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YJEFN3 Gene

protein-coding   GIFtS: 32
GCID: GC19P019639

YjeF N-Terminal Domain Containing 3

  Search for YJEFN3
at  

(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): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
YjeF N-Terminal Domain Containing 31 2     yjeF_N32
hYjeF_N32 3     YjeF N-Terminal Domain-Containing Protein 32
Apolipoprotein A1 Binding Protein2     YjeF_N33
hYjeF_N3-19p13.112     

External Ids:    HGNC: 247851   Entrez Gene: 3748872   Ensembl: ENSG000002500677   UniProtKB: A6XGL03   
ORGUL members:         

Export aliases for YJEFN3 gene to outside databases

Previous GC identifers: GC19P019501 GC19P019627 GC19P019201


(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 YJEFN3 Gene:
YJEFN3 (YjeF N-terminal domain containing 3) is a protein-coding gene. An important paralog of this gene is APOA1BP.

UniProtKB/Swiss-Prot: YJEN3_HUMAN, A6XGL0
Function: May play a role in spermiogenesis and oogenesis




(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 YJEFN3 gene promoter:
         ER-alpha   CUTL1   PPAR-gamma1   E2F   CP2   E2F-1   STAT3   PPAR-gamma2   ATF6   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidYJEFN3 promoter sequence
   Search Chromatin IP Primers for YJEFN3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat YJEFN3


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

Entrez Gene cytogenetic band: 19p13.11   Ensembl cytogenetic band:  19p13.11   HGNC cytogenetic band: 19p13.11

YJEFN3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
YJEFN3 gene location

GeneLoc information about chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19P019639:  view genomic region     (about GC identifiers)

Start:
19,627,036 bp from pter      End:
19,648,393 bp from pter
Size:
21,358 bases      Orientation:
plus 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: YJEN3_HUMAN, A6XGL0 (See protein sequence)
Recommended Name: YjeF N-terminal domain-containing protein 3  
Size: 299 amino acids; 32585 Da
Sequence caution: Sequence=BC020948; Type=Frameshift; Positions=200;
Secondary accessions: A6XGK9 Q4G1C0
Alternative splicing: 2 isoforms:  A6XGL0-1   A6XGL0-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for YJEFN3: NX_A6XGL0

Explore proteomics data for YJEFN3 at MOPED


See YJEFN3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts): 
NP_001177257.1  NP_940939.2  

ENSEMBL proteins: 
 ENSP00000398520   ENSP00000426964   ENSP00000477181  

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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:
 IPR004443 YjeF_N_dom

Graphical View of Domain Structure for InterPro Entry A6XGL0

ProtoNet protein and cluster: A6XGL0

UniProtKB/Swiss-Prot: YJEN3_HUMAN, A6XGL0
Similarity: Contains 1 YjeF N-terminal domain


YJEFN3 for domains           About GeneDecksing


(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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: YJEN3_HUMAN, A6XGL0
Function: May play a role in spermiogenesis and oogenesis

Animal Models:

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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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(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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Interactions:

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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 Tocris compounds for YJEFN3 (YJEN3)



(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, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for YJEFN3 gene (2 alternative transcripts): 
NM_001190328.1  NM_198537.3  

4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000436027(uc010ecf.2) ENST00000458210(uc021uqv.1 uc002nmu.2)
ENST00000514277 ENST00000608404
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Selected AceView cDNA sequences (see all 469):

BI860094 BM797483 BM668365 CB530047 AK094976 BM850820 F27361 BM839920 
AI357370 BE908146 BQ026764 BU956921 BM699888 AI311010 C04751 BC009189 
BU508729 BE389629 BM790018 AI056888 CD678943 F30223 BM665656 F30399 

GeneLoc Exon Structure


(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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YJEFN3 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: CTAGTGCCGT
YJEFN3 Expression
About this image

YJEFN3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

YJEFN3 Protein Expression

UniProtKB/Swiss-Prot: YJEN3_HUMAN, A6XGL0
Tissue specificity: Expressed in theca cells in ovary and in Leydig cells in testis (at protein level). Also
expressed in brain and mammary gland

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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 animals and fungi.

Orthologs for YJEFN3 gene from Selected species (see all 13)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Yjefn35 YjeF N-terminal domain containing 3   --   8 (34.02 cM) 69887788 
chicken
(Gallus gallus)
Aves LOC1008578311 yjeF N-terminal domain-containing protein 3-like 74.87(n)
74.35(a)
  100857831  XM_003643399.2  XP_003643447.2 
lizard
(Anolis carolinensis)
Reptilia YJEFN36
YjeF N-terminal domain containing 3
66(a)
1 ↔ 1
GL344325.1(24535-28585)
tropical clawed frog
(Xenopus tropicalis)
Amphibia yjefn31 YjeF N-terminal domain containing 3 62.13(n)
64.91(a)
  100491448  XM_004911021.1  XP_004911078.1 
zebrafish
(Danio rerio)
Actinopterygii yjefn31 YjeF N-terminal domain containing 3 62.41(n)
63.44(a)
  557840  NM_001044843.1  NP_001038308.1 
fruit fly
(Drosophila melanogaster)
Insecta CG29746
--
39(a)
1 → many
X(9978947-9980204)
worm
(Caenorhabditis elegans)
Secernentea Y18D10A.36
Protein Y18D10A.3 (Y18D10A.3) mRNA, complete cds
26(a)
1 → many
I(12810169-12815641) WBGene00012476
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes --
NADHX epimerase; catalyzes isomerization of (R)- a...
35(a)
1 → many
XIV(263713-264453) YNL200C


ENSEMBL Gene Tree for YJEFN3 (if available)
TreeFam Gene Tree for YJEFN3 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for YJEFN3 gene
APOA1BP2  
2 SIMAP similar genes for YJEFN3 using alignment to 3 protein entries:     YJEN3_HUMAN (see all proteins):
NDUFA13    APOA1BP

YJEFN3 for paralogs           About GeneDecksing



(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 YJEFN3 (see all 165)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 19 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1847207021,2
C--19639553(+) TGGCAC/GGAAAG 2 -- us2k10--------
rs1171368571,2
C--19639828(+) GGAGAC/TGGGCA 2 -- int11Minor allele frequency- T:0.01NA 120
rs614188341,2
C--19639903(+) GGGTCC/TGGGGA 2 -- int12Minor allele frequency- T:0.04WA 120
rs104267321,2
C,F,H--19640054(+) AGCTGC/TGTTGC 2 -- int18Minor allele frequency- T:0.03NS NA WA 914
rs1461935381,2
C--19640134(+) CCGAAC/GCCCAA 2 -- int10--------
rs2009802081,2
C--19640201(+) TTGCCA/GACATG 3 N D mis1 int10--------
rs2013921311,2
--19640270(+) CCTGGA/GGAAGG 3 R G mis1 int10--------
rs2018048371,2
C--19640271(+) CTGGGA/GAAGGC 3 E G mis1 int10--------
rs1481618971,2
C--19640309(+) CAGGGA/CCTGTT 3 T P mis1 int10--------
rs2012104661,2
C--19640319(+) TTGCCA/GGAGGT 3 Q R mis1 int10--------

HapMap Linkage Disequilibrium report for YJEFN3 (19627036 - 19648393 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for YJEFN3:    About this table    
Variant IDTypeSubtypePubMed ID
nsv509723CNV Insertion20534489
dgv3789n71CNV Loss21882294
nsv911305CNV Loss21882294

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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 YJEFN3 gene integrated from 10 sources:
(articles sorted by number of sources associating them with YJEFN3)
    Utopia: connect your pdf to the dynamic
world of online information

  1. ApoA-I-binding protein (AI-BP) and its homologues hYjeF_N2 and hYjeF_N3 comprise the YjeF_N domain protein family in humans with a role in spermiogenesis and oogenesis. (PubMed id 17533573)1, 2, 3 Rudolph C.... Schmitz G. (Horm. Metab. Res. 2007)
  2. The DNA sequence and biology of human chromosome 19. (PubMed id 15057824)1, 2 Grimwood J.... Lucas S.M. (Nature 2004)
  3. 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)
  4. Genome-wide association analysis identifies 13 new risk loci for schizophrenia. (PubMed id 23974872)1 Ripke S....Sullivan P.F. (Nat. Genet. 2013)
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
  6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  7. (PubMed id )2 

(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: 374887 HGNC: 24785 AceView: GRIM19andFLJ44968 Ensembl:ENSG00000250067 euGenes: HUgn374887
ECgene: YJEFN3 H-InvDB: YJEFN3

(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 YJEFN3 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 YJEFN3 gene:
Search GeneIP for patents involving YJEFN3

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, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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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

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