RetrogeneDB ID: | retro_mmus_1863 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 19:28742161..28742551(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000067351 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rps15a | ||
| Ensembl ID: | ENSMUSG00000008683 | ||
| Aliases: | Rps15a, A630031B11Rik | ||
| Description: | ribosomal protein S15A [Source:MGI Symbol;Acc:MGI:2389091] |
Retrocopy-Parental alignment summary:
>retro_mmus_1863
ATGGTGCGAATGAATGTTCTGGCAGATGCTCTCAAGAGCATCAACAACGCTGAGAAGAGAGGCAAACGCCAGGTCCTCAT
CAGGCCGTGTTCTAAAGTCATCGTTTGGTTTTTAACCGTGATGATGAAGCACGGGTACACTGGTGAATTCGAGATCATTG
ATGATCACAGAGATGGGAAGATCGTTGTGAACCTCACAGGAAGGTTGAACAAGTGTGGAGTTATAAGCCTTAGATTTGAT
GTTCAACTCAAAGACCTAGATAAATGGCAGAACAATCTGCTCCCTTTACGGCAGTTTGGCTTCATTGTGCTGACAACCTT
GGCTGGCATCATAGACCATGAAGAGGCAAGACGAAAACATACAGGAGGGAAAATCCTGGGATTCTTTTTT
ORF - retro_mmus_1863 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.85 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MVRMNVLADALKSINNAEKRGKRQVLIRPCSKVIVRFLTVMMKHGYIGEFEIIDDHRAGKIVVNLTGRLN |
| MVRMNVLADALKSINNAEKRGKRQVLIRPCSKVIV.FLTVMMKHGY.GEFEIIDDHR.GKIVVNLTGRLN | |
| Retrocopy | MVRMNVLADALKSINNAEKRGKRQVLIRPCSKVIVWFLTVMMKHGYTGEFEIIDDHRDGKIVVNLTGRLN |
| Parental | KCGVISPRFDVQLKDLEKWQNNLLPSRQFGFIVLTTSAGIMDHEEARRKHTGGKILGFFF |
| KCGVIS.RFDVQLKDL.KWQNNLLP.RQFGFIVLTT.AGI.DHEEARRKHTGGKILGFFF | |
| Retrocopy | KCGVISLRFDVQLKDLDKWQNNLLPLRQFGFIVLTTLAGIIDHEEARRKHTGGKILGFFF |
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 | 97 .00 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 80 .50 RPM |
| SRP007412_heart | 0 .06 RPM | 56 .78 RPM |
| SRP007412_kidney | 0 .00 RPM | 53 .23 RPM |
| SRP007412_liver | 0 .00 RPM | 40 .94 RPM |
| SRP007412_testis | 0 .00 RPM | 60 .70 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1863 was not detected
No EST(s) were mapped for retro_mmus_1863 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_63395 | 67 libraries | 163 libraries | 377 libraries | 224 libraries | 241 libraries |
The graphical summary, for retro_mmus_1863 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_1863 was not experimentally validated.