RetrogeneDB ID: | retro_mmus_168 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 1:159168156..159168642(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000061992 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Atp5h | ||
| Ensembl ID: | ENSMUSG00000034566 | ||
| Aliases: | Atp5h, 0610009D10Rik | ||
| Description: | ATP synthase, H+ transporting, mitochondrial F0 complex, subunit d [Source:MGI Symbol;Acc:MGI:1918929] |
Retrocopy-Parental alignment summary:
>retro_mmus_168
ATGGTTGGGTGTAAACTTGCTCTAAAAACCATTGATTGGGTATCTTTTGTGGAGATCATGCCCCCAAACCAGAAGGCAAT
TGGAAATGCCTTGAAGTCCTGGAATGAGACCTTCCACACCAGGTTGGCTAGTCTGTCTGAGAAACCACCTGCGATTGACT
GGGCTTACTACAAGGCCAGTGTGGCCAAGCCTGGCTTGGTGGATGATTTTGAAAAGAAGTATAATACCCTAAAGATTCCT
GTGCCTGAGGATAAATACACAGCCCTGGTGGACCAGGAGGAGGAGGAGGATGTGAAGAACTGTGCTGAGTTTGTGTCTGG
ATCTCAGCTCAGGATCCAGGAGTGTGAGAAGCAGCTGGAGAAAACGAGGAACATAATTCCCTTTGACCAGATGTCCATTG
GTGACTCGAATGAGATTTTCCCAGAAACCAAGCTGGACAAGAAGAAGTACCCGTACAGGCCCCACCAGCCCATCGAGAAC
CTATGA
ORF - retro_mmus_168 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.06 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAGRKLALKTIDWVSFVEVMPQNQKAIGNALKSWNETFHARLASLSEKPPAIDWAYYRANVAKPGLVDDF |
| M.G.KLALKTIDWVSFVE.MP.NQKAIGNALKSWNETFH.RLASLSEKPPAIDWAYY.A.VAKPGLVDDF | |
| Retrocopy | MVGCKLALKTIDWVSFVEIMPPNQKAIGNALKSWNETFHTRLASLSEKPPAIDWAYYKASVAKPGLVDDF |
| Parental | EKKYNALKIPVPEDKYTALVDQEEKEDVKSCAEFVSGSQLRIQEYEKQLEKMRNIIPFDQMTIDDLNEIF |
| EKKYN.LKIPVPEDKYTALVDQEE.EDVK.CAEFVSGSQLRIQE.EKQLEK.RNIIPFDQM.I.D.NEIF | |
| Retrocopy | EKKYNTLKIPVPEDKYTALVDQEEEEDVKNCAEFVSGSQLRIQECEKQLEKTRNIIPFDQMSIGDSNEIF |
| Parental | PETKLDKKKYPYWPHQPIENL |
| PETKLDKKKYPY.PHQPIENL | |
| Retrocopy | PETKLDKKKYPYRPHQPIENL |
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 | 86 .98 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 92 .53 RPM |
| SRP007412_heart | 0 .09 RPM | 368 .68 RPM |
| SRP007412_kidney | 0 .12 RPM | 241 .89 RPM |
| SRP007412_liver | 0 .00 RPM | 91 .29 RPM |
| SRP007412_testis | 0 .18 RPM | 58 .45 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_168 was not detected
No EST(s) were mapped for retro_mmus_168 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_70877 | 204 libraries | 287 libraries | 548 libraries | 30 libraries | 3 libraries |
The graphical summary, for retro_mmus_168 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_168 was not experimentally validated.