RetrogeneDB ID: | retro_mmus_2728 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 6:38376806..38377151(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000057696 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rpl30 | ||
| Ensembl ID: | ENSMUSG00000058600 | ||
| Aliases: | None | ||
| Description: | ribosomal protein L30 [Source:MGI Symbol;Acc:MGI:98037] |
Retrocopy-Parental alignment summary:
>retro_mmus_2728
ATGGTGGCCGCAAAGAAGACGAAAAAGTCTCTGGAGTCAATCAACTCTAGGCTCCAACTTGTTATGAAAAGTGGGAAGTA
CGTGCTGGGCTACAAACAGACTCTGAAGATGATCAGACAAGGCAAAGCGAAGTTGGTTATCCTTGCCAACAACTGTCCAG
CTTTGAGGAAATTTGAAATAGAGTACTATGCCATGTTGGCTAAAACTGGGGTCCATCACTACAGTGGCAATAATATTGAA
CTGGGCACAGCGTGTGGAAAATACTACAGAGTATGCACACTGGCTATCATTGACCCAGGTGATTCTGATATTATTAGAAG
CATGCCAGAACAGACTGGTGAGAAG
ORF - retro_mmus_2728 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.13 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MVAAKKTKKSLESINSRLQLVMKSGKYVLGYKQTLKMIRQGKAKLVILANNCPALRKSEIEYYAMLAKTG |
| MVAAKKTKKSLESINSRLQLVMKSGKYVLGYKQTLKMIRQGKAKLVILANNCPALRK.EIEYYAMLAKTG | |
| Retrocopy | MVAAKKTKKSLESINSRLQLVMKSGKYVLGYKQTLKMIRQGKAKLVILANNCPALRKFEIEYYAMLAKTG |
| Parental | VHHYSGNNIELGTACGKYYRVCTLAIIDPGDSDIIRSMPEQTGEK |
| VHHYSGNNIELGTACGKYYRVCTLAIIDPGDSDIIRSMPEQTGEK | |
| Retrocopy | VHHYSGNNIELGTACGKYYRVCTLAIIDPGDSDIIRSMPEQTGEK |
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 .05 RPM | 46 .73 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 28 .92 RPM |
| SRP007412_heart | 0 .03 RPM | 78 .98 RPM |
| SRP007412_kidney | 0 .19 RPM | 55 .54 RPM |
| SRP007412_liver | 0 .03 RPM | 64 .39 RPM |
| SRP007412_testis | 0 .00 RPM | 49 .99 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2728 was not detected
No EST(s) were mapped for retro_mmus_2728 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_121727 | 492 libraries | 443 libraries | 136 libraries | 0 libraries | 1 library |
The graphical summary, for retro_mmus_2728 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_2728 was not experimentally validated.