RetrogeneDB ID: | retro_mmus_1510 | ||
Retrocopylocation | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 16:35573319..35573556(-) | ||
| Located in intron of: | ENSMUSG00000052133 | ||
Retrocopyinformation | Ensembl ID: | ENSMUSG00000052192 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | Rps21 | ||
| Ensembl ID: | ENSMUSG00000039001 | ||
| Aliases: | Rps21, 1810049N11Rik, 2410030A14Rik | ||
| Description: | ribosomal protein S21 [Source:MGI Symbol;Acc:MGI:1913731] |
Retrocopy-Parental alignment summary:
>retro_mmus_1510
ATGCAGAACAACACCGGGGAGTTTGTGGACCTGTACGTGCCGCGGAAATGCTCCGCAAGCAACCGCATCATTGCTGCCAA
GGACCACTTGTCCATCCAGATGAACGTGGCCAAGGTTGATAGGACCACAGGCCAGTTTAAAACCTATGGCATCTGCAGGG
CCATTCGCAGGATGGGCGAGTCAGATGATTCTATTCTCCGATTGGCTAAGGCTGATGGAATTGTCTCAAAGAACTTT
ATGCAGAACAACACCGGGGAGTTTGTGGACCTGTACGTGCCGCGGAAATGCTCCGCAAGCAACCGCATCATTGCTGCCAA
GGACCACTTGTCCATCCAGATGAACGTGGCCAAGGTTGATAGGACCACAGGCCAGTTTAAAACCTATGGCATCTGCAGGG
CCATTCGCAGGATGGGCGAGTCAGATGATTCTATTCTCCGATTGGCTAAGGCTGATGGAATTGTCTCAAAGAACTTT
ORF - retro_mmus_1510 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.95 % |
| Parental protein coverage: | 100. % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MQNDAGEFVDLYVPRKCSASNRIIAAKDHASIQMNVAEVDRTTGRFNGQFKTYGICGAIRRMGESDDSIL |
| MQN..GEFVDLYVPRKCSASNRIIAAKDH.SIQMNVA.VDRTTG.F....KTYGIC.AIRRMGESDDSIL | |
| Retrocopy | MQNNTGEFVDLYVPRKCSASNRIIAAKDHLSIQMNVAKVDRTTGQF----KTYGICRAIRRMGESDDSIL |
| Parental | RLAKADGIVSKNF |
| RLAKADGIVSKNF | |
| Retrocopy | RLAKADGIVSKNF |
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 .09 RPM | 91 .23 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 56 .40 RPM |
| SRP007412_heart | 0 .19 RPM | 82 .68 RPM |
| SRP007412_kidney | 0 .17 RPM | 73 .67 RPM |
| SRP007412_liver | 0 .16 RPM | 64 .53 RPM |
| SRP007412_testis | 0 .05 RPM | 35 .77 RPM |
RNA Polymerase II actvity near the 5' end of retro_mmus_1510 was not detected
No EST(s) were mapped for retro_mmus_1510 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_46847 | 1 library | 0 libraries | 0 libraries | 1 library | 1070 libraries |
The graphical summary, for retro_mmus_1510 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_1510 was not experimentally validated.