RetrogeneDB ID: | retro_mmus_3171 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 8:4812822..4813152(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000095600 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rpl22 | ||
| Ensembl ID: | ENSMUSG00000028936 | ||
| Aliases: | Rpl22, 2700038K18Rik | ||
| Description: | ribosomal protein L22 [Source:MGI Symbol;Acc:MGI:99262] |
Retrocopy-Parental alignment summary:
>retro_mmus_3171
GTTTTGAAGTTCACCCTCAACTGCACTCATGCTGTAGTAGATGGAATCATGGATGCTGCCAATTTTGAGCAGTTCCCCCA
GGAGAGAATCAAGGTGAACAGGAAAGCTGGCAATCTCGGAGGAGGAGTTGTGACCATTGAGCAGAGCAAGAGCAAGATCA
CTGTCACTTCTGAGGTGCCTTTCTCCAAAAGGTATTTGAAATATCTCACCAAAGAATATTTGAAGAAGAACAACCTCCGA
GACTGGCTGCGTGTTGTCGCCAACAGCAAAGAGAGTTACGAGCTGCGTTACTTCCAGACTAACCAGGATGAAGAGCAGGA
GGATGACGAA
ORF - retro_mmus_3171 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.91 % |
| Parental protein coverage: | 85.94 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | VLKFTLDCTHPVEDGIMDAANFEQFLQERIKVNGKAGNLGGGVVTIERSKSKITVTSEVPFSKRYLKYLT |
| VLKFTL.CTH.V.DGIMDAANFEQF.QERIKVN.KAGNLGGGVVTIE.SKSKITVTSEVPFSKRYLKYLT | |
| Retrocopy | VLKFTLNCTHAVVDGIMDAANFEQFPQERIKVNRKAGNLGGGVVTIEQSKSKITVTSEVPFSKRYLKYLT |
| Parental | KKYLKKNNLRDWLRVVANSKESYELRYFQINQDEEEEEDE |
| K.YLKKNNLRDWLRVVANSKESYELRYFQ.NQDEE.E.DE | |
| Retrocopy | KEYLKKNNLRDWLRVVANSKESYELRYFQTNQDEEQEDDE |
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 | 61 .84 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 58 .79 RPM |
| SRP007412_heart | 0 .03 RPM | 91 .62 RPM |
| SRP007412_kidney | 0 .02 RPM | 115 .17 RPM |
| SRP007412_liver | 0 .00 RPM | 87 .71 RPM |
| SRP007412_testis | 0 .00 RPM | 47 .84 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3171 was not detected
No EST(s) were mapped for retro_mmus_3171 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_142622 | 379 libraries | 480 libraries | 208 libraries | 5 libraries | 0 libraries |
The graphical summary, for retro_mmus_3171 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_3171 was not experimentally validated.