RetrogeneDB ID: | retro_mmus_1067 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 13:118047317..118047735(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
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_1067
ATAGGCATCTCTCAGGATAACTGGCACAAGTGTGGCAAGACCAGGGTAAGAGAAAACCCTACCACGAGAAGTGGAAGTAT
GAGCTGGAACGGCCTGCTGCCAACACTAAGATTGGCCCTCTCCGCATACATACAGTCCGAGCTCAAGGAGGCAATAAGTA
CCATGCCCTGAGATTAGATGTGGGGAACTTTTCCTGGGCCTCTGAGTGTTGTACTTGCAAAACAAGGATCATTGATGGTG
TCTACAATGCATCCAATAATGAGCTTGTACATACCAAGACCCTGGTGAAAAACTGCATTGTGCTTATTGACAGCATACTC
TACCGACAGTGGTACGGGTCCCACTATGCACTGCCCCTGGGCCGCAAGTAGCGGGCAAGCTGACACCTGAGGAGGAAGAG
ATTTTAAACAGAAAACGA
ORF - retro_mmus_1067 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.82 % |
| Parental protein coverage: | 67.79 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MGISRDNWHKRRKTG-GKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRLDVGNFSWGS |
| .GIS.DNWHK..KT..GKRKPYH.K.KYEL.RPAANTKIGP.RIHTVR..GGNK.Y.ALRLDVGNFSW.S | |
| Retrocopy | IGISQDNWHKCGKTR<GKRKPYHEKWKYELERPAANTKIGPLRIHTVRAQGGNK-YHALRLDVGNFSWAS |
| Parental | ECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALPLGRK-KGAKLTPEEEEILN |
| ECCT.KTRIID.VYNASNNELV.TKTLVKNCIVLIDS..YRQWY.SHYALPLGRK....KLTPEEEEILN | |
| Retrocopy | ECCTCKTRIIDGVYNASNNELVHTKTLVKNCIVLIDSILYRQWYGSHYALPLGRK<VAGKLTPEEEEILN |
| Parental | KKR |
| .KR | |
| Retrocopy | RKR |
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 | 63 .94 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 45 .81 RPM |
| SRP007412_heart | 0 .00 RPM | 115 .74 RPM |
| SRP007412_kidney | 0 .00 RPM | 96 .29 RPM |
| SRP007412_liver | 0 .00 RPM | 88 .04 RPM |
| SRP007412_testis | 0 .00 RPM | 46 .29 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1067 was not detected
No EST(s) were mapped for retro_mmus_1067 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_26944 | 167 libraries | 295 libraries | 562 libraries | 42 libraries | 6 libraries |
The graphical summary, for retro_mmus_1067 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_1067 was not experimentally validated.