RetrogeneDB ID: | retro_mmus_474 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 1:102458658..102458922(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Lyrm2 | ||
| Ensembl ID: | ENSMUSG00000045854 | ||
| Aliases: | None | ||
| Description: | LYR motif containing 2 [Source:MGI Symbol;Acc:MGI:1917573] |
Retrocopy-Parental alignment summary:
>retro_mmus_474
ATGGCTGCTTCCTGCTTGCCACCTGCGGCCCTGATGCTGAAGCAGTTCATGAGAAGGCAGCAACTTCTCCTCCTCTACAG
AAAGATTTTGCAAGCAATTAGGCAAGTTCCAAGTGATTCTGACTGAAAATACCTTCAGGATTGGGCCAGGGAAGAATTTA
AAAGAAACAAAAGTGCCACAGAAGAGAATACAATCCGAATGATAATTATCCAAGGCAATATGCAGCTAAAGGAACTAGAA
AGGATGCTTGCCTTAGCCAACTCG
ORF - retro_mmus_474 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.77 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAASRLPPAALTLKQFMRRQQVLLLYRKILRAIRQVPSDSDRKYLQDWAREEFKRNKSATEEDTIRMMIT |
| MAAS.LPPAAL.LKQFMRRQQ.LLLYRKIL.AIRQVPSDSD.KYLQDWAREEFKRNKSATEE.TIRM.I. | |
| Retrocopy | MAASCLPPAALMLKQFMRRQQLLLLYRKILQAIRQVPSDSD*KYLQDWAREEFKRNKSATEENTIRMIII |
| Parental | QGNMQLKELERTLALANS |
| QGNMQLKELER.LALANS | |
| Retrocopy | QGNMQLKELERMLALANS |
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 | 8 .32 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 5 .78 RPM |
| SRP007412_heart | 0 .00 RPM | 15 .07 RPM |
| SRP007412_kidney | 0 .00 RPM | 18 .27 RPM |
| SRP007412_liver | 0 .00 RPM | 7 .13 RPM |
| SRP007412_testis | 0 .00 RPM | 11 .94 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_474 was not detected
No EST(s) were mapped for retro_mmus_474 retrocopy.
No TSS is located nearby retro_mmus_474 retrocopy 5' end.
retro_mmus_474 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_474 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 7 parental genes, and 9 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Macropus eugenii | ENSMEUG00000009916 | 1 retrocopy | |
| Microcebus murinus | ENSMICG00000012230 | 2 retrocopies | |
| Mus musculus | ENSMUSG00000045854 | 2 retrocopies |
retro_mmus_474 , retro_mmus_790,
|
| Otolemur garnettii | ENSOGAG00000034900 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000004324 | 1 retrocopy | |
| Ictidomys tridecemlineatus | ENSSTOG00000016198 | 1 retrocopy | |
| Tursiops truncatus | ENSTTRG00000007420 | 1 retrocopy |