RetrogeneDB ID: | retro_mmus_1449 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 16:21896505..21896919(+) | ||
| Located in intron of: | ENSMUSG00000033618 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000091580 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Psmb3 | ||
| Ensembl ID: | ENSMUSG00000069744 | ||
| Aliases: | Psmb3, AL033320, C10-II | ||
| Description: | proteasome (prosome, macropain) subunit, beta type 3 [Source:MGI Symbol;Acc:MGI:1347014] |
Retrocopy-Parental alignment summary:
>retro_mmus_1449
ATGTCTATTATGTCCTATAATGGAGGGGCCGTCATGGCCATGAAGGGAAAGAACTGTGTGGCCATCGCTGCAGACAGGCA
TTTCGGGATCCAGGCCCAGATGGTGACCACGGACTTCCAGAAGATCTTTCCCATGGGTGACAGGCTCTACATAGGCCTGG
CCGGCCTGGCCACTGACGTCCAGACAGTTGCCCAGCGTCTCAAGTTCCGACTGAACCTGTATGAGCTGAAAGAAGGTCGA
CAGATCAAGCCTTACACCCTCATGAGCATGGTGGCCAACCTCCTGTATGAGAAGCGGTTCGGTCCCTACTACACAGAGCC
TGTCATTGCTGGCCTGGACCCGAAGACCTTCAAGCCCTTCATTTGCTCTCTGGACCTCATTGGCTGCCCCATGGTGACTG
ATGACTTTGTGGTA
ORF - retro_mmus_1449 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.28 % |
| Parental protein coverage: | 67.32 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSIMSYNGGAVMAMKGKNCVAIAADRRFGIQAQMVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRLKFR |
| MSIMSYNGGAVMAMKGKNCVAIAADR.FGIQAQMVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRLKFR | |
| Retrocopy | MSIMSYNGGAVMAMKGKNCVAIAADRHFGIQAQMVTTDFQKIFPMGDRLYIGLAGLATDVQTVAQRLKFR |
| Parental | LNLYELKEGRQIKPYTLMSMVANLLYEKRFGPYYTEPVIAGLDPKTFKPFICSLDLIGCPMVTDDFVV |
| LNLYELKEGRQIKPYTLMSMVANLLYEKRFGPYYTEPVIAGLDPKTFKPFICSLDLIGCPMVTDDFVV | |
| Retrocopy | LNLYELKEGRQIKPYTLMSMVANLLYEKRFGPYYTEPVIAGLDPKTFKPFICSLDLIGCPMVTDDFVV |
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 | 22 .12 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 17 .19 RPM |
| SRP007412_heart | 0 .12 RPM | 26 .43 RPM |
| SRP007412_kidney | 0 .04 RPM | 22 .37 RPM |
| SRP007412_liver | 0 .05 RPM | 25 .83 RPM |
| SRP007412_testis | 0 .00 RPM | 9 .65 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1449 was not detected
No EST(s) were mapped for retro_mmus_1449 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_45696 | 628 libraries | 391 libraries | 52 libraries | 0 libraries | 1 library |
The graphical summary, for retro_mmus_1449 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_1449 was not experimentally validated.