RetrogeneDB ID: | retro_mmus_3666 | ||
Retrocopylocation | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:95211473..95211777(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | ENSMUSG00000083789 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | Ak1 | ||
| Ensembl ID: | ENSMUSG00000026817 | ||
| Aliases: | Ak1, Ak-1, B430205N08Rik | ||
| Description: | adenylate kinase 1 [Source:MGI Symbol;Acc:MGI:87977] |
Retrocopy-Parental alignment summary:
>retro_mmus_3666
ATGGAAGAGAAGCTGAATAAAGCCAAGATCATCTTTGTGGTGAGCCAGGTCTGGCTCAGGAAAGGGTACCCAATGTGAGA
AGATTGTGCAGAAATATGGCTACACCTACCTCTCTACTGGGGACCTGCTGCAAGCAGAAGTCAGCTCCGGATTGGAGAGG
GTCAAGATGCTGTCATCTGTTATGGAAAGGGGGAAGCTGGTGCTGCTGGAGACAGTGGTAGACATGCTCTGGGATGTTAT
GATAGCCAAAGTGGATTCTTCCAAGGGCTTCCTGATTGGTGGCTACCCAAGGGCAGCAAAACAG
ATGGAAGAGAAGCTGAATAAAGCCAAGATCATCTTTGTGGTGAGCCAGGTCTGGCTCAGGAAAGGGTACCCAATGTGAGA
AGATTGTGCAGAAATATGGCTACACCTACCTCTCTACTGGGGACCTGCTGCAAGCAGAAGTCAGCTCCGGATTGGAGAGG
GTCAAGATGCTGTCATCTGTTATGGAAAGGGGGAAGCTGGTGCTGCTGGAGACAGTGGTAGACATGCTCTGGGATGTTAT
GATAGCCAAAGTGGATTCTTCCAAGGGCTTCCTGATTGGTGGCTACCCAAGGGCAGCAAAACAG
ORF - retro_mmus_3666 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.47 % |
| Parental protein coverage: | 52.06 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MEEKLKKAKIIFVVGG-PGSGKGTQCEKIVQKYGYTHLSTGDLLRAEVSSGSERGKKLSAIMEKGELVPL |
| MEEKL.KAKIIFVV....GSGKGTQCEKIVQKYGYT.LSTGDLL.AEVSSG.ER.K.LS..ME.G.LV.L | |
| Retrocopy | MEEKLNKAKIIFVVSQ>SGSGKGTQCEKIVQKYGYTYLSTGDLLQAEVSSGLERVKMLSSVMERGKLVLL |
| Parental | DTVLDMLRDAMLAKVDSSNGFLIDGYPREVKQ |
| .TV.DML.D.M.AKVDSS.GFLI.GYPR..KQ | |
| Retrocopy | ETVVDMLWDVMIAKVDSSKGFLIGGYPRAAKQ |
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 | 71 .96 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 73 .43 RPM |
| SRP007412_heart | 0 .00 RPM | 548 .83 RPM |
| SRP007412_kidney | 0 .00 RPM | 126 .28 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .30 RPM |
| SRP007412_testis | 0 .09 RPM | 203 .13 RPM |
RNA Polymerase II actvity near the 5' end of retro_mmus_3666 was not detected
No EST(s) were mapped for retro_mmus_3666 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_158582 | 449 libraries | 245 libraries | 232 libraries | 43 libraries | 103 libraries |
The graphical summary, for retro_mmus_3666 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_3666 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3666 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000026817 | 1 retrocopy |
retro_mmus_3666 ,
|
| Mus musculus | ENSMUSG00000028719 | 1 retrocopy |