RetrogeneDB ID: | retro_mmus_2605 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 5:130188394..130188793(+) | ||
| Located in intron of: | ENSMUSG00000025340 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000080893 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ndufa12 | ||
| Ensembl ID: | ENSMUSG00000020022 | ||
| Aliases: | Ndufa12, 2410011G03Rik, AW112974 | ||
| Description: | NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 12 [Source:MGI Symbol;Acc:MGI:1913664] |
Retrocopy-Parental alignment summary:
>retro_mmus_2605
CAGGTCACCGGCCACGGCGGCCTGCGGGGCCTCCTACGGGTTTTCTTCAGGGCAAATGATATAAGGATTGGTACACTGGT
GGGAGAAGACAAATATGGGAATAAATACTACGAAGACAACAAGCAATTTTTTGGCCGCCACCGATGGGTCATCTACACCA
CCGAGATGAACGGCAAAAACACATTCTGGGATGTGGATGGAAGCATGGTGCCTCCTGAGTGGCACCGCTGGCTTCACTGC
ATGACTGACGACCCTCCGACGACTAATCCACCGACTGCTCGTAAATTCATCTGGACAAACCATAAATTCAATGTGTCTGC
CACTCCAGAGCAATACGTTCCTTATTCCACCACTAGAAAGAAGATTCATGAATGGGTCCCACCTTCGACACCTTACAAG
ORF - retro_mmus_2605 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 100.0 % |
| Parental protein coverage: | 89.26 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | QVTGHGGLRGLLRVFFRANDIRIGTLVGEDKYGNKYYEDNKQFFGRHRWVIYTTEMNGKNTFWDVDGSMV |
| QVTGHGGLRGLLRVFFRANDIRIGTLVGEDKYGNKYYEDNKQFFGRHRWVIYTTEMNGKNTFWDVDGSMV | |
| Retrocopy | QVTGHGGLRGLLRVFFRANDIRIGTLVGEDKYGNKYYEDNKQFFGRHRWVIYTTEMNGKNTFWDVDGSMV |
| Parental | PPEWHRWLHCMTDDPPTTNPPTARKFIWTNHKFNVSATPEQYVPYSTTRKKIHEWVPPSTPYK |
| PPEWHRWLHCMTDDPPTTNPPTARKFIWTNHKFNVSATPEQYVPYSTTRKKIHEWVPPSTPYK | |
| Retrocopy | PPEWHRWLHCMTDDPPTTNPPTARKFIWTNHKFNVSATPEQYVPYSTTRKKIHEWVPPSTPYK |
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 | 2 .20 RPM | 32 .22 RPM |
| SRP007412_cerebellum | 5 .04 RPM | 37 .82 RPM |
| SRP007412_heart | 0 .72 RPM | 119 .20 RPM |
| SRP007412_kidney | 10 .72 RPM | 91 .01 RPM |
| SRP007412_liver | 3 .06 RPM | 24 .28 RPM |
| SRP007412_testis | 10 .66 RPM | 84 .07 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2605 was not detected
No EST(s) were mapped for retro_mmus_2605 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_110270 | 472 libraries | 468 libraries | 131 libraries | 1 library | 0 libraries |
The graphical summary, for retro_mmus_2605 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_2605 was not experimentally validated.