RetrogeneDB ID: | retro_mmus_1995 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 2:156889466..156889748(+) | ||
| Located in intron of: | ENSMUSG00000080880 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000083831 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ndufb8 | ||
| Ensembl ID: | ENSMUSG00000025204 | ||
| Aliases: | Ndufb8, 2900010I05Rik, AI987932 | ||
| Description: | NADH dehydrogenase (ubiquinone) 1 beta subcomplex 8 [Source:MGI Symbol;Acc:MGI:1914514] |
Retrocopy-Parental alignment summary:
>retro_mmus_1995
GCAGCCGCTCGGGCTGCAGCCCTGGGAGTCTGATGGCTGCAAAGGACAACCCCACGTCGTGGTGCCACTGGAGGCACGGA
GAGCCTCCCACATGACCAAGGACATGTTGCTGAGGTCTAGGACCCCAGAGGAACGGGCCGAGGCCGCCAAGATGTATAAT
ATGCGTGTGGAAGACTCCGAGCCATACCCAGATGATGGCATGGGGTATGGTGACCACCCAGTGCTCCCCAACAATCACAG
CATGAGAGGGGTCCATGGTATGAATGGGACCACTTAGAACTG
ORF - retro_mmus_1995 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.61 % |
| Parental protein coverage: | 61.15 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | AAARAAALGVRWLQRTT-RGVVPLEARRAFHMTKDMLPGSYPRTPEERAAAAKKYNMRVEDYEPYPDDGM |
| AAARAAALGV.WLQRTT...VVPLEARRA.HMTKDML..S..RTPEERA.AAK.YNMRVED.EPYPDDGM | |
| Retrocopy | AAARAAALGV*WLQRTT>HVVVPLEARRASHMTKDMLLRS--RTPEERAEAAKMYNMRVEDSEPYPDDGM |
| Parental | GYGDYPMLPN-RSQHERDPWYQWDHSEL |
| GYGD.P.LPN..SQHER.PWY.WDH.EL | |
| Retrocopy | GYGDHPVLPN<QSQHERGPWYEWDHLEL |
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 | 47 .68 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 63 .31 RPM |
| SRP007412_heart | 0 .03 RPM | 215 .64 RPM |
| SRP007412_kidney | 0 .02 RPM | 151 .05 RPM |
| SRP007412_liver | 0 .03 RPM | 55 .25 RPM |
| SRP007412_testis | 0 .00 RPM | 49 .49 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1995 was not detected
No EST(s) were mapped for retro_mmus_1995 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_82278 | 570 libraries | 415 libraries | 85 libraries | 1 library | 1 library |
The graphical summary, for retro_mmus_1995 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_1995 was not experimentally validated.