RetrogeneDB ID: | retro_mmus_2998 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 7:13332864..13333257(-) | ||
| Located in intron of: | ENSMUSG00000033847 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000074547 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rps8 | ||
| Ensembl ID: | ENSMUSG00000047675 | ||
| Aliases: | None | ||
| Description: | ribosomal protein S8 [Source:MGI Symbol;Acc:MGI:98166] |
Retrocopy-Parental alignment summary:
>retro_mmus_2998
ATGGGCATCTCTCGGGACAACTGGCACAAGTGCCGCAAGACCGGGGGTAAGCGAAAACCCTACCACAAGAAGCGACGGCC
CGCTGCCAACACGAAGATTGGCCCTCGCCGCATACACACAGTCCGAGTTCGAGGAGGCAATAAGAAGTACCGTGCCCTGA
GATTGGATGTGGGGAACTTTTCCTGGGGCTCTGAGTGTTGTACTCGCAAAACAAGGATCATTGATGTTGTCTACAATGCA
TCCAACAACAAGCTTGTCCGCACCAAGACCCTGGTGAAGAACTGCATCGTGCTTATTGACAGCACACCGTACCAACAGTG
GTACGAGTCCCACTATGCACTGCCCCTGGGCCGCAAGAAGGGGGCCAAGCTGACTCCTGAGGAGGAAGAGATT
ORF - retro_mmus_2998 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.5 % |
| Parental protein coverage: | 65.38 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRLDVGNFSWGSE |
| MGISRDNWHK.RKT.G.......K......RPAANTKIGPRRIHTVRVRGGNKKYRALRLDVGNFSWGSE | |
| Retrocopy | MGISRDNWHKCRKT-GGKRKPYHKKR----RPAANTKIGPRRIHTVRVRGGNKKYRALRLDVGNFSWGSE |
| Parental | CCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPLGRKKGAKLTPEEEEI |
| CCTRKTRIIDVVYNASNN.LVRTKTLVKNCIVLIDSTPY.QWYESHYALPLGRKKGAKLTPEEEEI | |
| Retrocopy | CCTRKTRIIDVVYNASNNKLVRTKTLVKNCIVLIDSTPYQQWYESHYALPLGRKKGAKLTPEEEEI |
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 | 63 .94 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 45 .81 RPM |
| SRP007412_heart | 0 .03 RPM | 115 .74 RPM |
| SRP007412_kidney | 0 .06 RPM | 96 .29 RPM |
| SRP007412_liver | 0 .08 RPM | 88 .04 RPM |
| SRP007412_testis | 0 .00 RPM | 46 .29 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2998 was not detected
No EST(s) were mapped for retro_mmus_2998 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_129818 | 362 libraries | 504 libraries | 201 libraries | 3 libraries | 2 libraries |
The graphical summary, for retro_mmus_2998 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_2998 was not experimentally validated.