RetrogeneDB ID: | retro_mmus_2046 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 2:74591454..74591892(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000075279 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Mrpl23 | ||
| Ensembl ID: | ENSMUSG00000037772 | ||
| Aliases: | Mrpl23, L23mrp, Rpl23, Rpl23l | ||
| Description: | mitochondrial ribosomal protein L23 [Source:MGI Symbol;Acc:MGI:1196612] |
Retrocopy-Parental alignment summary:
>retro_mmus_2046
ATGGCGCGGAATGTGTTGTACCCCCTTTACCAACTGGGTGGCCCCCAGCTCCGTGTATTTCGAACTAACTTCTTCATTCA
GCTGGTGCGGCCTGGTACTGCACAGCCTGAAGATACCGTGCAGTTCCGGATCCCCATGGAGATGACCAGGGTGGACCTTC
GGAATTACCTTGAGCAGATTTACAATGTTCCCGTGGCTGCCGTGCGCACACGGGTGCAGCATGGCTCCAACAGGAGGAGG
GATCACAAGAATGTGAGGATCAAGAAACCAGACTACAAAGTGGCCTACGTGCAGCTGGCCCATGGGCAGACCTTCACTTT
CCCAGATCTTTTTCCAGAGAAGGACCCCCGTTCTCCAGAACCTCTGGAAGAGGAGCTACCCCAGCAGAGGCAAAGCAGCG
ACCTGAGGTGCCCTGGTATCCCTTCCTGGTTTGGCCTA
ORF - retro_mmus_2046 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 100.0 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MARNVLYPLYQLGGPQLRVFRTNFFIQLVRPGTAQPEDTVQFRIPMEMTRVDLRNYLEQIYNVPVAAVRT |
| MARNVLYPLYQLGGPQLRVFRTNFFIQLVRPGTAQPEDTVQFRIPMEMTRVDLRNYLEQIYNVPVAAVRT | |
| Retrocopy | MARNVLYPLYQLGGPQLRVFRTNFFIQLVRPGTAQPEDTVQFRIPMEMTRVDLRNYLEQIYNVPVAAVRT |
| Parental | RVQHGSNRRRDHKNVRIKKPDYKVAYVQLAHGQTFTFPDLFPEKDPRSPEPLEEELPQQRQSSDLRCPGI |
| RVQHGSNRRRDHKNVRIKKPDYKVAYVQLAHGQTFTFPDLFPEKDPRSPEPLEEELPQQRQSSDLRCPGI | |
| Retrocopy | RVQHGSNRRRDHKNVRIKKPDYKVAYVQLAHGQTFTFPDLFPEKDPRSPEPLEEELPQQRQSSDLRCPGI |
| Parental | PSWFGL |
| PSWFGL | |
| Retrocopy | PSWFGL |
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 .07 RPM | 2 .17 RPM |
| SRP007412_cerebellum | 0 .09 RPM | 2 .52 RPM |
| SRP007412_heart | 0 .25 RPM | 4 .67 RPM |
| SRP007412_kidney | 0 .27 RPM | 3 .25 RPM |
| SRP007412_liver | 0 .11 RPM | 1 .83 RPM |
| SRP007412_testis | 0 .00 RPM | 0 .50 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2046 was not detected
No EST(s) were mapped for retro_mmus_2046 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_88878 | 19 libraries | 1 library | 53 libraries | 222 libraries | 777 libraries |
The graphical summary, for retro_mmus_2046 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_2046 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2046 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000000103 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000031268 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000037772 | 1 retrocopy |
retro_mmus_2046 ,
|
| Nomascus leucogenys | ENSNLEG00000026950 | 1 retrocopy | |
| Otolemur garnettii | ENSOGAG00000029988 | 1 retrocopy | |
| Sarcophilus harrisii | ENSSHAG00000002716 | 1 retrocopy |