RetrogeneDB ID: | retro_mmus_259 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 15:5120652..5121135(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000068706 | |
| 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_259
ATGGCTGGGCGTAAACTTGCTCTAAAAACCATTGATTGGGTATCTTTTGTGGAGGTCATGCCCCAAAATCAGAAGGCAAT
TGGAAATGCCCTGAAGTCCTGGAATGAGACCTTCCACGCCAGGTTGGCTAGTCTGTCTGAGAAACCACCTGCGATTGACT
GGGCTTACTACAGGGCCAATGTGGCCAAGCCTGGCTTGGTGGATGATTTTGAAAAGAAGTATAATGCCCTGAAGATTCCT
GTGCCTGAGGATAAATACACAGCCCTGGTGGACCAGGAGGAGAAGGAGGATGTGAAGAGCTGTGCTGAATTTGTGTCTGG
ATCCCAGCTCAGGATCCAGGAGTATGAGAAGCAGCTGGAGAAAATGAGGAACATAATTCCCTTTGACCAGATGACCATTG
ATGACTTGAATGAGATCTTCCCAGAAACCAAGCTGGACAAGAAGTACCCGTACTGGCCCCACCAGCCCATCGAGAACCTG
TGA
ORF - retro_mmus_259 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.38 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAGRKLALKTIDWVSFVEVMPQNQKAIGNALKSWNETFHARLASLSEKPPAIDWAYYRANVAKPGLVDDF |
| MAGRKLALKTIDWVSFVEVMPQNQKAIGNALKSWNETFHARLASLSEKPPAIDWAYYRANVAKPGLVDDF | |
| Retrocopy | MAGRKLALKTIDWVSFVEVMPQNQKAIGNALKSWNETFHARLASLSEKPPAIDWAYYRANVAKPGLVDDF |
| Parental | EKKYNALKIPVPEDKYTALVDQEEKEDVKSCAEFVSGSQLRIQEYEKQLEKMRNIIPFDQMTIDDLNEIF |
| EKKYNALKIPVPEDKYTALVDQEEKEDVKSCAEFVSGSQLRIQEYEKQLEKMRNIIPFDQMTIDDLNEIF | |
| Retrocopy | EKKYNALKIPVPEDKYTALVDQEEKEDVKSCAEFVSGSQLRIQEYEKQLEKMRNIIPFDQMTIDDLNEIF |
| Parental | PETKLDKKKYPYWPHQPIENL |
| PETKLDKK.YPYWPHQPIENL | |
| Retrocopy | PETKLDKK-YPYWPHQPIENL |
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 .47 RPM | 86 .98 RPM |
| SRP007412_cerebellum | 0 .30 RPM | 92 .53 RPM |
| SRP007412_heart | 3 .70 RPM | 368 .68 RPM |
| SRP007412_kidney | 1 .48 RPM | 241 .89 RPM |
| SRP007412_liver | 0 .30 RPM | 91 .29 RPM |
| SRP007412_testis | 0 .37 RPM | 58 .45 RPM |
RNA Polymerase II activity may be related with retro_mmus_259 in 4 libraries
| ENCODE library ID | Target | ChIP-Seq Peak coordinates |
|---|---|---|
| ENCFF001XVA | POLR2A | 15:5121126..5121857 |
| ENCFF001XVA | POLR2A | 15:5121904..5122256 |
| ENCFF001YIJ | POLR2A | 15:5115190..5123695 |
| ENCFF001YJZ | POLR2A | 15:5121070..5122908 |
| ENCFF001YKA | POLR2A | 15:5115258..5125624 |
No EST(s) were mapped for retro_mmus_259 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_40346 | 127 libraries | 371 libraries | 547 libraries | 24 libraries | 3 libraries |
The graphical summary, for retro_mmus_259 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_259 was not experimentally validated.