RetrogeneDB ID: | retro_mmus_3707 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:145601839..145602301(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000051428 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Pfdn5 | ||
| Ensembl ID: | ENSMUSG00000001289 | ||
| Aliases: | None | ||
| Description: | prefoldin 5 [Source:MGI Symbol;Acc:MGI:1928753] |
Retrocopy-Parental alignment summary:
>retro_mmus_3707
ATGGCGCAGTCGATTAACATCACGGAGCTGAATCTGCCACAACTGGAAATGCTCAAGAACCAGCTGGACCAGGAAGTGGA
GTTTTTGTCCACGTCCATTGCTCAGCTCAAGGTGGTCCAGACCAAGTGCGTGGAAGCCAAGCACTGTCTGAACGTGCTGA
ACAAGAGCAACGAGGGCAAAGAATTACTGGTCCCACTGACGAGTTCTACGTACATCCCCAGGAAGCTACACGATGTGGAG
TATGAACTTATTGATGTGGGAACTGGCTACTACGTGGAGAAGACAGCTGAGGACGCCAAGGACTTCTTCAAAAGGAAGAT
AGACTTCCTCACCAAACAGATGGAGAAAATCCAGCCAGCGCTGCAGGAGAAGCATGCCATGAAACAGGCTGTCACGGAAA
TGATGAGCCAGAAGATTCAGCAGCTCACAGCCCTGGGGGCAGCGCAGGCCACGGCCAAGGCC
ORF - retro_mmus_3707 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.16 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MAQSINITELNLPQLEMLKNQLDQEVEFLSTSIAQLKVVQTKYVEAKDCLNVLNKSNEGKELLVPLTSSM |
| MAQSINITELNLPQLEMLKNQLDQEVEFLSTSIAQLKVVQTK.VEAK.CLNVLNKSNEGKELLVPLTSS. | |
| Retrocopy | MAQSINITELNLPQLEMLKNQLDQEVEFLSTSIAQLKVVQTKCVEAKHCLNVLNKSNEGKELLVPLTSST |
| Parental | YVPGKLHDVEHVLIDVGTGYYVEKTAEDAKDFFKRKIDFLTKQMEKIQPALQEKHAMKQAVMEMMSQKIQ |
| Y.P.KLHDVE..LIDVGTGYYVEKTAEDAKDFFKRKIDFLTKQMEKIQPALQEKHAMKQAV.EMMSQKIQ | |
| Retrocopy | YIPRKLHDVEYELIDVGTGYYVEKTAEDAKDFFKRKIDFLTKQMEKIQPALQEKHAMKQAVTEMMSQKIQ |
| Parental | QLTALGAAQATVKA |
| QLTALGAAQAT.KA | |
| Retrocopy | QLTALGAAQATAKA |
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 | 69 .04 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 50 .67 RPM |
| SRP007412_heart | 0 .25 RPM | 50 .49 RPM |
| SRP007412_kidney | 0 .27 RPM | 58 .04 RPM |
| SRP007412_liver | 0 .05 RPM | 31 .68 RPM |
| SRP007412_testis | 0 .23 RPM | 105 .02 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3707 was not detected
No EST(s) were mapped for retro_mmus_3707 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_155753 | 337 libraries | 546 libraries | 188 libraries | 1 library | 0 libraries |
The graphical summary, for retro_mmus_3707 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_3707 was not experimentally validated.