Mus musculus complex locus EG668879andEif4e, encoding eukaryotic translation initiation factor 4E and predicted gene, EG668879.
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SUMMARY back to top
RefSeq annotates one representative transcript from 2 predicted genes that we see see as a single gene (NM included in AceView variant.b), but Mus musculus cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 6 spliced variants.

AceView synopsis, each blue text links to tables and details
Note that this locus merges 2 different NCBI genes, because some GenBank cDNA has significant sequence overlap or common intron boundaries with both gene models.
Expression: According to AceView, this gene is expressed at high level, 3.5 times the average gene in this release. The sequence of this gene is defined by 711 GenBank accessions, some from 8-cell stage embryo (seen 10 times), mammary (9), brain (8), eye (7), head (7), otocysts (7), upper head (7) and 70 other tissues.
Alternative mRNA variants and regulation: The gene contains 11 distinct gt-ag introns. Transcription produces 9 different mRNAs, 6 alternatively spliced variants and 3 unspliced forms. There are 4 probable alternative promotors and 7 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, presence or absence of 2 cassette exons, overlapping exons with different boundaries.
Function: There are 37 articles specifically referring to this gene in PubMed. Functionally, the gene has been proposed to participate in pathways (Insulin signaling pathway, mTOR signaling pathway) and processes (translation, translational initiation, regulation of translation). Proteins are expected to have molecular functions (protein binding, RNA binding, translation initiation factor activity) and to localize in cytoplasm.
Please see the Jackson Laboratory Mouse Genome Database/Informatics site MGI_95305, MGI_3649046 for in depth functional annotation of this gene.
Protein coding potential: 6 spliced and the unspliced mRNAs putatively encode good proteins, altogether 7 different isoforms (3 complete, 2 COOH complete, 2 partial), some containing Eukaryotic translation initiation factor 4E (eIF-4E) domain [Pfam]. The remaining 2 mRNA variants (2 unspliced) appear not to encode good proteins.
Isoform EG668879andEif4e.cSep07 is annotated using as Met a Kozak-compatible a..AAGg start, thereby gaining 81 amino acids N-terminal to the first AUG.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 3, links to other databases and other names
Map: This gene EG668879andEif4e maps on chromosome 3, at 3 G3-H1 according to Entrez Gene. In AceView, it covers 32.01 kb, from 138188890 to 138220899 (NCBI 37a, Aug 2007), on the direct strand.
Links to: manual annotations from MGI_95305, MGI_3649046, KEGG_04150, KEGG_04910, the SNP view, SNP view, gene overviews from Gene 668879, 13684, expression data from Gene 668879, 13684, molecular and other annotations from UCSC.
Other names: The gene is also known as EG668879andEif4e, If4e, eIF-4E, Eif4e-ps, MGC103177, Eif4e, EG668879 or LOC668879, LOC13684.
Closest AceView homologs in other species ?
The closest human gene, according to BlastP, is the AceView gene EIF4E (e=3 10-31).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene ife-3 (e=9 10-57), which may contain interesting functional annotation.
The closest A.thaliana genes, according to BlastP, are the AceView genes EIF4E (e=3 10-31), AT1G29550 (e=7 10-31), AT1G29590 (e=10-30), LSP1 (e=5 10-29), NCBP (e=10-27), which may contain interesting functional annotation
          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the HTML5/SVG version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Gene EG668879andEif4e 5' 3' encoded on plus strand of chromosome 3 from 138,188,890 to 138,220,899 a b [NM] c d e f-u h-u g i-u 1 2kb 0 130 bp exon 130 bp exon 19006 bp [gt-ag] intron 106 GenBank accessions 107 bp exon 1231 bp [gt-ag] intron 119 GenBank accessions 96 bp exon 2508 bp [gt-ag] intron 121 GenBank accessions 64 bp exon 566 bp [gt-ag] intron 119 GenBank accessions 114 bp exon 2575 bp [gt-ag] intron 116 GenBank accessions 140 bp exon 1668 bp [gt-ag] intron 97 GenBank accessions 170 bp exon 6 accessions, some from brain (seen once) embryonic limb, maxilla and mandible (once) 170 bp exon 116 bp exon 973 bp [gt-ag] intron 12 GenBank accessions 47 bp exon 47 bp exon 19006 bp [gt-ag] intron 106 GenBank accessions 107 bp exon 1231 bp [gt-ag] intron 119 GenBank accessions 96 bp exon 2508 bp [gt-ag] intron 121 GenBank accessions 64 bp exon 566 bp [gt-ag] intron 119 GenBank accessions 114 bp exon 2575 bp [gt-ag] intron 116 GenBank accessions 140 bp exon 1668 bp [gt-ag] intron 97 GenBank accessions 2541 bp exon 188 accessions, NM_007917 some from 8-cell stage embryo (seen 10 times) mammary (8), eye (7) otocysts (7), brain (6) Validated 3' end, 10 accessions Validated 3' end, 1 accession Validated 3' end, 17 accessions Validated 3' end, 3 accessions Validated 3' end, 4 accessions Validated 3' end, 6 accessions Validated 3' end, 1 accession 2541 bp exon 37 bp exon 6061 bp [gt-ag] intron 1 GenBank accession 136 bp exon 136 bp exon 12809 bp [gt-ag] intron 1 GenBank accession 107 bp exon 1231 bp [gt-ag] intron 119 GenBank accessions 96 bp exon 2508 bp [gt-ag] intron 121 GenBank accessions 64 bp exon 566 bp [gt-ag] intron 119 GenBank accessions 114 bp exon 2575 bp [gt-ag] intron 116 GenBank accessions 140 bp exon 1668 bp [gt-ag] intron 97 GenBank accessions 99 bp exon 1 accession from mammary from tumor gross tissue 99 bp exon 35 bp exon 35 bp exon 19006 bp [gt-ag] intron 106 GenBank accessions 107 bp exon 3835 bp [gt-ag] intron 6 GenBank accessions 64 bp exon 566 bp [gt-ag] intron 119 GenBank accessions 114 bp exon 2575 bp [gt-ag] intron 116 GenBank accessions 140 bp exon 1668 bp [gt-ag] intron 97 GenBank accessions 582 bp exon 6 accessions, some from kidney: TCDD (DMSO verhicle) treated 48hours IP injections (seen 2 times) blood (once), head (once) lung (once), macrophage (once) 582 bp exon 157 bp exon 157 bp exon 174 bp [gt-ag] intron 3 GenBank accessions 114 bp exon 2575 bp [gt-ag] intron 116 GenBank accessions 140 bp exon 1668 bp [gt-ag] intron 97 GenBank accessions 417 bp exon 3 accessions, some from heart: TCCD (DMSO vehicle) treated 48 hoursip injection (seen 3 times) 417 bp exon 1169 bp exon 15 accessions, some from placenta (seen 4 times) testis (3), kidney (2) brain (once), hematopoietic stem cells (once) 1169 bp exon 2088 bp exon 2088 bp exon 11 accessions, some from thymus (seen 4 times) spinal ganglion (3), upper head (2) head (once) 2088 bp exon 152 bp exon 152 bp exon 2575 bp [gt-ag] intron 116 GenBank accessions 134 bp exon 1 accession from muscle 134 bp exon 774 bp exon 774 bp exon 2 accessions, some from pancreas (seen 2 times) total pancreas (once) 774 bp exon Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
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Sequences: click on the numbers to get the DNA back to top


Click on the headers to reorder the lines
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR uORF Upstream sequence Transcription
unit
pre-mRNA		 Downstream sequence
aSep07 821 bp 254 aa   55 bp 762 bp 2kb 28375 bp 1kb
bSep07 3225 bp 217 aa 145 bp 2426 bp 651 bp 2kb possibly including promoter 31752 bp 1kb
cSep07 793 bp 207 aa 170 bp     2kb probably including promoter 28211 bp 1kb
dSep07 1042 bp 185 aa 17 bp 467 bp 555 bp 2kb probably including promoter 28692 bp 1kb
eSep07 828 bp 133 aa 124 bp 302 bp 399 bp 2kb possibly including promoter 5245 bp 1kb
fSep07-unspliced 1169 bp 133 aa   767 bp   2kb 1169 bp 1kb
gSep07 286 bp 77 aa 53 bp     2kb possibly including promoter 2861 bp 1kb
hSep07-unspliced 2088 bp 36 aa 1948 bp 29 bp   2kb 2088 bp 1kb
iSep07-unspliced 774 bp 36 aa 101 bp 562 bp   2kb 774 bp 1kb
Gene neighbors and Navigator on chromosome 3 G3-H1 back to top
G C R Rg9mtd2 C R P P Adh7 D C R P Adh1 D C R P Adh6a C R P R C G C R Adh4 C R P Adh5 D C R P EG668879andEif4e C R P C P R R Tspan5 C R P P D C R P Mttp R C R 4930579F01Rik R R C R Metap1 C EG545570 G R R G C C R P Rap1gds1 C 100kb 0 LOC100039528, 5 accessions muhako, 2 accessions Rg9mtd2, 247 accessions 9 variants gluskor, 2 accessions Adh7, 80 accessions, 4 variants Adh1, 587 accessions, 6 variants Adh6a, 21 accessions, 2 variants hihako, 3 accessions ADH_zinc_N.0, 12 accessions 2 variants LOC639769, 5 accessions 3 variants Adh4, 22 accessions, 4 variants Adh5, 564 accessions, 8 variants EG668879andEif4e, 233 accessions 9 variants sunarara, 75 accessions huhako, 9 accessions, 2 variants kenarara, 37 accessions Tspan5, 246 accessions 11 variants renirara, 10 accessions gopley, 1 accession fleyskor, 1 accession tinarara, 11 accessions glaskor, 1 accession glyskor, 1 accession garpley, 4 accessions tenarara, 2 accessions sanarara, 2 accessions glerskor, 1 accession glorskor, 1 accession gloyskor, 1 accession klaskor, 4 accessions kluskor, 3 accessions 2 variants kloskor, 5 accessions kleeskor, 1 accession klerskor, 1 accession senarara, 11 accessions sonarara, 1 accession kleyskor, 1 accession kinarara, 1 accession kloyskor, 1 accession plaskor, 1 accession pluskor, 1 accession ploskor, 1 accession pleeskor, 1 accession wanirara, 3 accessions rinirara, 1 accession pleyskor, 4 accessions plorskor, 1 accession yanirara, 2 accessions yunirara, 6 accessions 2 variants minirara, 5 accessions skarskor, 1 accession munirara, 1 accession skawskor, 3 accessions 2 variants skeeskor, 1 accession skeyskor, 3 accessions slaskor, 1 accession hinirara, 2 accessions slyskor, 2 accessions sloskor, 1 accession slarskor, 2 accessions sleeskor, 1 accession slerskor, 2 accessions hunirara, 1 accession henirara, 1 accession ninirara, 1 accession nenirara, 1 accession fleeskor, 1 accession EG329763, 4 accessions flerskor, 4 accessions tanarara, 1 accession tunarara, 1 accession florskor, 1 accession floyskor, 2 accessions tonarara, 1 accession gloskor, 2 accessions glarskor, 1 accession glawskor, 1 accession gleeskor, 1 accession gleyskor, 1 accession klyskor, 1 accession klarskor, 1 accession klawskor, 1 accession sinarara, 4 accessions 2 variants kanarara, 1 accession klorskor, 1 accession kunarara, 1 accession plyskor, 1 accession plarskor, 3 accessions konarara, 1 accession plawskor, 3 accessions plerskor, 1 accession runirara, 7 accessions ronirara, 1 accession ployskor, 1 accession yonirara, 1 accession manirara, 5 accessions skaskor, 1 accession skyskor, 1 accession skuskor, 2 accessions skoskor, 1 accession menirara, 1 accession skerskor, 1 accession skorskor, 1 accession skoyskor, 1 accession monirara, 1 accession hanirara, 1 accession sluskor, 1 accession slawskor, 1 accession slorskor, 1 accession sloyskor, 1 accession smaskor, 5 accessions 2 variants Transposase_22.378, 28 accessions smyskor, 1 accession honirara, 2 accessions smuskor, 1 accession nanirara, 2 accessions nunirara, 2 accessions smoskor, 1 accession nonirara, 6 accessions Mttp, 81 accessions, 3 variants mehako, 14 accessions 4930579F01Rik, 15 accessions 2 variants mohako, 10 accessions 4 variants hahako, 2 accessions Metap1, 250 accessions 10 variants EG545570, 3 accessions LOC668881, 1 accession hehako, 3 accessions ranirara, 1 accession LOC620771, 15 accessions Rap1gds1, 377 accessions 11 variants sleyskor, 3 accessions ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               37 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f-u, .g, .h-u, .i-u Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes C

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

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