RetrogeneDB ID: | retro_mmus_1978 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 2:142570507..142570943(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000081125 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rpl26 | ||
| Ensembl ID: | ENSMUSG00000060938 | ||
| Aliases: | Rpl26, SIG-20 | ||
| Description: | ribosomal protein L26 [Source:MGI Symbol;Acc:MGI:106022] |
Retrocopy-Parental alignment summary:
>retro_mmus_1978
ATGAAGTTCAATCCCTTTGTGACTTCTGACAGAAGCATGAAACACAAATGGCATTTCAATGCACCTTCTCACATACTAAG
GAAGATCATGTCTTCCCCTCTTTCCAAAGAGCTGAGACAGAAGTATAATGTTCAGTCTATGCCCACTCAAAAGGATGATG
AAGTTCAGGTTGTTCGAGGACACTACGAAGGCCAGCAGATTGGCAAGGTGGTCCAAGTGTACAGGAAAAAATATGTCATC
TACATCAAACAAGTCGAGCGAGAGAAGGCTAATGGCACAACTGTCCGAGTGGGCATCCACCCCAGCAAGGTGGTTATCAC
AAGGCTAAAGCTGGGAGGAGGACCGCAAGAAGATCCTAGAAAGAAAAGCCAAGTTCTGACAAGTAGGAAAGGAGAAGGGC
AAATACAAGGAAGAAACGATCGAGACGGTACAGGAG
ORF - retro_mmus_1978 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.3 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MKFNPFVTSDRSKNRKRHFNAPSHIRRKIMSSPLSKELRQKYNVRSMPIRKDDEVQVVRGHYKGQQIGKV |
| MKFNPFVTSDRS...K.HFNAPSHI.RKIMSSPLSKELRQKYNV.SMP..KDDEVQVVRGHY.GQQIGKV | |
| Retrocopy | MKFNPFVTSDRSMKHKWHFNAPSHILRKIMSSPLSKELRQKYNVQSMPTQKDDEVQVVRGHYEGQQIGKV |
| Parental | VQVYRKKYVIYIERVQREKANGTTVHVGIHPSKVVITRLKL-DKDRKKILERKAKSRQVGKEKGKYKEET |
| VQVYRKKYVIYI..V.REKANGTTV.VGIHPSKVVITRLKL...DRKKILERKAK..QVGKEKGKYKEET | |
| Retrocopy | VQVYRKKYVIYIKQVEREKANGTTVRVGIHPSKVVITRLKL>EEDRKKILERKAKF*QVGKEKGKYKEET |
| Parental | IEKMQE |
| IE..QE | |
| Retrocopy | IETVQE |
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 .00 RPM | 82 .07 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 43 .77 RPM |
| SRP007412_heart | 0 .00 RPM | 61 .58 RPM |
| SRP007412_kidney | 0 .00 RPM | 56 .40 RPM |
| SRP007412_liver | 0 .00 RPM | 60 .43 RPM |
| SRP007412_testis | 0 .00 RPM | 61 .02 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1978 was not detected
No EST(s) were mapped for retro_mmus_1978 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_80997 | 323 libraries | 518 libraries | 228 libraries | 3 libraries | 0 libraries |
The graphical summary, for retro_mmus_1978 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_1978 was not experimentally validated.