RetrogeneDB ID: | retro_mmus_2338 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 4:32051811..32052209(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000082398 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ndufs3 | ||
| Ensembl ID: | ENSMUSG00000005510 | ||
| Aliases: | Ndufs3, 0610010M09Rik, CI-30kD | ||
| Description: | NADH dehydrogenase (ubiquinone) Fe-S protein 3 [Source:MGI Symbol;Acc:MGI:1915599] |
Retrocopy-Parental alignment summary:
>retro_mmus_2338
GGGCGACCCTCAGTGTTGTTGCAGTGCGTAAGAAGGGAGAATGTGGTGGCTGAGAAGCGCCCCACTGTCAGACCCCAGAG
TGATATGACCCACAAGCAACTCTCAGCATTTGGAGAGCATGTGGCTGAAATCTTACCCAATTAAGTCCAACAAGTTTAGG
TGACCTGCCTTGATGAGTTAGAAATCTGTATCCATCCCGATGGAGTCATCCCAACACTGACGTTTCTCAGGGATCGCACC
AATGCACAATTCAGATCCTTGGCTGACTTGACACAGTGGATGTCCCAACTCGGCAGAACCGTTTTGATATTGTCTACAAC
CTGCTGTCTCTGTGGTTCAACTCTAGGATTTGGGTGAAGACCTATGTAGATGAGCTGACGTCCACTAACTCTATAGTT
ORF - retro_mmus_2338 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.09 % |
| Parental protein coverage: | 50.57 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | GRPSVLWQHVRRESAAADKRPTVRPRSDVTHKQLSAFGEYVAEILPKYVQQVQVSCLDELEICIHPDGVI |
| GRPSVL.Q.VRRE...A.KRPTVRP.SD.THKQLSAFGE.VAEILP..VQQV.V.CLDELEICIHPDGVI | |
| Retrocopy | GRPSVLLQCVRRENVVAEKRPTVRPQSDMTHKQLSAFGEHVAEILPN*VQQV*VTCLDELEICIHPDGVI |
| Parental | PTLTFLRDHTNAQFKSLADLT-AVDVPTRQNRFEIVYNLLSLRFNSRIRVKTYADELTPIDSIV |
| PTLTFLRD.TNAQF.SLADLT..VDVPTRQNRF.IVYNLLSL.FNSRI.VKTY.DELT...SIV | |
| Retrocopy | PTLTFLRDRTNAQFRSLADLT<TVDVPTRQNRFDIVYNLLSLWFNSRIWVKTYVDELTSTNSIV |
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 .02 RPM | 42 .82 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 40 .47 RPM |
| SRP007412_heart | 0 .00 RPM | 141 .98 RPM |
| SRP007412_kidney | 0 .00 RPM | 93 .96 RPM |
| SRP007412_liver | 0 .00 RPM | 49 .65 RPM |
| SRP007412_testis | 0 .09 RPM | 36 .00 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2338 was not detected
No EST(s) were mapped for retro_mmus_2338 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_104252 | 114 libraries | 281 libraries | 166 libraries | 283 libraries | 228 libraries |
The graphical summary, for retro_mmus_2338 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_2338 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2338 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000008411 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000020194 | 1 retrocopy | |
| Equus caballus | ENSECAG00000013454 | 1 retrocopy | |
| Erinaceus europaeus | ENSEEUG00000007356 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000005510 | 2 retrocopies |
retro_mmus_2338 , retro_mmus_792,
|