RetrogeneDB ID: | retro_mmus_1990 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 2:153826170..153826605(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000083097 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Tomm20 | ||
| Ensembl ID: | ENSMUSG00000093904 | ||
| Aliases: | Tomm20, 1810060K07Rik, BB284719, Gm19268, MAS20, MOM19, TOM20, mKIAA0016 | ||
| Description: | translocase of outer mitochondrial membrane 20 homolog (yeast) [Source:MGI Symbol;Acc:MGI:1915202] |
Retrocopy-Parental alignment summary:
>retro_mmus_1990
ATGGTGGGCCGGAACAGCGCCATCGCCGCGGGCGTGTGCGGTGCCCTCTTCATCGGGTACTGTATCTACTTCGACCGCAA
AAGGCGGAGTGACCCCAACTTCAAGAACAGGCTTCGAGAACGAAGAAAGAAACAGAAGCTTGCTAAGGAGAGAGCTGGGC
TTTCCAAGTTACCTGATTTAAAAGATGCTGAAGCAGTTCAGAAATTCTTCCTTGAAGAGATACAGCTTGGTGAAGAGTTA
CTAGCACAAGGTGACTACGAGAAGGGTGTGGACCACCTGACAAATGCCATTGCTGTGTGTGGACAGCCTCAGCAGCTGCT
GCAAGTGTTACAGCAGACTCTTCCACCACCAGTGTTCCAGATGCTTCTGACCAAGCTTCCGACCATTAGTCAGAGAATTG
TAAGTGCTCAGAGCTTGGCTGAAGATGATGTGGAA
ORF - retro_mmus_1990 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 | MVGRNSAIAAGVCGALFIGYCIYFDRKRRSDPNFKNRLRERRKKQKLAKERAGLSKLPDLKDAEAVQKFF |
| MVGRNSAIAAGVCGALFIGYCIYFDRKRRSDPNFKNRLRERRKKQKLAKERAGLSKLPDLKDAEAVQKFF | |
| Retrocopy | MVGRNSAIAAGVCGALFIGYCIYFDRKRRSDPNFKNRLRERRKKQKLAKERAGLSKLPDLKDAEAVQKFF |
| Parental | LEEIQLGEELLAQGDYEKGVDHLTNAIAVCGQPQQLLQVLQQTLPPPVFQMLLTKLPTISQRIVSAQSLA |
| LEEIQLGEELLAQGDYEKGVDHLTNAIAVCGQPQQLLQVLQQTLPPPVFQMLLTKLPTISQRIVSAQSLA | |
| Retrocopy | LEEIQLGEELLAQGDYEKGVDHLTNAIAVCGQPQQLLQVLQQTLPPPVFQMLLTKLPTISQRIVSAQSLA |
| Parental | EDDVE |
| EDDVE | |
| Retrocopy | EDDVE |
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 .16 RPM | 273 .49 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 132 .87 RPM |
| SRP007412_heart | 0 .12 RPM | 19 .55 RPM |
| SRP007412_kidney | 0 .12 RPM | 62 .31 RPM |
| SRP007412_liver | 0 .00 RPM | 19 .12 RPM |
| SRP007412_testis | 0 .09 RPM | 19 .16 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1990 was not detected
No EST(s) were mapped for retro_mmus_1990 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_81823 | 123 libraries | 283 libraries | 58 libraries | 97 libraries | 511 libraries |
| TSS #2 | TSS_81824 | 591 libraries | 257 libraries | 217 libraries | 5 libraries | 2 libraries |
The graphical summary, for retro_mmus_1990 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_1990 was not experimentally validated.