RetrogeneDB ID: | retro_mmus_1506 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 16:28950921..28951356(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
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_1506
ATGAAGTTCAATCCCTTCCTGACTTCTGACCGAAGCAAGAACTGCAAACGGCATTTCAACGCACCCTCTCACATTCGGAG
GAAGATCATTTCTTCCCCTCTTTCCAAAGAACTGAGACAGAAGTAGAACGTTCGGTCTATGCCCATTCGGAAGGATGATG
AAGTTCATGTTGTTCGCGGACACTACAAAGGCCAGCAGATTGGCAAGGTGGTCCAAGTGTACAGGAAGAAGTACGTCATC
TACATTGAACGTGTCCAGCGACAGAAGGCTAATGGCACAACCGTCCACGTGGGCATCCACCCCAGCAAGGTCGTTATCAC
CAGGCTAAAGCTGGACAAGGACCGCAAGAAGATCCTGGAGAGGAAAGCCAAGTCCTGACAAGTAGGAAAGGAGAAGGACA
AATACAAGGAAGAAACGATCGAGAAGATGCAGGAG
ORF - retro_mmus_1506 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.48 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MKFNPFVTSDRSKNRKRHFNAPSHIRRKIMSSPLSKELRQKYNVRSMPIRKDDEVQVVRGHYKGQQIGKV |
| MKFNPF.TSDRSKN.KRHFNAPSHIRRKI.SSPLSKELRQK.NVRSMPIRKDDEV.VVRGHYKGQQIGKV | |
| Retrocopy | MKFNPFLTSDRSKNCKRHFNAPSHIRRKIISSPLSKELRQK*NVRSMPIRKDDEVHVVRGHYKGQQIGKV |
| Parental | VQVYRKKYVIYIERVQREKANGTTVHVGIHPSKVVITRLKLDKDRKKILERKAKSRQVGKEKGKYKEETI |
| VQVYRKKYVIYIERVQR.KANGTTVHVGIHPSKVVITRLKLDKDRKKILERKAKS.QVGKEK.KYKEETI | |
| Retrocopy | VQVYRKKYVIYIERVQRQKANGTTVHVGIHPSKVVITRLKLDKDRKKILERKAKS*QVGKEKDKYKEETI |
| Parental | EKMQE |
| EKMQE | |
| Retrocopy | EKMQE |
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 .05 RPM | 82 .07 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 43 .77 RPM |
| SRP007412_heart | 0 .12 RPM | 61 .58 RPM |
| SRP007412_kidney | 0 .04 RPM | 56 .40 RPM |
| SRP007412_liver | 0 .03 RPM | 60 .43 RPM |
| SRP007412_testis | 0 .00 RPM | 61 .02 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1506 was not detected
No EST(s) were mapped for retro_mmus_1506 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_46244 | 544 libraries | 475 libraries | 52 libraries | 0 libraries | 1 library |
The graphical summary, for retro_mmus_1506 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_1506 was not experimentally validated.