RetrogeneDB ID: | retro_mmus_53 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 19:23619741..23620320(+) | ||
| Located in intron of: | ENSMUSG00000033053 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000044424 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rps7 | ||
| Ensembl ID: | ENSMUSG00000061477 | ||
| Aliases: | Rps7, Mtu, Rps7A, S7 | ||
| Description: | ribosomal protein S7 [Source:MGI Symbol;Acc:MGI:1333818] |
Retrocopy-Parental alignment summary:
>retro_mmus_53
AGCCATGTCGCCAAGATCGTGAAGCCCAATGGTGAGAAGCCGGACGAGTTCGAGTCTGGCATCTCTCAGGCGCTGCTCGA
GCTGGAGATGAACTCCGATCTCAAGGCGCAGCTGCGGGAACTCAACATCACCGCAGCCAAGGAAATCGAAGTTGGTGGTG
GTCGGAAAGCTATCATAATTTTTGTACCAGTTCCTCAGCTTAAATCTTTCCAGAAAATCCAAGTCCGGCTAGTTCGTGAA
TTGGAGAAAAAGTTCAGTGGCAAGCACGTGGTCTTCATTGCTCAGAGGAGGATTCTGCCCAAGCCAACCCAGAAAAGCCG
TACGAAAAATAAGCAGAAGCGCCCCAGAAGCCGTACCCTGACAGCAGTACACGACGCCATCCTTGAGGACTTAGTCTTCC
CAAGTGAAATTGTGGGTAAGAGGATCCGTGTGAAACTGGATGGCAGCCGGCTCATAAAAGTTCACTTAGACAAAGCACAG
CAGAACAACGTGGAACACAAGGTTGAAACTTTTTCTGGTGTGTACAAGAAGCTCACAGGCAAGGATGTTAATTTTGAATT
CCCAGAGTTTCAGTTGTAA
ORF - retro_mmus_53 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.44 % |
| Parental protein coverage: | 98.97 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | SSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFVPVPQLKSF |
| S..AKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFVPVPQLKSF | |
| Retrocopy | SHVAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFVPVPQLKSF |
| Parental | QKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTAVHDAILEDLVFPSEIVGK |
| QKIQVRLVRELEKKFSGKHVVFIAQRRILPKPT.KSRTKNKQKRPRSRTLTAVHDAILEDLVFPSEIVGK | |
| Retrocopy | QKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTQKSRTKNKQKRPRSRTLTAVHDAILEDLVFPSEIVGK |
| Parental | RIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTGKDVNFEFPEFQL |
| RIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTGKDVNFEFPEFQL | |
| Retrocopy | RIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTGKDVNFEFPEFQL |
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 .07 RPM | 49 .34 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 26 .79 RPM |
| SRP007412_heart | 0 .03 RPM | 53 .70 RPM |
| SRP007412_kidney | 0 .00 RPM | 49 .68 RPM |
| SRP007412_liver | 0 .05 RPM | 60 .30 RPM |
| SRP007412_testis | 0 .09 RPM | 79 .63 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_53 was not detected
No EST(s) were mapped for retro_mmus_53 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_63143 | 146 libraries | 256 libraries | 607 libraries | 52 libraries | 11 libraries |
The graphical summary, for retro_mmus_53 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_53 was not experimentally validated.