RetrogeneDB ID: | retro_mmus_1027 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 13:67586385..67586622(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | 2200002D01Rik | ||
| Ensembl ID: | ENSMUSG00000030587 | ||
| Aliases: | None | ||
| Description: | RIKEN cDNA 2200002D01 gene [Source:MGI Symbol;Acc:MGI:1919525] |
Retrocopy-Parental alignment summary:
>retro_mmus_1027
ATGGAGTTTGACTTGGTGCAGTCCTGGGCCCTGGTTCTAAGAAGCCAGAGGGGGCAGGTCAAGTGAGAGATCCCAAATGC
TGTCCTCGTAAAGCACTGGGGTGGGTTAGAGGCAGGCAGGAAGCATGGCCCTAGGAGCTCCTCCCACTCCAGCAACAGTA
GCAGGTACGCTGGCTGAAAGAAGCATGAACGCTCCTCAGACAAGGTCAAGAAACCCAAAGTGAAGAAGGAGAAGAAG
ORF - retro_mmus_1027 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 50.62 % |
| Parental protein coverage: | 69.3 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MEFDLA-AALGPGSKKPEGAGHVGDPKHCPLKAP-GGPEAGAAHKPRRVSGSSSDSSSSSSSSDSEAEGK |
| MEFDL..A.LGPGSKKPEGAG.V.DPK.CP.KA..GG.EAG..H.PR..S.SS..S.............K | |
| Retrocopy | MEFDLV<AVLGPGSKKPEGAGQVRDPKCCPRKAL>GGLEAGRKHGPRSSSHSSNSSRYAG*KKHERSSDK |
| Parental | EYAAGCKKHER |
| ......KK... | |
| Retrocopy | VKKPKVKKEKK |
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 | 0 .09 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 0 .61 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .68 RPM |
| SRP007412_kidney | 0 .00 RPM | 1 .54 RPM |
| SRP007412_liver | 0 .00 RPM | 2 .40 RPM |
| SRP007412_testis | 0 .00 RPM | 0 .41 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1027 was not detected
No EST(s) were mapped for retro_mmus_1027 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_30806 | 515 libraries | 250 libraries | 137 libraries | 39 libraries | 131 libraries |
The graphical summary, for retro_mmus_1027 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_1027 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1027 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000030587 | 1 retrocopy |
retro_mmus_1027 ,
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