

ENSEMBL:
Gene Tree for YIPF1 (if available)
TreeFam:
Gene Tree for YIPF1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for YIPF1: view image
Alliance of Genome Resources:
Additional Orthologs for YIPF1

Paralogs for YIPF1 Gene

Paralogs for YIPF1 Gene

(1) SIMAP similar genes for YIPF1 Gene using alignment to 4 proteins:

  • YIPF1_HUMAN
  • B7Z6F5_HUMAN
  • C9JFB2_HUMAN
  • L8ECI1_HUMAN
genes like me logo Genes that share paralogs with YIPF1: view

Variants for YIPF1 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for YIPF1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for YIPF1 Gene

Variant ID Type Subtype PubMed ID
esv27981 CNV loss 19812545
esv3586078 CNV loss 21293372
nsv1011262 CNV gain 25217958
nsv1113119 CNV deletion 24896259

Variation tolerance for YIPF1 Gene

Residual Variation Intolerance Score: 62.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.91; 83.80% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for YIPF1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
YIPF1
Leiden Open Variation Database (LOVD)
YIPF1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for YIPF1 Gene

Disorders for YIPF1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for YIPF1 Gene - From: COP

Disorder Aliases PubMed IDs
de quervain disease
  • radial styloid tenosynovitis
synostoses, tarsal, carpal, and digital
  • calcaneonavicular coalition
critical illness polyneuropathy
  • polyneuropathy, critical illness
- elite association - COSMIC cancer census association via MalaCards
Search YIPF1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for YIPF1

genes like me logo Genes that share disorders with YIPF1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for YIPF1 Gene

Publications for YIPF1 Gene

  1. YIPF1, YIPF2, and YIPF6 are medial-/trans-Golgi and trans-Golgi network-localized Yip domain family proteins, which play a role in the Golgi reassembly and glycan synthesis. (PMID: 28286305) Soonthornsit J … Nakamura N (Experimental cell research 2017) 2 3 4
  2. 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
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains. (PMID: 32814053) Haenig C … Wanker EE (Cell reports 2020) 3
  5. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3

Products for YIPF1 Gene

Sources for YIPF1 Gene