RetrogeneDB ID: | retro_mmus_519 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 1:189277445..189277823(-) | ||
| Located in intron of: | ENSMUSG00000037624 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Pdcd5 | ||
| Ensembl ID: | ENSMUSG00000030417 | ||
| Aliases: | Pdcd5, 2200003D22Rik, AA408513, Tfar19 | ||
| Description: | programmed cell death 5 [Source:MGI Symbol;Acc:MGI:1913538] |
Retrocopy-Parental alignment summary:
>retro_mmus_519
ATGGCGGACGAAGAACTTGAGGCGCTGAGGAAGCAGAGGCTGGCCGAGTTGCAGGCCAAGCATGGAGATCCTGGTGATGC
AGCCCAACAGGAAGCAAAGCAAAGGGAAGCAGAAATGAGAAACAGTATCTTAGCCCAAGTTCTGGATCAGTCAGCCCGGG
CCAGATTAAGTAACTTAGCACTTGTAAAGCCTGAAAAAACTAAAGCAGTGGAGAACTACCTTATACAGATGGCGCGGTAT
GGACAGCTAAGTGGGAAGGTGTCAGAACAAGGTTTGATAGAAATACTTGAGAAAGTCAGCCAACAGACAGAAAAGAAAAC
AACAGTGAAATTCAACAGAAGAAAAGTAATGGACTCCGATGAAGACGACGCCGATTAC
ORF - retro_mmus_519 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 | MADEELEALRKQRLAELQAKHGDPGDAAQQEAKQREAEMRNSILAQVLDQSARARLSNLALVKPEKTKAV |
| MADEELEALRKQRLAELQAKHGDPGDAAQQEAKQREAEMRNSILAQVLDQSARARLSNLALVKPEKTKAV | |
| Retrocopy | MADEELEALRKQRLAELQAKHGDPGDAAQQEAKQREAEMRNSILAQVLDQSARARLSNLALVKPEKTKAV |
| Parental | ENYLIQMARYGQLSGKVSEQGLIEILEKVSQQTEKKTTVKFNRRKVMDSDEDDADY |
| ENYLIQMARYGQLSGKVSEQGLIEILEKVSQQTEKKTTVKFNRRKVMDSDEDDADY | |
| Retrocopy | ENYLIQMARYGQLSGKVSEQGLIEILEKVSQQTEKKTTVKFNRRKVMDSDEDDADY |
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 .14 RPM | 15 .84 RPM |
| SRP007412_cerebellum | 0 .13 RPM | 19 .11 RPM |
| SRP007412_heart | 1 .03 RPM | 38 .48 RPM |
| SRP007412_kidney | 0 .54 RPM | 33 .28 RPM |
| SRP007412_liver | 0 .11 RPM | 17 .94 RPM |
| SRP007412_testis | 1 .19 RPM | 182 .50 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_519 was not detected
No EST(s) were mapped for retro_mmus_519 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_73221 | 277 libraries | 512 libraries | 272 libraries | 6 libraries | 5 libraries |
The graphical summary, for retro_mmus_519 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_519 was not experimentally validated.