RetrogeneDB ID: | retro_mmus_2766 | ||
Retrocopylocation | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 6:98275762..98276072(+) | ||
| Located in intron of: | ENSMUSG00000090667 | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | Arhgdia | ||
| Ensembl ID: | ENSMUSG00000025132 | ||
| Aliases: | Arhgdia, 5330430M07Rik, Gdi-1, Rho-GDI, RhoDGI, RhoGDI-1 | ||
| Description: | Rho GDP dissociation inhibitor (GDI) alpha [Source:MGI Symbol;Acc:MGI:2178103] |
Retrocopy-Parental alignment summary:
>retro_mmus_2766
CCCCTGGAACTGGGCCTGAAAGGTGATCTGGAGAGCTTCAAGAAACAGTCGTTTGTCTTGAAGAAAGGTGTGGAGTACCG
GATAAAAATTTCTTTCCGGGTGAACAGAGAGATCGTGTCAGGCATGAAGTACACTCAGCACACAGAACAGGAAAGGGGTC
AAAATCGACAAGACTGACTACATGGTCGGGAGCTATGGACTGAGGGCTCAGGAGTACGAGTTTCTGACACCCACGGAGGA
GGCTCCCAAAGGCACGCTTGCTCGGGGCAGTTACAACATCAAGTCTTGCTTCACCAATGATGACAAAACT
CCCCTGGAACTGGGCCTGAAAGGTGATCTGGAGAGCTTCAAGAAACAGTCGTTTGTCTTGAAGAAAGGTGTGGAGTACCG
GATAAAAATTTCTTTCCGGGTGAACAGAGAGATCGTGTCAGGCATGAAGTACACTCAGCACACAGAACAGGAAAGGGGTC
AAAATCGACAAGACTGACTACATGGTCGGGAGCTATGGACTGAGGGCTCAGGAGTACGAGTTTCTGACACCCACGGAGGA
GGCTCCCAAAGGCACGCTTGCTCGGGGCAGTTACAACATCAAGTCTTGCTTCACCAATGATGACAAAACT
ORF - retro_mmus_2766 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.46 % |
| Parental protein coverage: | 50.49 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | PLELDLTGDLESFKKQSFVLKEGVEYRIKISFRVNREIVSGMKYIQHTY-RKGVKIDKTDYMVGSYGPRA |
| PLEL.L.GDLESFKKQSFVLK.GVEYRIKISFRVNREIVSGMKY.QHT..RKGVKIDKTDYMVGSYG.RA | |
| Retrocopy | PLELGLKGDLESFKKQSFVLKKGVEYRIKISFRVNREIVSGMKYTQHTE>RKGVKIDKTDYMVGSYGLRA |
| Parental | EEYEFLTPMEEAPKGMLARGSYNIKSRFTDDDKT |
| .EYEFLTP.EEAPKG.LARGSYNIKS.FT.DDKT | |
| Retrocopy | QEYEFLTPTEEAPKGTLARGSYNIKSCFTNDDKT |
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 | 200 .22 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 159 .44 RPM |
| SRP007412_heart | 0 .00 RPM | 141 .77 RPM |
| SRP007412_kidney | 0 .00 RPM | 215 .52 RPM |
| SRP007412_liver | 0 .00 RPM | 76 .30 RPM |
| SRP007412_testis | 0 .05 RPM | 59 .87 RPM |
RNA Polymerase II actvity near the 5' end of retro_mmus_2766 was not detected
No EST(s) were mapped for retro_mmus_2766 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_126232 | 525 libraries | 248 libraries | 293 libraries | 5 libraries | 1 library |
| TSS #2 | TSS_126233 | 183 libraries | 321 libraries | 550 libraries | 16 libraries | 2 libraries |
The graphical summary, for retro_mmus_2766 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_2766 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2766 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 | |
|---|---|---|---|
| Felis catus | ENSFCAG00000030567 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000025132 | 1 retrocopy |
retro_mmus_2766 ,
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