RetrogeneDB ID: | retro_mmus_162 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 6:117213655..117214048(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000090549 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rpl28 | ||
| Ensembl ID: | ENSMUSG00000030432 | ||
| Aliases: | Rpl28, D7Wsu21e | ||
| Description: | ribosomal protein L28 [Source:MGI Symbol;Acc:MGI:101839] |
Retrocopy-Parental alignment summary:
>retro_mmus_162
TGGATGGTCGTTCAGAACTGCTTCAGTTTCTTGATTAAGAGGAAAAAGCAGACCTACATCACAGAACCAAATAATCTGAA
GGCCCGAAACTCCTTCAGTTACAACAGGCAAATTCACCGCAAGACTGTCAGAGTGCAGCCCGAGACCGATGGCAAAGGGG
TTGTGGTAGTTACGAAACGCAGATACGATCAGCAGAAACCTGCCAATTCTTACGTGAGGACCACCATCAACAAGAATGGT
CTGGCTACTCTCAGCAGCATCAGGCACATGATCCGAAAGAACAAGTATCGCCCTGATCTACGTATGGAGGCCATCCTCAG
GGCCAGTGCCATCCTTCAAAGCCAGAAGCCTGTGGTGGTACCCGCCCCACCAAGAGCTCCTGAGCCCCATACC
ORF - retro_mmus_162 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.5 % |
| Parental protein coverage: | 87.59 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | WMVVRNCSSFLIKRNKQTYSTEPNNLKARNSFRYNGLIHRKTVGVEPAADGKGVVVVMKRRSGQRKPATS |
| WMVV.NC.SFLIKR.KQTY.TEPNNLKARNSF.YN..IHRKTV.V.P..DGKGVVVV.KRR..Q.KPA.S | |
| Retrocopy | WMVVQNCFSFLIKRKKQTYITEPNNLKARNSFSYNRQIHRKTVRVQPETDGKGVVVVTKRRYDQQKPANS |
| Parental | YVRTTINKNARATLSSIRHMIRKNKYRPDLRMAAIRRASAILRSQKPVVV |
| YVRTTINKN..ATLSSIRHMIRKNKYRPDLRM.AI.RASAIL.SQKPVVV | |
| Retrocopy | YVRTTINKNGLATLSSIRHMIRKNKYRPDLRMEAILRASAILQSQKPVVV |
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 | 32 .57 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 34 .13 RPM |
| SRP007412_heart | 0 .00 RPM | 95 .91 RPM |
| SRP007412_kidney | 0 .02 RPM | 78 .85 RPM |
| SRP007412_liver | 0 .00 RPM | 81 .84 RPM |
| SRP007412_testis | 0 .00 RPM | 58 .32 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_162 was not detected
No EST(s) were mapped for retro_mmus_162 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_117615 | 354 libraries | 555 libraries | 161 libraries | 2 libraries | 0 libraries |
The graphical summary, for retro_mmus_162 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_162 was not experimentally validated.