RetrogeneDB ID: | retro_mmus_2697 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 5:129128079..129128517(-) | ||
| Located in intron of: | ENSMUSG00000044017 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000060419 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rps16 | ||
| Ensembl ID: | ENSMUSG00000037563 | ||
| Aliases: | Rps16, AA420385, AI317031 | ||
| Description: | ribosomal protein S16 [Source:MGI Symbol;Acc:MGI:98118] |
Retrocopy-Parental alignment summary:
>retro_mmus_2697
ATGCCGTCCAAGGGTCCGCTGCAGTCCGTGCAGGTCTTCGGACGCAAGAAAACAGCCACGGCTGTGGCCCACTGCAAACG
GGGAAATGGGCTCATCAAGGTGAACGGACGTCCCCTGGAGATGATCGAGCCGCGCACGCTGCAGTACAAGTTACTGGAGC
CTGTTTTGCTTCTGGGCAAGGAGCGATTTGCTGGTGTGGATATTCGGGTCCGTGTGAAGGGTGGTGGACATGTGGCCCAA
ATTTATGCCATCCGACAGTCCATCTCAAAGGCCCTGGTAGCTTATTACCAAAAATATGTGGATGAAGCCTCCAAGAAGGA
GATCAAAGATATCCTCATCCAATACGATCGGACCCTGCTTGTAGCTGACCCCCGTCGCTGCGAATCCAAAAAGTTTGGAG
GTCCTGGTGCCCGTGCCCGATACCAGAAATCCTACCGA
ORF - retro_mmus_2697 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 100.0 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MPSKGPLQSVQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEPVLLLGKERFAGVDIRV |
| MPSKGPLQSVQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEPVLLLGKERFAGVDIRV | |
| Retrocopy | MPSKGPLQSVQVFGRKKTATAVAHCKRGNGLIKVNGRPLEMIEPRTLQYKLLEPVLLLGKERFAGVDIRV |
| Parental | RVKGGGHVAQIYAIRQSISKALVAYYQKYVDEASKKEIKDILIQYDRTLLVADPRRCESKKFGGPGARAR |
| RVKGGGHVAQIYAIRQSISKALVAYYQKYVDEASKKEIKDILIQYDRTLLVADPRRCESKKFGGPGARAR | |
| Retrocopy | RVKGGGHVAQIYAIRQSISKALVAYYQKYVDEASKKEIKDILIQYDRTLLVADPRRCESKKFGGPGARAR |
| Parental | YQKSYR |
| YQKSYR | |
| Retrocopy | YQKSYR |
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 .30 RPM | 27 .17 RPM |
| SRP007412_cerebellum | 0 .09 RPM | 26 .83 RPM |
| SRP007412_heart | 0 .65 RPM | 63 .01 RPM |
| SRP007412_kidney | 0 .62 RPM | 70 .40 RPM |
| SRP007412_liver | 0 .85 RPM | 66 .99 RPM |
| SRP007412_testis | 0 .27 RPM | 33 .53 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2697 was not detected
No EST(s) were mapped for retro_mmus_2697 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_110178 | 54 libraries | 157 libraries | 687 libraries | 134 libraries | 40 libraries |
The graphical summary, for retro_mmus_2697 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_2697 was not experimentally validated.