RetrogeneDB ID: | retro_mmus_3317 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 9:17502355..17502703(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Iscu | ||
| Ensembl ID: | ENSMUSG00000025825 | ||
| Aliases: | Iscu, 2310020H20Rik, AA407971, Nifu, Nifun | ||
| Description: | IscU iron-sulfur cluster scaffold homolog (E. coli) [Source:MGI Symbol;Acc:MGI:1913633] |
Retrocopy-Parental alignment summary:
>retro_mmus_3317
TCGGCTGGACCGGGCCGTCTAAGGCGGGCAGCGTCCGCCACGCTGCTGCTCTGGAGCCCATGCCTGCCTGCTCGGGAGCT
GTAAGCTCCAGCCAGGCTCTACCACAAGGAAGTTGTGGATCATTATGAAAACCCTGGGAACGTGGGGTCCCTTGACAAGA
CATGTAAAAATGTTGGAACCGGATTGGTGGGGGTTCCAGCATATGGTGACATCATGAAATTGCTGCTCTAGGTGGATGAA
AAGGGGAAGATTGTGGACGCCAGATTCAAAACGTTTGGCTGCAGCTCTGCCATGGCCTACAGCTCCTCAGCCATGGAGTG
GGTAAAGGGTAAAACGGTAGAGGAAGCC
ORF - retro_mmus_3317 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.9 % |
| Parental protein coverage: | 68.45 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ATGAGRLRRAASA-LLLRSPRLPARELSAPARLYHKKVVDHYENPRNVGSLDKTSKNVGTGLVGAPACGD |
| ..G.GRLRRAASA.LLL.SP.LPAREL.APARLYHK.VVDHYENP.NVGSLDKT.KNVGTGLVG.PA.GD | |
| Retrocopy | SAGPGRLRRAASATLLLWSPCLPAREL*APARLYHKEVVDHYENPGNVGSLDKTCKNVGTGLVGVPAYGD |
| Parental | VMKLQIQVDEKGKIVDARFKTFGCGSAIASSSLATEWVKGKTVEEA |
| .MKL...VDEKGKIVDARFKTFGC.SA.A.SS.A.EWVKGKTVEEA | |
| Retrocopy | IMKLLL*VDEKGKIVDARFKTFGCSSAMAYSSSAMEWVKGKTVEEA |
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 | 33 .29 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 49 .67 RPM |
| SRP007412_heart | 0 .00 RPM | 57 .19 RPM |
| SRP007412_kidney | 0 .00 RPM | 107 .16 RPM |
| SRP007412_liver | 0 .03 RPM | 47 .38 RPM |
| SRP007412_testis | 0 .00 RPM | 38 .33 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3317 was not detected
No EST(s) were mapped for retro_mmus_3317 retrocopy.
No TSS is located nearby retro_mmus_3317 retrocopy 5' end.
retro_mmus_3317 was not experimentally validated.