RetrogeneDB ID: | retro_mmus_271 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:152909535..152910120(-) | ||
| Located in intron of: | ENSMUSG00000083440 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000095597 | |
| 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_271
ATGTTCAGCTCGAGCGCCAAGATCGGGAAGCCCAATGGCGAGAAGCCAGACGAGTTCGAGTCTGGCATCTCTCAGGCGCT
GCTCGAGCTGGAGATGAACTCCGATCTCAAGGCGCAGCTGCGTGAACTCAACATCACCGCAGCCAAGGAAATCGAAGTTG
GTGGTGGTCGGAAAGCTATCATAATTTTTGTACCAGTTCCTCAGCTTAAATCTTTCCAGAAAATCCAAGTCCGGCTAGTT
CGTGAATTGGAGAAAAAGTTCAGTGGCAAGCACGTGGTCTTCATTGCTCAGAGGAGGATTCTGCCCAAGCCAACCCGGAA
AAGCCGTACGAAAAATAAGCAGAAGCGCCCCAGAAGCCGTACCCTGACAGCAGTGCACGACGCCATCCTTGAGGACTTAG
TCTTCCCAAGTGAAATTGTGGGTAAGAGGATCCGTGTGAAACTGGATGGCAGCCGGCTCATAAAAGTTCACTTAGACAAA
GCACAGCAGAACAACGTGGAACACAAGGTTGAAACTTTTTCTGGTGTGTACAAGAAGCTCACAGGCAAGGATGTTAATTT
TGAATTCCCAGAGTTTCAGTTGTAA
ORF - retro_mmus_271 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.48 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFVPVPQLK |
| MFSSSAKI.KPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFVPVPQLK | |
| Retrocopy | MFSSSAKIGKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFVPVPQLK |
| Parental | SFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTAVHDAILEDLVFPSEIV |
| SFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTAVHDAILEDLVFPSEIV | |
| Retrocopy | SFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTAVHDAILEDLVFPSEIV |
| Parental | GKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTGKDVNFEFPEFQL |
| GKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTGKDVNFEFPEFQL | |
| Retrocopy | GKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKLTGKDVNFEFPEFQL |
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 | 1 .03 RPM | 49 .34 RPM |
| SRP007412_cerebellum | 1 .43 RPM | 26 .79 RPM |
| SRP007412_heart | 0 .09 RPM | 53 .70 RPM |
| SRP007412_kidney | 2 .41 RPM | 49 .68 RPM |
| SRP007412_liver | 2 .24 RPM | 60 .30 RPM |
| SRP007412_testis | 5 .26 RPM | 79 .63 RPM |
RNA Polymerase II activity may be related with retro_mmus_271 in 1 libraries
| ENCODE library ID | Target | ChIP-Seq Peak coordinates |
|---|---|---|
| ENCFF001YKA | POLR2A | X:152909819..152910183 |
No EST(s) were mapped for retro_mmus_271 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_155931 | 53 libraries | 39 libraries | 428 libraries | 317 libraries | 235 libraries |
The graphical summary, for retro_mmus_271 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_271 was not experimentally validated.