RetrogeneDB ID: | retro_mmus_1869 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 19:33447615..33447798(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Mrpl33 | ||
| Ensembl ID: | ENSMUSG00000029142 | ||
| Aliases: | Mrpl33, 0610009M10Rik, L33mt, MRP-L33 | ||
| Description: | mitochondrial ribosomal protein L33 [Source:MGI Symbol;Acc:MGI:2137225] |
Retrocopy-Parental alignment summary:
>retro_mmus_1869
ATGCTGCTTTCTGCTGTCCCATTTGCCAAGAGCAAGTCAAACTTGCTGGTGTGCCAAACCAAGACAGGTTTCTCCTTCAT
CCACAAAAGAAGCCAACTTTGAGAGAACCTGACCCTTCTGCACTATGATCCAATGGTGAACCAAAAGGTTCTCCTTGTGG
AACAGAAAAAAATATATTCCCTC
ORF - retro_mmus_1869 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 70.77 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MLLSAVSFAKSKSKTILVKLVSQAGTGFSFNHKRSRLREKLSLLHYDPIVNKKVLFVEQKKIRSL |
| MLLSAV.FAKSKS......LV.Q..TGFSF.HKRS.L.E.L.LLHYDP.VN.KVL.VEQKKI.SL | |
| Retrocopy | MLLSAVPFAKSKSNL----LVCQTKTGFSFIHKRSQL*ENLTLLHYDPMVNQKVLLVEQKKIYSL |
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 | 16 .03 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 12 .11 RPM |
| SRP007412_heart | 0 .00 RPM | 34 .59 RPM |
| SRP007412_kidney | 0 .00 RPM | 28 .87 RPM |
| SRP007412_liver | 0 .00 RPM | 17 .37 RPM |
| SRP007412_testis | 0 .00 RPM | 17 .47 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1869 was not detected
No EST(s) were mapped for retro_mmus_1869 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_63855 | 619 libraries | 420 libraries | 33 libraries | 0 libraries | 0 libraries |
The graphical summary, for retro_mmus_1869 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_1869 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1869 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000015881 | 1 retrocopy | |
| Echinops telfairi | ENSETEG00000003239 | 2 retrocopies | |
| Mus musculus | ENSMUSG00000029142 | 2 retrocopies |
retro_mmus_1869 , retro_mmus_1870,
|