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Aliases for YIPF1 Gene

Aliases for YIPF1 Gene

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

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. 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

Additional gene information for YIPF1 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for YIPF1 Gene

Genomics for YIPF1 Gene

GeneHancer (GH) Regulatory Elements for YIPF1 Gene

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
GH01J053942 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.2 -55.5 -55478 5.4 HDGF SMAD1 ARID4B SIN3A YBX1 FEZF1 ZNF2 YY1 POLR2B ZNF766 HSPB11 LRRC42 YIPF1 SSBP3-AS1 MAGOH ENSG00000228838 NDC1 ENSG00000226938 CYB5RL PARS2
GH01J053889 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 655.8 -0.2 -160 2 HDGF HNRNPUL1 PKNOX1 ARNT ARID4B SIN3A ZNF2 SLC30A9 POLR2B ZNF213 DIO1 YIPF1 GC01P053890 ENSG00000228838 MAGOH SSBP3-AS1 ENSG00000226938 LOC100652967 ENSG00000279049 LRRC42
GH01J053891 Enhancer 0.6 ENCODE 650.7 -1.4 -1369 0.2 MTA2 SOX6 TEAD4 TAL1 CBFA2T3 DPF2 ZEB2 EP300 TCF12 NCOR1 GC01P053890 YIPF1 DIO1
GH01J053835 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 6.1 +52.7 52702 4.1 MLX DMAP1 YBX1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 MEF2D NDC1 MAGOH SSBP3-AS1 HSPB11 LRRC42 ECHDC2 ENSG00000256407 CYB5RL C1orf123 ENSG00000279049
GH01J053981 Enhancer 1.1 Ensembl ENCODE 11.1 -92.8 -92775 1.6 ELF3 ARID4B DMAP1 ZNF48 RAD21 RARA YY1 EGR1 ZNF143 THAP11 TCEANC2 HSPB11 LRRC42 LDLRAD1 YIPF1 DIO1 TMEM59 HNRNPA3P12 GC01P054015
- 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 UCSC Golden Path with GeneCards custom track

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

Genomic Locations for YIPF1 Gene

Genomic Locations for YIPF1 Gene
chr1:53,849,790-53,889,834
(GRCh38/hg38)
Size:
40,045 bases
Orientation:
Minus strand
chr1:54,317,392-54,356,407
(GRCh37/hg19)
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=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for YIPF1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for YIPF1 Gene

Post-translational modifications for YIPF1 Gene

  • Ubiquitination at isoforms=1107 and isoforms=63
  • Glycosylation at isoforms=2297
  • 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

Protein Domains for YIPF1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for YIPF1 Gene

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 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>

Animal Model Products

CRISPR Products

miRNA for YIPF1 Gene

miRTarBase miRNAs that target YIPF1

Inhibitory RNA Products

  • 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
endosome 4
plasma membrane 3
nucleus 3
cytoskeleton 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
cytosol 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for YIPF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000138 Golgi trans cisterna IDA 28286305
GO:0005768 endosome IEA --
GO:0005794 Golgi apparatus IBA --
GO:0005797 Golgi medial cisterna IDA 28286305
GO:0005802 trans-Golgi network IDA 28286305
genes like me logo Genes that share ontologies with YIPF1: view

Pathways & Interactions for YIPF1 Gene

SuperPathways for YIPF1 Gene

No Data Available

Interacting Proteins for YIPF1 Gene

Gene Ontology (GO) - Biological Process for YIPF1 Gene

None

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

Unigene Clusters for YIPF1 Gene

Yip1 domain family, member 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • 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
ECgene alternative splicing isoforms for
YIPF1

Expression for YIPF1 Gene

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

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

NURSA nuclear receptor signaling pathways regulating expression of YIPF1 Gene:

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(4.2)
  • Pancreas(4.2)
  • Muscle(3)
  • Heart(2)
genes like me logo Genes that share expression patterns with YIPF1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , 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 34 33
  • 99.78 (n)
OneToOne
dog
(Canis familiaris)
Mammalia YIPF1 34 33
  • 92.13 (n)
OneToOne
cow
(Bos Taurus)
Mammalia YIPF1 33
  • 90.96 (n)
rat
(Rattus norvegicus)
Mammalia Yipf1 33
  • 84.2 (n)
mouse
(Mus musculus)
Mammalia Yipf1 16 34 33
  • 83.77 (n)
oppossum
(Monodelphis domestica)
Mammalia YIPF1 34
  • 81 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia YIPF1 34
  • 80 (a)
OneToOne
chicken
(Gallus gallus)
Aves YIPF1 34 33
  • 75.61 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia YIPF1 34
  • 78 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia yipf1 33
  • 67.01 (n)
zebrafish
(Danio rerio)
Actinopterygii yipf1 34 33
  • 61.99 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG4645 34 33
  • 50.55 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP006951 33
  • 48.19 (n)
worm
(Caenorhabditis elegans)
Secernentea Y25C1A.7 34 33
  • 51.47 (n)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YIP5 36
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G27490 33
  • 47.59 (n)
rice
(Oryza sativa)
Liliopsida Os01g0610500 33
  • 47.4 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU05276 33
  • 44.74 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC227.06 33
  • 44.25 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 41 (a)
OneToMany
Species where no ortholog for YIPF1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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

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

Sequence variations from dbSNP and Humsavar for YIPF1 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000125411 -- 53,862,952(-) C/T intron_variant
rs1000197616 -- 53,864,422(-) T/C intron_variant
rs1000198653 -- 53,879,023(-) A/G intron_variant
rs1000219304 -- 53,883,011(-) T/C intron_variant, non_coding_transcript_variant
rs1000246903 -- 53,863,271(-) A/G intron_variant

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for YIPF1 Gene

Disorders for YIPF1 Gene

Additional Disease Information for YIPF1

No disorders were found for YIPF1 Gene.

No data available for MalaCards , 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) 3 4 58
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  3. 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
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for YIPF1 Gene

Sources for YIPF1 Gene

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