Aliases for YIPF5 Gene

Aliases for YIPF5 Gene

  • Yip1 Domain Family Member 5 2 3 5
  • SMAP-5 2 3 4
  • Five-Pass Transmembrane Protein Localizing In The Golgi Apparatus And The Endoplasmic Reticulum 5 3 4
  • YPT-Interacting Protein 1 A 3 4
  • YIP1 Family Member 5 3 4
  • Protein YIPF5 3 4
  • FinGER5 2 3
  • YIP1A 3 4
  • Smooth Muscle Cell Associated Protein 5 3
  • Smooth Muscle Cell-Associated Protein 5 4
  • Yip1 Domain Family, Member 5 2
  • Golgi Membrane Protein SB140 3
  • FINGER5 4
  • SB140 3
  • SMAP5 3
  • YIPF5 5

External Ids for YIPF5 Gene

Previous GeneCards Identifiers for YIPF5 Gene

  • GC05M143520
  • GC05M138685

Summaries for YIPF5 Gene

GeneCards Summary for YIPF5 Gene

YIPF5 (Yip1 Domain Family Member 5) is a Protein Coding gene. Diseases associated with YIPF5 include Ulnar Neuropathy and 3-Methylglutaconic Aciduria, Type Vii. An important paralog of this gene is YIPF7.

UniProtKB/Swiss-Prot Summary for YIPF5 Gene

Gene Wiki entry for YIPF5 Gene

Additional gene information for YIPF5 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for YIPF5 Gene

Genomics for YIPF5 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for YIPF5 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
GH05J144169 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 642.2 +0.5 513 2.8 CREB1 PRDM10 ZNF629 ZNF512 RFX1 POLR2A GABPA ZNF143 RBFOX2 NR2C1 YIPF5 KCTD16 lnc-NR3C1-2 RN7SL87P lnc-KCTD16-2 RF00017-4981 HMHB1
GH05J144187 Enhancer 1.4 FANTOM5 ENCODE dbSUPER 28.2 -19.6 -19647 6.1 SP1 CREB1 CTCF PRDM10 ZNF629 FOXA1 GABPA ZNF143 RELA RAD21 YIPF5 KCTD16 piR-37895-137
GH05J143241 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 19.8 +926.4 926413 6.2 CREB1 YBX1 PRDM10 ZNF629 LEF1 IKZF1 ZNF692 ZNF174 ZHX2 JUND lnc-NR3C1-3 YIPF5 RPL7P21 ENSG00000261757 NR3C1 ARHGAP26 lnc-ARHGAP26-5
GH05J144198 Enhancer 0.8 FANTOM5 Ensembl 36.5 -28.0 -27987 1.4 POLR2A REST SCRT2 SP1 FOSL2 ZNF189 MAFK KLF17 PRDM6 TRIM28 YIPF5 KCTD16 piR-37895-137
GH05J143394 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 10 +770.4 770413 12.6 HNRNPL GATAD2A PRDM10 REST ZNF629 TFE3 SIX5 KDM1A CTCF ZNF692 NR3C1 KU921432 RPL7P21 YIPF5 U01351 lnc-ARHGAP26-9 ARHGAP26
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around YIPF5 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for YIPF5

Top Transcription factor binding sites by QIAGEN in the YIPF5 gene promoter:
  • AML1a
  • FOXO3a
  • FOXO3b
  • GATA-1
  • GR
  • GR-alpha
  • GR-beta
  • Nkx2-5
  • RP58
  • SRY

Genomic Locations for YIPF5 Gene

Genomic Locations for YIPF5 Gene
chr5:144,158,162-144,170,714
(GRCh38/hg38)
Size:
12,553 bases
Orientation:
Minus strand
chr5:143,537,723-143,550,278
(GRCh37/hg19)
Size:
12,556 bases
Orientation:
Minus strand

Genomic View for YIPF5 Gene

Genes around YIPF5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
YIPF5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for YIPF5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for YIPF5 Gene

Proteins for YIPF5 Gene

  • Protein details for YIPF5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q969M3-YIPF5_HUMAN
    Recommended name:
    Protein YIPF5
    Protein Accession:
    Q969M3
    Secondary Accessions:
    • D3DQF5
    • Q4VSN6
    • Q53EX4
    • Q8NHE5
    • Q9H338
    • Q9H3U4

    Protein attributes for YIPF5 Gene

    Size:
    257 amino acids
    Molecular mass:
    27989 Da
    Quaternary structure:
    • Interacts with the COPII coat components Sec23 (SEC23A and/or SEC23B) and Sec24 (SEC24A and/or SEC24B) (PubMed:11489904). Interacts with YIF1A (PubMed:15990086). May interact with RAB1A (PubMed:15611160). Interacts with YIPF3 and YIPF4 (PubMed:27999994).

    Alternative splice isoforms for YIPF5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for YIPF5 Gene

Post-translational modifications for YIPF5 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for YIPF5 Gene

No data available for DME Specific Peptides for YIPF5 Gene

Domains & Families for YIPF5 Gene

Gene Families for YIPF5 Gene

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

Protein Domains for YIPF5 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for YIPF5 Gene

GenScript: Design optimal peptide antigens:
  • YPT-interacting protein 1 A (YIPF5_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q969M3

UniProtKB/Swiss-Prot:

YIPF5_HUMAN :
  • Belongs to the YIP1 family.
Family:
  • Belongs to the YIP1 family.
genes like me logo Genes that share domains with YIPF5: view

Function for YIPF5 Gene

Molecular function for YIPF5 Gene

UniProtKB/Swiss-Prot Function:
Plays a role in transport between endoplasmic reticulum and Golgi.
UniProtKB/Swiss-Prot Induction:
By TGFB1.

Phenotypes From GWAS Catalog for YIPF5 Gene

Gene Ontology (GO) - Molecular Function for YIPF5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 23736259
genes like me logo Genes that share ontologies with YIPF5: view
genes like me logo Genes that share phenotypes with YIPF5: view

Animal Models for YIPF5 Gene

MGI Knock Outs for YIPF5:
  • Yipf5 Yipf5<tm1b(EUCOMM)Hmgu>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for YIPF5

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for YIPF5 Gene

Localization for YIPF5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for YIPF5 Gene

Endoplasmic reticulum membrane. Multi-pass membrane protein. Golgi apparatus, cis-Golgi network membrane. Multi-pass membrane protein. Cytoplasmic vesicle, COPII-coated vesicle. Note=Enriched at the endoplasmic reticulum exit sites. Colocalizes with RAB1A. Incorporated into COPII-coated vesicles.

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 YIPF5 gene
Compartment Confidence
nucleus 4
endoplasmic reticulum 4
golgi apparatus 4
plasma membrane 3
extracellular 1
cytoskeleton 1
mitochondrion 1
endosome 1
cytosol 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endoplasmic reticulum (3)
  • Golgi apparatus (3)
  • Vesicles (3)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for YIPF5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0005783 endoplasmic reticulum IEA,IDA --
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0005794 Golgi apparatus IEA,IDA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with YIPF5: view

Pathways & Interactions for YIPF5 Gene

PathCards logo

SuperPathways for YIPF5 Gene

No Data Available

Gene Ontology (GO) - Biological Process for YIPF5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015031 protein transport IEA --
GO:0016192 vesicle-mediated transport IEA --
GO:0060628 regulation of ER to Golgi vesicle-mediated transport IEA --
genes like me logo Genes that share ontologies with YIPF5: view

No data available for Pathways by source and SIGNOR curated interactions for YIPF5 Gene

Drugs & Compounds for YIPF5 Gene

No Compound Related Data Available

Transcripts for YIPF5 Gene

mRNA/cDNA for YIPF5 Gene

3 REFSEQ mRNAs :
22 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for YIPF5

Alternative Splicing Database (ASD) splice patterns (SP) for YIPF5 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b · 5c ^ 6a · 6b ^ 7a · 7b · 7c
SP1: - -
SP2: - - - -
SP3: - - - -
SP4: - -
SP5: -
SP6:

Relevant External Links for YIPF5 Gene

GeneLoc Exon Structure for
YIPF5

Expression for YIPF5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for YIPF5 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for YIPF5 Gene

This gene is overexpressed in Bone (15.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for YIPF5 Gene



Protein tissue co-expression partners for YIPF5 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for YIPF5

SOURCE GeneReport for Unigene cluster for YIPF5 Gene:

Hs.372050

mRNA Expression by UniProt/SwissProt for YIPF5 Gene:

Q969M3-YIPF5_HUMAN
Tissue specificity: Ubiquitously expressed. Highly expressed in coronary smooth muscles.

Evidence on tissue expression from TISSUES for YIPF5 Gene

  • Liver(4.5)
  • Kidney(4.3)
  • Heart(4.3)
  • Eye(4.3)
  • Nervous system(4.2)
  • Muscle(2)
genes like me logo Genes that share expression patterns with YIPF5: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for YIPF5 Gene

Orthologs for YIPF5 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for YIPF5 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia YIPF5 30 31
  • 99.87 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia YIPF5 30 31
  • 94.94 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia YIPF5 30 31
  • 93.77 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia YIPF5 31
  • 93 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia YIPF5 31
  • 91 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Yipf5 30 17 31
  • 88.85 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Yipf5 30
  • 88.59 (n)
Chicken
(Gallus gallus)
Aves YIPF5 30 31
  • 81.63 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia YIPF5 31
  • 88 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia yipf5 30
  • 75.65 (n)
Str.6252 30
African clawed frog
(Xenopus laevis)
Amphibia smap-5-prov 30
Zebrafish
(Danio rerio)
Actinopterygii yipf5 30 31
  • 73.18 (n)
OneToOne
zgc56513 30
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2330 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG12404 30 31
  • 51.27 (n)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea F32D8.14 30 31
  • 53.87 (n)
OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YIP1 30 31 33
  • 48.84 (n)
OneToMany
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F15015g 30
  • 48.72 (n)
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_AAL135C 30
  • 47.76 (n)
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT2G36300 30
  • 47.53 (n)
Rice
(Oryza sativa)
Liliopsida Os03g0289200 30
  • 45.1 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPCC61.04c 30
  • 51.21 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.977 31
  • 51 (a)
OneToMany
Bread mold
(Neurospora crassa)
Ascomycetes NCU05514 30
  • 47.46 (n)
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.3073 30
Species where no ortholog for YIPF5 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • 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 YIPF5 Gene

ENSEMBL:
Gene Tree for YIPF5 (if available)
TreeFam:
Gene Tree for YIPF5 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for YIPF5: view image

Paralogs for YIPF5 Gene

Paralogs for YIPF5 Gene

(1) SIMAP similar genes for YIPF5 Gene using alignment to 3 proteins:

  • YIPF5_HUMAN
  • E5RGR9_HUMAN
  • E5RHH4_HUMAN
genes like me logo Genes that share paralogs with YIPF5: view

Variants for YIPF5 Gene

Additional dbSNP identifiers (rs#s) for YIPF5 Gene

Structural Variations from Database of Genomic Variants (DGV) for YIPF5 Gene

Variant ID Type Subtype PubMed ID
nsv1128196 CNV deletion 24896259

Variation tolerance for YIPF5 Gene

Residual Variation Intolerance Score: 66.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.48; 28.88% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for YIPF5 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
YIPF5

SNP Genotyping and Copy Number Assay Products

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 YIPF5 Gene

Disorders for YIPF5 Gene

MalaCards: The human disease database

(3) MalaCards diseases for YIPF5 Gene - From: DISEASES

- elite association - COSMIC cancer census association via MalaCards
Search YIPF5 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for YIPF5

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with YIPF5: view

No data available for UniProtKB/Swiss-Prot and Genatlas for YIPF5 Gene

Publications for YIPF5 Gene

  1. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 2 3 4
  2. Functional characterisation of the YIPF protein family in mammalian cells. (PMID: 27999994) Kranjc T … Simpson JC (Histochemistry and cell biology 2017) 3 4
  3. Fine mapping of the CELIAC2 locus on chromosome 5q31-q33 in the Finnish and Hungarian populations. (PMID: 19845895) Koskinen LL … Saavalainen P (Tissue antigens 2009) 3 41
  4. YIPF5 and YIF1A recycle between the ER and the Golgi apparatus and are involved in the maintenance of the Golgi structure. (PMID: 18718466) Yoshida Y … Nakamura N (Experimental cell research 2008) 2 3
  5. Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. (PMID: 15592455) Rush J … Comb MJ (Nature biotechnology 2005) 3 4

Products for YIPF5 Gene

Sources for YIPF5 Gene