RetrogeneDB ID: | retro_mmus_743 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 11:98185399..98186104(+) | ||
| Located in intron of: | ENSMUSG00000018160 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000085897 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rps6 | ||
| Ensembl ID: | ENSMUSG00000028495 | ||
| Aliases: | None | ||
| Description: | ribosomal protein S6 [Source:MGI Symbol;Acc:MGI:98159] |
Retrocopy-Parental alignment summary:
>retro_mmus_743
GTCATCGAGGTGGTTGACGAGCGCAAGCTCCACATCTTCTATGAGAAGCACATGGCCACGGAAGTAGCCGCTAATGCTCT
TGGTGAAGAGTGGAAGGGTTATGTGGTCCGGATCAGTGGTGGGAATGACAAGCAAGGTTTTCCCATGAAGCACGGTGCTC
TGACCCATGGCAGAGTGCGCCTGCTGTTGAATAGGGGGCATCCCTGTTACAGACCAAGGAGAACTGGAGAGAGGAAGCGC
AAGTCTGTTCGCGGATGCATCGTGGATGCTAATCTCAGTGTTCTCAACTTGGTTATTGTAAAGAAAGGAGAGAAGGATAT
TCCTGGACTGACAGACACGACTGTGCCTCCTCGGTTGGGACCTAAAAGAGCTAGTAGAATCCGAAAGCTTTTTAATCTCT
CTAAAGAAGATGATGTCAGCCAGTATGTTGTCAGGAAGCCCTTAAACAAAGAAGGTAAGAAGCCCAGGACCAAAGCACCC
AAGATTCAGCATCTTGTTACTCCATGCGTCCTGCAACACAAACTCCGATGTATTGCTCTGAAGAAACAACGCACTAAGAA
GAACAAGGAGGAGGCTGCAGAATATGCTAAACTTTTGGCCAAGAGAATGAAGGAAGCCAAAGAAAAGCGCCAGGAACAGA
TTGCCAAGAGACGTAGGCTGTCCTCGCTGAGAGCTTCTACTTCTAAGTCTGAGTCCAGTCAAAAA
ORF - retro_mmus_743 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.77 % |
| Parental protein coverage: | 94.38 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQGFPMKQGVLTHGRVRLLLSKGHSCY |
| .IEV.DERKL..FYEK.MATEVAA.ALGEEWKGYVVRISGGNDKQGFPMK.G.LTHGRVRLLL..GH.CY | |
| Retrocopy | VIEVVDERKLHIFYEKHMATEVAANALGEEWKGYVVRISGGNDKQGFPMKHGALTHGRVRLLLNRGHPCY |
| Parental | RPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVR |
| RPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKDIPGLTDTTVP.RLGPKRASRIRKLFNLSKEDDV. | |
| Retrocopy | RPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKDIPGLTDTTVPPRLGPKRASRIRKLFNLSKEDDVS |
| Parental | QYVVRKPLNKEGKKPRTKAPKIQRLVTPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKR |
| QYVVRKPLNKEGKKPRTKAPKIQ.LVTP.VLQHK.R.IALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKR | |
| Retrocopy | QYVVRKPLNKEGKKPRTKAPKIQHLVTPCVLQHKLRCIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKR |
| Parental | QEQIAKRRRLSSLRASTSKSESSQK |
| QEQIAKRRRLSSLRASTSKSESSQK | |
| Retrocopy | QEQIAKRRRLSSLRASTSKSESSQK |
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 | 43 .48 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 37 .30 RPM |
| SRP007412_heart | 0 .00 RPM | 69 .30 RPM |
| SRP007412_kidney | 0 .08 RPM | 72 .19 RPM |
| SRP007412_liver | 0 .00 RPM | 80 .59 RPM |
| SRP007412_testis | 0 .09 RPM | 43 .50 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_743 was not detected
No EST(s) were mapped for retro_mmus_743 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_19848 | 171 libraries | 319 libraries | 518 libraries | 55 libraries | 9 libraries |
The graphical summary, for retro_mmus_743 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_743 was not experimentally validated.