RetrogeneDB ID: | retro_mmus_2577 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 5:72047566..72048085(+) | ||
| Located in intron of: | ENSMUSG00000029212 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rpl5 | ||
| Ensembl ID: | ENSMUSG00000058558 | ||
| Aliases: | Rpl5, U21RNA | ||
| Description: | ribosomal protein L5 [Source:MGI Symbol;Acc:MGI:102854] |
Retrocopy-Parental alignment summary:
>retro_mmus_2577
AGTGGAGGTGAATACAATGTGGAAAGCATTGATGGTCAGCCTGGTGCCTTCACTTGCTATCTGGATGCAGGTCTTGCCCA
AACTACAACTGGCAATAAAGTTTTTGGGGCCCTGAAGGGAGCTGTGGATGGAGGCTTGTCTATCCCTCATAGTACCAAAT
GATTCCCTGGTTATGACTCTGAAAGCAAGGAGTTCAATGCAGAGGTACATGCTCGGAAGCACACCATGGATCAGGATGTG
GCAGACTACATGCGCTACCTAATGGAGGAAGATGAAGATGCGTATAAGAAACAGTTCTCTCAGTACATCAGGAACAACGT
AACTCCAGACATGATGGAGGAGATGTATAAGAAAGCTCATGCTGCTATCCGAGAGAATCCAGTCTATGAGAAGAAGCCCA
AGAGAGAAGTGAAGGAGAAGAGGTGGAATCATTCCAAAATGTCTTTTGCCCAGTAGAGAAACCGGGTTGCTCAAAAGAAG
GCAAGCTTCCTCAGAGCTCAGGAAAGTTCTGCTGAAAGC
ORF - retro_mmus_2577 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.17 % |
| Parental protein coverage: | 57.91 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | NGGEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFPGYDSESKEFNAEVH |
| .GGEYNVESIDGQPGAFTCYLDAGLA.TTTGNKVFGALKGAVDGGLSIPHSTK.FPGYDSESKEFNAEVH | |
| Retrocopy | SGGEYNVESIDGQPGAFTCYLDAGLAQTTTGNKVFGALKGAVDGGLSIPHSTK*FPGYDSESKEFNAEVH |
| Parental | -RKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMYKKAHAAIRENPVYEKKPKREVKKK |
| .RKH.M.Q.VADYMRYLMEEDEDAYKKQFSQYI.NNVTPDMMEEMYKKAHAAIRENPVYEKKPKREVK.K | |
| Retrocopy | ARKHTMDQDVADYMRYLMEEDEDAYKKQFSQYIRNNVTPDMMEEMYKKAHAAIRENPVYEKKPKREVKEK |
| Parental | RWNRPKMSLAQKKDRVAQKKASFLRAQERAAES |
| RWN..KMS.AQ...RVAQKKASFLRAQE..AES | |
| Retrocopy | RWNHSKMSFAQ*RNRVAQKKASFLRAQESSAES |
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 .26 RPM | 46 .80 RPM |
| SRP007412_cerebellum | 0 .39 RPM | 34 .26 RPM |
| SRP007412_heart | 0 .16 RPM | 57 .28 RPM |
| SRP007412_kidney | 0 .17 RPM | 78 .35 RPM |
| SRP007412_liver | 0 .08 RPM | 59 .15 RPM |
| SRP007412_testis | 0 .00 RPM | 29 .04 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2577 was not detected
No EST(s) were mapped for retro_mmus_2577 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_115130 | 55 libraries | 74 libraries | 592 libraries | 255 libraries | 96 libraries |
The graphical summary, for retro_mmus_2577 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_2577 was not experimentally validated.