RetrogeneDB ID: | retro_mmus_1500 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 16:20822145..20822640(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000063427 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rps10 | ||
| Ensembl ID: | ENSMUSG00000052146 | ||
| Aliases: | Rps10, 2210402A09Rik | ||
| Description: | ribosomal protein S10 [Source:MGI Symbol;Acc:MGI:1914347] |
Retrocopy-Parental alignment summary:
>retro_mmus_1500
ATGTTGATGCCTAAGAAGAATCGGATTGCCATCTACGAACTCCTTTTTAAGGAGGGCGTGATGGTCGCCAAAAAGGATGT
CCACATGCCTAAGCACCCGGAGCTGGCAGACAAAAATGTGCCCAACCTTCATGTAATGAAGGCCATGCAGTCTCTCAAGT
CTCGAGGCTACGTGAAGGAACAGTTTGCTTGGAGACATTTCTACTGGTACCTTACGAACGAGGGCATCCAGTATCTCCGA
GACTACCTGCACCTACCCCCGGAGATCGTGCCCGCCACCCTGCGTCGCAGCCGTCCCGAGACCGGCAGGCCTCGGCCCAA
AGGTCCAGAGGGTGAGCGACCTGCAAGATTCACAAGAGGGGAGGCTGACAGAGACACCTACAGAAGGAGCGCCGTGCCCC
CTGGAGCCGACAAGAAAGCTGAGGCTGGGGCTGGCTGGGCCACTGAGTTCCAGTTTAGAGGCGGCTTTGGTCATGGACGT
GGTCAGCCACCTCAG
ORF - retro_mmus_1500 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.79 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKEQFAWRHFYWY |
| MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKEQFAWRHFYWY | |
| Retrocopy | MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKEQFAWRHFYWY |
| Parental | LTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGPEGERPARFTRGEADRDTYRRSAVPPGADKKA |
| LTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGPEGERPARFTRGEADRDTYRRSAVPPGADKKA | |
| Retrocopy | LTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGPEGERPARFTRGEADRDTYRRSAVPPGADKKA |
| Parental | EAGAGSATEFQFRGGFGRGRGQPPQ |
| EAGAG.ATEFQFRGGFG.GRGQPPQ | |
| Retrocopy | EAGAGWATEFQFRGGFGHGRGQPPQ |
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 .14 RPM | 28 .50 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 20 .41 RPM |
| SRP007412_heart | 0 .16 RPM | 54 .48 RPM |
| SRP007412_kidney | 0 .12 RPM | 36 .63 RPM |
| SRP007412_liver | 0 .11 RPM | 39 .08 RPM |
| SRP007412_testis | 0 .00 RPM | 18 .20 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1500 was not detected
No EST(s) were mapped for retro_mmus_1500 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_45639 | 72 libraries | 80 libraries | 465 libraries | 241 libraries | 214 libraries |
| TSS #2 | TSS_45640 | 1047 libraries | 20 libraries | 5 libraries | 0 libraries | 0 libraries |
The graphical summary, for retro_mmus_1500 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_1500 was not experimentally validated.