RetrogeneDB ID: | retro_mmus_1919 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 2:53551925..53552282(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000080716 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Fam96a | ||
| Ensembl ID: | ENSMUSG00000032381 | ||
| Aliases: | Fam96a, 5730536A07Rik | ||
| Description: | family with sequence similarity 96, member A [Source:MGI Symbol;Acc:MGI:1915500] |
Retrocopy-Parental alignment summary:
>retro_mmus_1919
ATGGAGCGAGTGTCTGGGTTGCTTTCCTGGACGCTGAGCAGGGTCCTATGGCTCTCAGGGTTTTCTGAGCACGGAGCTGC
CTGGCAGCCCCAGATCATGGAAGAGAAAGCGCTAGAAGTTTATGATTTGATTTGAACTATCCAGGACCCAGAAAAGCCCA
ATGCTTTAGAAGAACTGGAAGTGGTCACAGAGAGTTGTGTGGAAGTTCAAGAAATAAATGAAGATAACTATTTGGTTATT
ATCAAGTTCACACCAACAGTGCCTCATTGCTCTTTGGCAACTCTTATTGGGCTGTGCTTAAGAGTAAAGCTCTAGCGGTG
TCTGCCGTTCACTGGACAGAAGAAGATATCAACAAGC
ORF - retro_mmus_1919 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.08 % |
| Parental protein coverage: | 74.38 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MERVSGLLSWTLSRVLWLSGFSEHGAAWQPRIMEEKALEVYDLIRTIRDPEKPNTLEELEVVTESCVEVQ |
| MERVSGLLSWTLSRVLWLSGFSEHGAAWQP.IMEEKALEVYDLI.TI.DPEKPN.LEELEVVTESCVEVQ | |
| Retrocopy | MERVSGLLSWTLSRVLWLSGFSEHGAAWQPQIMEEKALEVYDLI*TIQDPEKPNALEELEVVTESCVEVQ |
| Parental | EINEDDYLVIIKFTPTVPHCSLATLIGLCLRVKLQRCLPFKHKLEIYIS |
| EINED.YLVIIKFTPTVPHCSLATLIGLCLRVKL.RCLPF.....I..S | |
| Retrocopy | EINEDNYLVIIKFTPTVPHCSLATLIGLCLRVKL*RCLPFTGQKKISTS |
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 | 11 .10 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 9 .34 RPM |
| SRP007412_heart | 0 .00 RPM | 19 .71 RPM |
| SRP007412_kidney | 0 .04 RPM | 33 .46 RPM |
| SRP007412_liver | 0 .00 RPM | 20 .65 RPM |
| SRP007412_testis | 0 .00 RPM | 13 .90 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1919 was not detected
No EST(s) were mapped for retro_mmus_1919 retrocopy.
No TSS is located nearby retro_mmus_1919 retrocopy 5' end.
retro_mmus_1919 was not experimentally validated.