RetrogeneDB ID: | retro_mmus_502 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 1:151520446..151520687(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Cox7b | ||
| Ensembl ID: | ENSMUSG00000031231 | ||
| Aliases: | Cox7b, 1100001F07Rik, 1110004F07Rik, C80563 | ||
| Description: | cytochrome c oxidase subunit VIIb [Source:MGI Symbol;Acc:MGI:1913392] |
Retrocopy-Parental alignment summary:
>retro_mmus_502
ATGTTGCCCTTAGCCAAAAACGCACTAAGCCGCCTCCAAGTTCGAAGCATTCAGCAAGTGGTGGCAAGGCAGAGCCACCC
AGAAGAGGACACCTAGTTTCCATGACAAATATGGGAATACTATATTAGCAGGTAGAGCCATCTTCTGTGTTTCTACATGG
ACCTATACAGCTACACAAATTGGAACAGAATGGAACATGTCCCCTGTTGGCAGAGTCACCCCAAAGGAATGGAGAGATCA
G
ORF - retro_mmus_502 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.83 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MLPLAKNALSRLQVRSIQQVVARQSH-QKRAPSFHDKYGNAILAGGAIFCVSTWTYTATQIGIEWNMSPV |
| MLPLAKNALSRLQVRSIQQVVARQSH.QKR.PSFHDKYGN.ILAG.AIFCVSTWTYTATQIG.EWNMSPV | |
| Retrocopy | MLPLAKNALSRLQVRSIQQVVARQSH>QKRTPSFHDKYGNTILAGRAIFCVSTWTYTATQIGTEWNMSPV |
| Parental | GRVTPKEWRDQ |
| GRVTPKEWRDQ | |
| Retrocopy | GRVTPKEWRDQ |
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 .05 RPM | 100 .97 RPM |
| SRP007412_cerebellum | 0 .09 RPM | 108 .08 RPM |
| SRP007412_heart | 0 .56 RPM | 430 .53 RPM |
| SRP007412_kidney | 0 .25 RPM | 240 .39 RPM |
| SRP007412_liver | 0 .05 RPM | 132 .50 RPM |
| SRP007412_testis | 0 .18 RPM | 3 .61 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_502 was not detected
No EST(s) were mapped for retro_mmus_502 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_70324 | 532 libraries | 480 libraries | 60 libraries | 0 libraries | 0 libraries |
The graphical summary, for retro_mmus_502 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_502 was not experimentally validated.