RetrogeneDB ID: | retro_mmus_656 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 10:74862990..74863416(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000072407 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Mrpl42 | ||
| Ensembl ID: | ENSMUSG00000062981 | ||
| Aliases: | Mrpl42, 2700009F22Rik, 2900055D03Rik, D10Ertd322e, HSPC204, L31mt, MRP-L31, PTD007, Rpml31 | ||
| Description: | mitochondrial ribosomal protein L42 [Source:MGI Symbol;Acc:MGI:1333774] |
Retrocopy-Parental alignment summary:
>retro_mmus_656
ATGGCGGGTGCAGTAAAATGGGCGATATCAAACAGAACTATCTGGAAGCATTTATTTCCAATCCAAAACGGAGCTTTGTC
TAGTGCTTGTCACAAATCCACATACTCTTCTCTTCCGGATGACTACAATTGCCAGGTGGACCTCGCCTTGACAGCCGACG
GCAGGACAATAGTGTGCTACCACCCTTCTGTGGACATCCCCTATGAACACTCCAAACCCACCCCTCAGCCAGATCTTCTG
CATAATAATGAGGAAACCCACGAGCAGATCCCGAAAGCCAAGTTAGAAGTTAGAAAGCGCAAGCCGCTGGAGCAAGGGCC
CATGTTAGAACAACTGAGCAAGGTGTTCTACACCACGAAGCATCGCTGGTACCCGCACGGACAGTATCACAGTCGTCGTA
AGAAACAGAATCCTCCCAAAAACAGA
ORF - retro_mmus_656 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.55 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAAAVKWAISNRTIWKHLLPIQNGALSSACHKSTYSSLPDDYNCQVDLALTADGRTIVCYHPSVDIPYEH |
| MA.AVKWAISNRTIWKHL.PIQNGALSSACHKSTYSSLPDDYNCQVDLALTADGRTIVCYHPSVDIPYEH | |
| Retrocopy | MAGAVKWAISNRTIWKHLFPIQNGALSSACHKSTYSSLPDDYNCQVDLALTADGRTIVCYHPSVDIPYEH |
| Parental | TKPIPQPDLLHNNEETHEQILKAKLEVRKSKQLEQGPMIEQLSKVFYTTKHRWYPHGQYHNRRKKLNPPR |
| .KP.PQPDLLHNNEETHEQI.KAKLEVRK.K.LEQGPM.EQLSKVFYTTKHRWYPHGQYH.RRKK.NPP. | |
| Retrocopy | SKPTPQPDLLHNNEETHEQIPKAKLEVRKRKPLEQGPMLEQLSKVFYTTKHRWYPHGQYHSRRKKQNPPK |
| Parental | DR |
| .R | |
| Retrocopy | NR |
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 | 22 .50 RPM |
| SRP007412_cerebellum | 0 .09 RPM | 26 .49 RPM |
| SRP007412_heart | 0 .44 RPM | 174 .17 RPM |
| SRP007412_kidney | 0 .33 RPM | 91 .44 RPM |
| SRP007412_liver | 0 .08 RPM | 34 .38 RPM |
| SRP007412_testis | 0 .00 RPM | 12 .94 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_656 was not detected
No EST(s) were mapped for retro_mmus_656 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_5127 | 30 libraries | 3 libraries | 68 libraries | 192 libraries | 779 libraries |
The graphical summary, for retro_mmus_656 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_656 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_656 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 23 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000062981 | 7 retrocopies |
retro_mmus_1432, retro_mmus_1492, retro_mmus_1756, retro_mmus_2140, retro_mmus_656 , retro_mmus_721, retro_mmus_722,
|
| Rattus norvegicus | ENSRNOG00000042740 | 4 retrocopies | |
| Ictidomys tridecemlineatus | ENSSTOG00000026544 | 12 retrocopies |