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YIPF2 Gene

protein-coding   GIFtS: 42
GCID: GC19M011033

Yip1 Domain Family, Member 2

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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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This gene clusters with an RNA gene
Subcategory (RNA class): antisense

Quality score for the ORGUL clustered with this gene is 3

Aliases
Yip1 Domain Family, Member 21 2
YIP1 Family Member 22 3
FinGER22
Protein YIPF22

External Ids:    HGNC: 284761   Entrez Gene: 789922   Ensembl: ENSG000001307337   UniProtKB: Q9BWQ63   
ORGUL members:         

Export aliases for YIPF2 gene to outside databases

Previous GC identifers: GC19M010895 GC19M010611


(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 YIPF2 Gene:
YIPF2 (Yip1 domain family, member 2) is a protein-coding gene. An important paralog of this gene is YIPF1.


(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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Regulatory elements:
   Regulatory transcription factor binding sites in the YIPF2 gene promoter:
         NF-1   Elk-1   Pax-2   XBP-1   Pax-2a   c-Ets-1   Egr-4   PPAR-alpha   Ik-2   TGIF   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidYIPF2 promoter sequence
   Search Chromatin IP Primers for YIPF2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat YIPF2


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

Entrez Gene cytogenetic band: 19p13.2   Ensembl cytogenetic band:  19p13.2   HGNC cytogenetic band: 19p13.2

YIPF2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
YIPF2 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M011033:  view genomic region     (about GC identifiers)

Start:
11,033,444 bp from pter      End:
11,039,357 bp from pter
Size:
5,914 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, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: YIPF2_HUMAN, Q9BWQ6 (See protein sequence)
Recommended Name: Protein YIPF2  
Size: 316 amino acids; 35151 Da

Explore the universe of human proteins at neXtProt for YIPF2: NX_Q9BWQ6

Explore proteomics data for YIPF2 at MOPED


See YIPF2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_076934.1  
ENSEMBL proteins: 
 ENSP00000466055   ENSP00000253031   ENSP00000467829   ENSP00000467156   ENSP00000465257  
 ENSP00000467019   ENSP00000466408   ENSP00000465943   ENSP00000468436   ENSP00000464839  

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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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HGNC Gene Families:
YIPF: Yip1 domain family

1 InterPro protein domain:
 IPR006977 Yip1

Graphical View of Domain Structure for InterPro Entry Q9BWQ6

ProtoNet protein and cluster: Q9BWQ6

UniProtKB/Swiss-Prot: YIPF2_HUMAN, Q9BWQ6
Similarity: Belongs to the YIP1 family


Find genes that share domains with YIPF2           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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:
   genOway: Develop your customized and physiologically relevant rodent model for YIPF2

miRNA
Products:
    
miRTarBase miRNAs that target YIPF2:
hsa-mir-16-5p (MIRT051142), hsa-mir-34a-5p (MIRT025577), hsa-mir-340-5p (MIRT019579)

Block miRNA regulation of human, mouse, rat YIPF2 using miScript Target Protectors
Selected qRT-PCR Assays for microRNAs that regulate YIPF2 (see all 10):
hsa-miR-448 hsa-miR-34b* hsa-miR-4328 hsa-miR-324-3p hsa-miR-410 hsa-miR-153 hsa-miR-146a* hsa-miR-548t
SwitchGear 3'UTR luciferase reporter plasmidYIPF2 3' UTR sequence
Inhib. RNA
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GenScript: all cDNA clones in your preferred vector: YIPF2 (NM_024029)
Sino Biological Human cDNA Clone for YIPF2
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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat YIPF2

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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for YIPF2


(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
YIPF2_HUMAN, Q9BWQ6: Membrane; Multi-pass membrane protein (Potential)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
plasma membrane3
golgi apparatus1
mitochondrion1
nucleus1

Gene Ontology (GO): 3 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0016020membrane ----
GO:0016021integral component of membrane IEA--
GO:0030133transport vesicle IDA--

Find genes that share ontologies with YIPF2           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 YIPF2
Interactions:

    Search GeneGlobe Interaction Network for YIPF2

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

Selected Interacting proteins for YIPF2 (Q9BWQ63 ENSP000002530314) via UniProtKB, MINT, STRING, and/or I2D (see all 35)
InteractantInteraction Details
GeneCardExternal ID(s)
YIPF6Q96EC83, ENSP000004175734I2D: score=2 STRING: ENSP00000417573
FATE1Q969F03I2D: score=1 
ARFGAP1ENSP000003146154STRING: ENSP00000314615
YIPF5ENSP000002744964STRING: ENSP00000274496
YIPF7ENSP000004126964STRING: ENSP00000412696
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(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 YIPF2



(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 YIPF2 gene: 
NM_024029.3  

12 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000586748 ENST00000253031(uc002mqb.3 uc002mqc.3) ENST00000592646
ENST00000589971 ENST00000591872 ENST00000590329 ENST00000586575 ENST00000587943
ENST00000588347 ENST00000585858 ENST00000588962 ENST00000592505
miRNA
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Block miRNA regulation of human, mouse, rat YIPF2 using miScript Target Protectors
Selected qRT-PCR Assays for microRNAs that regulate YIPF2 (see all 10):
hsa-miR-448 hsa-miR-34b* hsa-miR-4328 hsa-miR-324-3p hsa-miR-410 hsa-miR-153 hsa-miR-146a* hsa-miR-548t
SwitchGear 3'UTR luciferase reporter plasmidYIPF2 3' UTR sequence
Inhib. RNA
Products:
     
OriGene RNAi products in human, mouse, rat for YIPF2
Predesigned siRNA for gene silencing in human, mouse, rat YIPF2
Clone
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OriGene clones in human, mouse for YIPF2 (see all 7)
OriGene ORF clones in mouse, rat for YIPF2
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GenScript: all cDNA clones in your preferred vector: YIPF2 (NM_024029)
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Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat YIPF2
Primer
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OriGene qPCR primer pairs and template standards for YIPF2
OriGene qSTAR qPCR primer pairs in human, mouse for YIPF2
Pre-validated RT2 qPCR Primer Assay in human, mouse, rat YIPF2
  QuantiTect SYBR Green Assays in human, mouse, rat YIPF2
  QuantiFast Probe-based Assays in human, mouse, rat YIPF2

Selected AceView cDNA sequences (see all 245):

AI243064 BU753892 BX387531 BC000056 BU552626 BQ676152 AI380798 BM563834 
BQ877701 BU860060 BI829175 BU944073 BM554546 BX641860 BM975967 BC013014 
AI659144 BM906269 BM718992 BX332273 AI420432 BG762911 BU625482 BE387991 

GeneLoc Exon Structure

5 Alternative Splicing Database (ASD) splice patterns (SP) for YIPF2    About this scheme

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


ECgene alternative splicing isoforms for YIPF2

(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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YIPF2 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GGCTGTAAGT
YIPF2 Expression
About this image

YIPF2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

YIPF2 Protein Expression
    Custom PCR Arrays for YIPF2
Primer
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QuantiFast Probe-based Assays in human, mouse, rat YIPF2
In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for YIPF2

(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 YIPF2 gene from Selected species (see all 16)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Yipf21 , 5 Yip1 domain family, member 21, 5 79.76(n)1
82.47(a)1
  9 (7.83 cM)5
747661  NM_001205158.11  NP_001192087.11 
 215887095 
lizard
(Anolis carolinensis)
Reptilia YIPF26
Yip1 domain family, member 2
56(a)
1 ↔ 1
2(80878265-80894452)
African clawed frog
(Xenopus laevis)
Amphibia BU910210.12   -- 76.06(n)    BU910210.1 
zebrafish
(Danio rerio)
Actinopterygii yipf21 Yip1 domain family, member 2 55.78(n)
51.85(a)
  445106  NM_001003500.1  NP_001003500.1 
fruit fly
(Drosophila melanogaster)
Insecta CG46456
--
26(a)
1 → many
X(12803986-12805948)
worm
(Caenorhabditis elegans)
Secernentea Y25C1A.76
Protein Y25C1A.7, isoform b (Y25C1A.7) mRNA, compl...
23(a)
1 → many
II(3062540-3071381) WBGene00021294
soybean
(Glycine max)
eudicotyledons Gma.7392 Transcribed sequence with moderate similarity to protein more 71.08(n)  


ENSEMBL Gene Tree for YIPF2 (if available)
TreeFam Gene Tree for YIPF2 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for YIPF2 gene
YIPF12  
1 SIMAP similar gene for YIPF2 using alignment to 9 protein entries:     YIPF2_HUMAN (see all proteins):
YIPF1

Find genes that share paralogs with YIPF2           About GenesLikeMe



(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 YIPF2 (see all 256)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 19 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1906175901,2
C--10969773(+) GCCCCA/GCCGAG 1 -- int10--------
rs129728751,2
C--10969776(+) CCGCCA/GAGGCT 1 -- int10--------
rs1829046361,2
--10969917(+) CCCCCA/GCCCCC 1 -- int10--------
rs1995723331,2
C--10969935(+) AGAGT-/AGAGCA 1 -- int10--------
rs1878762581,2
--10970221(+) GCAGCA/GCAGGC 1 -- ut310--------
rs1918749891,2
--10970296(+) CCGCCA/GTGTGT 1 -- ut310--------
rs1829807301,2
C--10970453(+) CCCTCG/TCCCGC 1 -- ut310--------
rs1876562031,2
--10970457(+) CGCCCA/GCCTTT 1 -- ut310--------
rs1925174271,2
--10970526(+) AGTCTA/GGAAAG 1 -- ut310--------
rs1853887121,2
--10970669(+) CTTGAC/GTGGGA 1 -- int10--------

HapMap Linkage Disequilibrium report for YIPF2 (11033444 - 11039357 bp)

Structural Variations
     Database of Genomic Variants (DGV) 4 variations for YIPF2:    About this table    
Variant IDTypeSubtypePubMed ID
nsv911050CNV Loss21882294
nsv911051CNV Loss21882294
nsv833749CNV Loss17160897
nsv833748CNV Loss17160897

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing YIPF2
DNA2.0 Custom Variant and Variant Library Synthesis for YIPF2

(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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2 diseases from the University of Copenhagen DISEASES database for YIPF2:
Denys-Drash syndrome     Nephroblastoma

Find genes that share disorders with YIPF2           About GenesLikeMe


Export disorders for YIPF2 gene to outside databases

(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 YIPF2 gene integrated from 10 sources:
(articles sorted by number of sources associating them with YIPF2)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  3. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
  4. N-terminal acetylome analyses and functional insights of the N- terminal acetyltransferase NatB. (PubMed id 22814378)2 Van Damme P....Aldabe R. (Proc. Natl. Acad. Sci. U.S.A. 2012)
  5. Ubiquitin-mediated proteolysis of HuR by heat shock. (PubMed id 19322201)1 Abdelmohsen K....Gorospe M. (EMBO J. 2009)
  6. The LIFEdb database in 2006. (PubMed id 16381901)1 Mehrle A....Wiemann S. (Nucleic Acids Res. 2006)
  7. Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)1 Rual J.F....Vidal M. (Nature 2005)
  8. From ORFeome to biology: a functional genomics pipeline. (PubMed id 15489336)1 Wiemann S....Poustka A. (Genome Res. 2004)
  9. Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. (PubMed id 11256614)1 Simpson J.C.... Wiemann S. (EMBO Rep. 2000)
  10. DNA cloning using in vitro site-specific recombination. (PubMed id 11076863)1 Hartley J.L....Brasch M.A. (Genome Res. 2000)

(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: 78992 HGNC: 28476 AceView: MGC3262 Ensembl:ENSG00000130733 euGenes: HUgn78992
ECgene: YIPF2 H-InvDB: YIPF2

(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 YIPF2 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 YIPF2 gene:
Search GeneIP for patents involving YIPF2

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



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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