RetrogeneDB ID: | retro_mmus_3462 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:61785380..61785779(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000050900 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Eif4e | ||
| Ensembl ID: | ENSMUSG00000028156 | ||
| Aliases: | Eif4e, EG668879, Eif4e-ps, If4e, eIF-4E | ||
| Description: | eukaryotic translation initiation factor 4E [Source:MGI Symbol;Acc:MGI:95305] |
Retrocopy-Parental alignment summary:
>retro_mmus_3462
ATGGCGACTGTGGAACCGGAAACCACCCCTACCACTAATCCCCCACCTGCAGAAGAGGAAAAAACAGAGTCTAATCAGGA
GGTTGCTAACCCAGAGCACTATATTAAACACCCTCTACAGAACAGGTGGGCACTCTGGTTTTTTAAAAATGATAAAAGCA
AAACTAGGCAAGCAAACCTTCGATTGATCTCTAAGTTTGATACTGTTGAAGACTTTTGGGCTCTATACAACCATATCCAG
TTGTCTAGTAATTTAATGCCTGGCTGTGACTACTCACTTTTAAAGGATGGTATTGAGCCTATGTGGGAAGATGAGAAAAA
CAAACGAGGAGGACGGTGGCTGATCACACTGAACAAGCAGCAGAGACGGAGTGACCTCGATCGCTTCTGGCTAGACACT
ORF - retro_mmus_3462 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.74 % |
| Parental protein coverage: | 61.29 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MATVEPETTPTTNPPPAEEEKTESNQEVANPEHYIKHPLQNRWALWFFKNDKSKTWQANLRLISKFDTVE |
| MATVEPETTPTTNPPPAEEEKTESNQEVANPEHYIKHPLQNRWALWFFKNDKSKT.QANLRLISKFDTVE | |
| Retrocopy | MATVEPETTPTTNPPPAEEEKTESNQEVANPEHYIKHPLQNRWALWFFKNDKSKTRQANLRLISKFDTVE |
| Parental | DFWALYNHIQLSSNLMPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLET |
| DFWALYNHIQLSSNLMPGCDYSL.KDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWL.T | |
| Retrocopy | DFWALYNHIQLSSNLMPGCDYSLLKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLDT |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP007412_brain | 0 .07 RPM | 55 .63 RPM |
| SRP007412_cerebellum | 0 .13 RPM | 43 .68 RPM |
| SRP007412_heart | 0 .19 RPM | 80 .47 RPM |
| SRP007412_kidney | 0 .12 RPM | 55 .05 RPM |
| SRP007412_liver | 0 .05 RPM | 25 .45 RPM |
| SRP007412_testis | 0 .14 RPM | 113 .80 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3462 was not detected
No EST(s) were mapped for retro_mmus_3462 retrocopy.
| TSS No. | TSS Name | TSS expression level (Expr) in TPM range: | ||||
|---|---|---|---|---|---|---|
| no expression | 0 < Expr ≤ 1 | 1 < Expr ≤ 5 | 5 < Expr ≤ 10 | Expr > 10 | ||
| TSS #1 | TSS_157515 | 60 libraries | 22 libraries | 263 libraries | 444 libraries | 283 libraries |
The graphical summary, for retro_mmus_3462 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)
retro_mmus_3462 was not experimentally validated.