RetrogeneDB ID: | retro_mmus_1010 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 13:50950221..50950972(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
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_1010
ATGAAGCTAAACATCTCCTTCCCTGCCACTGGCTGTCAGAAATGCATTGAAGTGGATGACGAACGCAAGCTTTACACGTT
CTATGAGAAGCGCATGGATACAGAAATTGCTGCTGCTGCTGCTCTTGGTGAAGAGCGAAAGGGTTGTGTGGTCCGGATCA
GCAGTGGGAATGACAAGCAAGGTTTTCCCATGAAGCAAGGTGTTCTGACCCATGGCAGAGTGCGCCTGCTGTTGAATAGG
GGGCATTCCTGTTACAGACTAAGGAGAACTGGAGAGAGGAAGCGCAAGTCTGTTCGCAGATGCATTGTGGACGCTAATCT
CAGTGTTCTCAACTTGGTCATTGTAAAGAAAGGAGAGAAGGATATTCCTGGACTGACAGATACTACTGTGCCTTGTCGGT
TGGGACTTAAAAGAACTAGTAGAATCCGAAAGCTTTTTAATCTCTCCAAAAAGATGATGTCCGCCAGTATGTTGTCAGGA
AGCCCTTAAACAAAGAAGGTAAGAAGCCCAGGACCAAAGCACCCAAGATTCAATCAATGTCTTGTTACTCTACGGGTCCT
GCAACACAAACGCTGACATATTTCTCTGAAGAAACAACGCAAAGAAAAACAAGGAGGAGGCTGCAGATTACGCTAAACTT
TTGGCCAAGAGAATGGAGGAAGCCAAAGAAAAGCGCCAGGAACAGATTGCCAAGAGACGTAGGCTGTTCTCCCTAAGAGC
CTCTATTTCTAAGTCTGAGTCCAGTCAAAAA
ORF - retro_mmus_1010 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.04 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADA-LGEEWKGYVVRISGGNDKQGFPMKQGVLT |
| MKLNISFPATGCQK.IEVDDERKL.TFYEKRM.TE.AA.A.LGEE.KG.VVRIS.GNDKQGFPMKQGVLT | |
| Retrocopy | MKLNISFPATGCQKCIEVDDERKLYTFYEKRMDTEIAAAAALGEERKGCVVRISSGNDKQGFPMKQGVLT |
| Parental | HGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKDIPGLTDTTVPRRLGPKRAS |
| HGRVRLLL..GHSCYR.RRTGERKRKSVR.CIVDANLSVLNLVIVKKGEKDIPGLTDTTVP.RLG.KR.S | |
| Retrocopy | HGRVRLLLNRGHSCYRLRRTGERKRKSVRRCIVDANLSVLNLVIVKKGEKDIPGLTDTTVPCRLGLKRTS |
| Parental | RIRKLFNLSKE-DDVRQYVVRKPLNKEGKKPRTKA-PKI-QRLVTPRVLQHKRRRIALKKQRTKK-NKEE |
| RIRKLFNLSK..DDVRQYVVRKPLNKEGKKPRTKA.P...Q.LVT.RVLQHKR..I.LKKQR..K...E. | |
| Retrocopy | RIRKLFNLSKK<DDVRQYVVRKPLNKEGKKPRTKA>PRFNQCLVTLRVLQHKR*HISLKKQRKEK>KEEA |
| Parental | AAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRASTSKSESSQK |
| A..YAKLLAKRM.EAKEKRQEQIAKRRRL.SLRAS.SKSESSQK | |
| Retrocopy | A-DYAKLLAKRMEEAKEKRQEQIAKRRRLFSLRASISKSESSQK |
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 | 43 .48 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 37 .30 RPM |
| SRP007412_heart | 0 .12 RPM | 69 .30 RPM |
| SRP007412_kidney | 0 .06 RPM | 72 .19 RPM |
| SRP007412_liver | 0 .03 RPM | 80 .59 RPM |
| SRP007412_testis | 0 .05 RPM | 43 .50 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1010 was not detected
No EST(s) were mapped for retro_mmus_1010 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_29596 | 470 libraries | 510 libraries | 84 libraries | 4 libraries | 4 libraries |
The graphical summary, for retro_mmus_1010 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_1010 was not experimentally validated.