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YIF1B Gene

protein-coding   GIFtS: 48
GCID: GC19M038794

Yip1 Interacting Factor Homolog B (S. Cerevisiae)

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Yip1 Interacting Factor Homolog B (S. Cerevisiae)1 2
YIP1-Interacting Factor Homolog B2 3
FinGER82
Protein YIF1B2

External Ids:    HGNC: 305111   Entrez Gene: 905222   Ensembl: ENSG000001676457   UniProtKB: Q5BJH73   

Export aliases for YIF1B gene to outside databases

Previous GC identifers: GC19M043488 GC19M035242


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for YIF1B Gene:
YIF1B (Yip1 interacting factor homolog B (S. cerevisiae)) is a protein-coding gene. An important paralog of this gene is YIF1A.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000019.9  NT_011109.17  NC_018930.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the YIF1B gene promoter:
         AhR   Arnt   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidYIF1B promoter sequence
   Search Chromatin IP Primers for YIF1B

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat YIF1B


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 19q13.2   Ensembl cytogenetic band:  19q13.2   HGNC cytogenetic band: 19q13.2

YIF1B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
YIF1B gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M038794:  view genomic region     (about GC identifiers)

Start:
38,794,200 bp from pter      End:
38,807,913 bp from pter
Size:
13,714 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: YIF1B_HUMAN, Q5BJH7 (See protein sequence)
Recommended Name: Protein YIF1B  
Size: 314 amino acids; 34435 Da
Secondary accessions: H7BXS8 Q5JPC2 Q8WY70 Q96C02 Q96IC4
Alternative splicing: 6 isoforms:  Q5BJH7-1   Q5BJH7-2   Q5BJH7-3   Q5BJH7-4   Q5BJH7-5   Q5BJH7-6   (Gene prediction based on EST data)

Explore the universe of human proteins at neXtProt for YIF1B: NX_Q5BJH7

Explore proteomics data for YIF1B at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys123
  • Modification sites at PhosphoSitePlus

  • See YIF1B Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (7 alternative transcripts): 
    NP_001034760.1  NP_001034761.1  NP_001034762.1  NP_001138933.1  NP_001138934.1  NP_001138935.1  NP_291035.1  

    ENSEMBL proteins: 
     ENSP00000466428   ENSP00000337411   ENSP00000375971   ENSP00000343435   ENSP00000467489  
     ENSP00000329559   ENSP00000465230   ENSP00000465446   ENSP00000468358   ENSP00000468463  
     ENSP00000465277  

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    antibodies-online antibodies for YIF1B (11 products) 

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR005578 Hrf1

    Graphical View of Domain Structure for InterPro Entry Q5BJH7

    ProtoNet protein and cluster: Q5BJH7

    UniProtKB/Swiss-Prot: YIF1B_HUMAN, Q5BJH7
    Similarity: Belongs to the YIF1 family


    Find genes that share domains with YIF1B           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for YIF1B
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    miRNA
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    miRTarBase miRNAs that target YIF1B:
    hsa-mir-103a-3p (MIRT027066), hsa-mir-92a-3p (MIRT049802), hsa-mir-16-5p (MIRT001396)

    Block miRNA regulation of human, mouse, rat YIF1B using miScript Target Protectors
    3 qRT-PCR Assays for microRNAs that regulate YIF1B:
    hsa-miR-3065-3p hsa-miR-143 hsa-miR-143*
    SwitchGear 3'UTR luciferase reporter plasmidYIF1B 3' UTR sequence
    Inhib. RNA
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    YIF1B_HUMAN, Q5BJH7: Membrane; Multi-pass membrane protein (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane3
    golgi apparatus1
    mitochondrion1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016020membrane ----
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with YIF1B           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for YIF1B
    Interactions:

        Search GeneGlobe Interaction Network for YIF1B

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for YIF1B (Q5BJH73 ENSP000003434354) via UniProtKB, MINT, STRING, and/or I2D (see all 65)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CAPN15O758083I2D: score=2 
    RGS16O154923I2D: score=2 
    UBE2E2Q96LR53I2D: score=2 
    YIPF5Q969M33I2D: score=2 
    DESI2Q9BSY93I2D: score=1 
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for YIF1B



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for YIF1B gene (9 alternative transcripts): 
    NM_001013617.1  NM_001031731.1  NM_001039671.2  NM_001039672.2  NM_001039673.2  NM_001145461.1  NM_001145462.1  NM_001145463.1  
    NM_033557.3  

    Unigene Cluster for YIF1B:

    Yip1 interacting factor homolog B (S. cerevisiae)
    Hs.280741  [show with all ESTs]
    Unigene Representative Sequence: NM_033557
    16 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000592694 ENST00000337679(uc002oia.2 uc002oib.3) ENST00000392124(uc002ohw.2)
    ENST00000586319 ENST00000339413(uc002ohy.2 uc002ohz.2) ENST00000592246
    ENST00000329420(uc002ohx.2 uc010xtx.1 uc010xty.1) ENST00000591784
    ENST00000589151 ENST00000591755 ENST00000589644 ENST00000588002 ENST00000585563
    ENST00000589247 ENST00000587361 ENST00000587039
    miRNA
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    3 qRT-PCR Assays for microRNAs that regulate YIF1B:
    hsa-miR-3065-3p hsa-miR-143 hsa-miR-143*
    SwitchGear 3'UTR luciferase reporter plasmidYIF1B 3' UTR sequence
    Inhib. RNA
    Products:
         
    OriGene RNAi products in human, mouse, rat for YIF1B
    Predesigned siRNA for gene silencing in human, mouse, rat YIF1B
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    GenScript: all cDNA clones in your preferred vector (see all 7): YIF1B (NM_001039672)
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    Primer
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    OriGene qPCR primer pairs and template standards for YIF1B
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      QuantiTect SYBR Green Assays in human, mouse, rat YIF1B
      QuantiFast Probe-based Assays in human, mouse, rat YIF1B

    Additional mRNA sequence: 

    AF258578.3 AK027130.1 AL833382.1 AY358965.1 BC007644.1 BC014974.1 BC025257.1 BC091477.1 

    Selected DOTS entries (see all 28):

    DT.310298  DT.100762081  DT.121483044  DT.97846838  DT.100755105  DT.100755106  DT.92424415  DT.100772849 
    DT.100755104  DT.121483028  DT.92431507  DT.121482967  DT.92431508  DT.100692309  DT.100713714  DT.75118830 
    DT.102831790  DT.86854239  DT.87016176  DT.92431504  DT.95190672  DT.121482970  DT.121483079  DT.75101399 

    Selected AceView cDNA sequences (see all 218):

    AI184105 BX092259 CR598537 BQ680270 BM695737 BU620538 AI810818 BM665108 
    BI963081 AW271667 CB961267 C02248 BF339777 CF457219 AW002546 BU615679 
    CR601973 BQ648279 BX354499 AI085552 AF258578 BC014974 AI380916 BM717386 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for YIF1B (see all 12)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11a · 11b
    SP1:              -     -     -     -     -     -     -                 -                                               -               
    SP2:                    -     -     -     -     -     -                 -                                               -               
    SP3:              -     -     -     -     -     -     -                 -                                                               
    SP4:                                      -     -     -                 -                                                               
    SP5:                                            -     -                 -                                                               


    ECgene alternative splicing isoforms for YIF1B

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    YIF1B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    YIF1B Expression
    About this image

    YIF1B Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    YIF1B Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.280741
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    In Situ
    Assay Products:
     

     
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for YIF1B gene from Selected species (see all 18)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Yif1b1 , 5 Yip1 interacting factor homolog B (S. cerevisiae)1, 5 87.67(n)1
    91(a)1
      7 (16.94 cM)5
    772541  NM_029887.31  NP_084163.21 
     292383295 
    lizard
    (Anolis carolinensis)
    Reptilia YIF1B6
    Yip1 interacting factor homolog B (S. cerevisiae)
    74(a)
    1 ↔ 1
    LGf(1868343-1873155)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.122812 Xenopus laevis transcribed sequence with weak similarity to protein refNP_065203.1 (H.sapiens) putative transmembrane protein; homolog of yeast Golgi membrane protein Yif1p (Yip1p-interacting factor) [Homo sapiens] less 74.87(n)    48041647 
    zebrafish
    (Danio rerio)
    Actinopterygii yif1b1 Yip1 interacting factor homolog B (S. cerevisiae) 69.86(n)
    72.95(a)
      492462  NM_001007334.1  NP_001007335.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG54841 CG5484 56.54(n)
    47.7(a)
      43217  NM_170284.1  NP_733163.1 
    worm
    (Caenorhabditis elegans)
    Secernentea yif-16
    Protein YIF-1, isoform b (yif-1) mRNA, complete cd...
    23(a)
    1 → many
    V(10049862-10054913) WBGene00010178
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes YIF1(YNL263C)4 Integral membrane protein required for the fusion of ER-derived COPII transport vesicles with the Golgi; interacts with Yip1p and Yos1p; localizes to the Golgi, the ER, and COPII vesicles; homolog of human YIPF3 less   --   14(147840-146896) 855458  NP_014136.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT3G595001 AT3G59500 46.41(n)
    35.44(a)
      825119  NM_115812.3  NP_191509.2 
    rice
    (Oryza sativa)
    Liliopsida Os04g01654001 Os04g0165400 46.78(n)
    32.51(a)
      4335045  NM_001058667.1  NP_001052132.1 


    ENSEMBL Gene Tree for YIF1B (if available)
    TreeFam Gene Tree for YIF1B (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for YIF1B gene
    YIF1A2  
    1 SIMAP similar gene for YIF1B using alignment to 6 protein entries:     YIF1B_HUMAN (see all proteins):
    YIF1A

    Find genes that share paralogs with YIF1B           About GenesLikeMe


    1 Pseudogenes.org Pseudogene for YIF1B
    PGOHUM00000259329


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for YIF1B (see all 287)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 19 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1826982981,2
    --35250244(+) ATCACC/TAGGTC 1 -- us2k10--------
    rs1487136851,2
    --35250331(+) GGTGCA/GTGCCT 1 -- us2k10--------
    rs1859624931,2
    --35250392(+) ACCGGA/GGAGGT 1 -- us2k10--------
    rs2022413921,2
    --38796159(+) GGGAAA/GGAGAG 7 -- int10--------
    rs72519141,2
    C,H--38796164(+) AGAGAG/AAGAGG 7 -- int1 trp36Minor allele frequency- A:0.00NS EA NA 414
    rs1167437511,2
    C,F--38796178(+) CAAGGG/AATTTA 7 -- int11Minor allele frequency- A:0.02WA 118
    rs770271921,2
    C,F--38796286(+) GCCTCA/GGGTTT 7 -- int11Minor allele frequency- G:0.03NA 120
    rs746197031,2
    C--38796383(+) GTTCCA/GTACTC 7 -- int15Minor allele frequency- G:0.16CSA WA NA EA 361
    rs1920234061,2
    --38796413(+) GGAGCC/GGGTGA 7 -- int10--------
    rs1123118401,2
    C--38796572(+) GGTGCG/ATTGGC 7 -- int14Minor allele frequency- A:0.11CSA WA NA EA 359

    HapMap Linkage Disequilibrium report for YIF1B (38794200 - 38807913 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for YIF1B:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv911658CNV Loss21882294
    nsv833822CNV Loss17160897

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for YIF1B gene, integrated from 10 sources (see all 18):
    (articles sorted by number of sources associating them with YIF1B)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2, 3 Clark H.F.... Gray A.M. (Genome Res. 2003)
    2. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (Cell 2012)
    3. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    4. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    5. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (amp 2011)
    6. Global identification of modular cullin-RING ligase substrates. (PubMed id 21963094)1 Emanuele M.J....Elledge S.J. (Cell 2011)
    7. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. (PubMed id 20068231)2 Olsen J.V....Mann M. (Sci. Signal. 2010)
    8. Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. (PubMed id 19690332)2 Mayya V.... Han D.K. (Sci. Signal. 2009)
    9. A quantitative atlas of mitotic phosphorylation. (PubMed id 18669648)2 Dephoure N.... Gygi S.P. (Proc. Natl. Acad. Sci. U.S.A. 2008)
    10. Quantitative analysis of global ubiquitination in HeLa cells by mass spectrometry. (PubMed id 18781797)1 Meierhofer D.... Kaiser P. (J. Proteome Res. 2008)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 90522 HGNC: 30511 AceView: LOC90522 Ensembl:ENSG00000167645 euGenes: HUgn90522
    ECgene: YIF1B H-InvDB: YIF1B

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for YIF1B Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for YIF1B gene:
    Search GeneIP for patents involving YIF1B

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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