RetrogeneDB ID: | retro_mmus_346 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 1:95498620..95499148(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000081051 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rpl18a | ||
| Ensembl ID: | ENSMUSG00000045128 | ||
| Aliases: | Rpl18a, 2510019J09Rik | ||
| Description: | ribosomal protein L18A [Source:MGI Symbol;Acc:MGI:1924058] |
Retrocopy-Parental alignment summary:
>retro_mmus_346
ATGAAGGCCTCGGGCACGCTTCGGGAGTACAAGGTGGTGGGGCGCTGCTTGCCAACCCCAAAATGCCACACACCACCACT
GTACCGTATGCGAATCTTTGCACCCAACCATGTGGTGGCCAAGTCCCGCTTCTGGTACTTTGTGTCACAGCTGAAGAAGA
TGAAGAAGTCATCCGGGGAAATTGTGTACTGCAGACAGGTGTTTGAGAAGTCACCCCTGCGTGTGAAGAACTTTGGCATC
TGGCTGCGCTATGACTCCCGCAGTGGCACACACAACATGTATCGGGAGTACAGGGACCTGACCACTGCTGGTGCAGTCAC
ACAGTGCTACCGAGACATGGGTGCCCGACACCGTGCCCGTGCCCACTCCATCCAGATCATGAAGGTGGAAGAGATTGCAG
CTGGCAAGTGCCGCCGGCCAGCTGTCAAGCAGTTCCACGACTCCAAGATCAAATTCCCACTGCCCCACCGTGTGTTGCGG
AGCCAGCACAAGCCACGCTTCACCACCAAGAGGCCCAACACCTTCTTC
ORF - retro_mmus_346 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.86 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MKASGTLREYKVVGRCLPTPKCHTPPLYRMRIFAPNHVVAKSRFWYFVSQLKKMKKSSGEIVYCGQVFEK |
| MKASGTLREYKVVGRCLPTPKCHTPPLYRMRIFAPNHVVAKSRFWYFVSQLKKMKKSSGEIVYC.QVFEK | |
| Retrocopy | MKASGTLREYKVVGRCLPTPKCHTPPLYRMRIFAPNHVVAKSRFWYFVSQLKKMKKSSGEIVYCRQVFEK |
| Parental | SPLRVKNFGIWLRYDSRSGTHNMYREYRDLTTAGAVTQCYRDMGARHRARAHSIQIMKVEEIAAGKCRRP |
| SPLRVKNFGIWLRYDSRSGTHNMYREYRDLTTAGAVTQCYRDMGARHRARAHSIQIMKVEEIAAGKCRRP | |
| Retrocopy | SPLRVKNFGIWLRYDSRSGTHNMYREYRDLTTAGAVTQCYRDMGARHRARAHSIQIMKVEEIAAGKCRRP |
| Parental | AVKQFHDSKIKFPLPHRVLRRQHKPRFTTKRPNTFF |
| AVKQFHDSKIKFPLPHRVLR.QHKPRFTTKRPNTFF | |
| Retrocopy | AVKQFHDSKIKFPLPHRVLRSQHKPRFTTKRPNTFF |
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 | 38 .62 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 40 .86 RPM |
| SRP007412_heart | 0 .25 RPM | 83 .68 RPM |
| SRP007412_kidney | 0 .38 RPM | 75 .27 RPM |
| SRP007412_liver | 0 .14 RPM | 65 .79 RPM |
| SRP007412_testis | 0 .14 RPM | 43 .31 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_346 was not detected
No EST(s) were mapped for retro_mmus_346 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_77941 | 19 libraries | 20 libraries | 307 libraries | 91 libraries | 635 libraries |
| TSS #2 | TSS_77942 | 380 libraries | 419 libraries | 263 libraries | 9 libraries | 1 library |
The graphical summary, for retro_mmus_346 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_346 was not experimentally validated.