RetrogeneDB ID: | retro_cfam_388 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 10:43544352..43544799(-) | ||
| Located in intron of: | ENSCAFG00000002297 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ISCU | ||
| Ensembl ID: | ENSCAFG00000011324 | ||
| Aliases: | LOC477527, ISCU | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cfam_388
ATGGTGTCAGCTGGAGCTGGTGGTCTGAGGCCGGCAGCGTCGGCCTTGCTGCTCCGGAGCCCACACCTGCCTGCCCGAGA
ACTGTCGGCTCCGGCTCGGCTGTATCACAAGAAGGTTGTTGATCATTATGAAAATCCTAGAAACATGGGGGTCCCTGGAC
AAGACATCAAAAAATTTTGGAACTGGATTGGTGGGGGCTCCAGCATGTGGTGACTAATGAAATTGCAGATTCAAGTGGAT
GAAAAGGAGAAGATTGTGGATGCCAGGTTTAAAACATTTGGCTGTGGGTCTGAAATTGCCTCCAGCTCCTTAGCCACTGA
CTGGGTAAAAGGCAAGACGGTGGAGGAAGCCTTGACCATCAAGAACACCGACATCGCCAAGGAGCTCTGCCCTCCCTCTG
TGAGAAACTGCACTGCCCTATGCTGGCCGAAGATGCAATCAAGGCTG
ORF - retro_cfam_388 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.58 % |
| Parental protein coverage: | 89.82 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MAAAGAGRLRRAASALLLRSPRLPARELSAPARLYHKKVVDHYENPRNV-GSLDKTSKNVGTGLVGAPAC |
| M..AGAG.LR.AASALLLRSP.LPARELSAPARLYHKKVVDHYENPRN..GSLDKTSKN.GTGLVGAPAC | |
| Retrocopy | MVSAGAGGLRPAASALLLRSPHLPARELSAPARLYHKKVVDHYENPRNM>GSLDKTSKNFGTGLVGAPAC |
| Parental | GD-VMKLQIQVDEKGKIVDARFKTFGCGSAIASSSLATEWVKGKTVEEALTIKNTDIAKELCLPPVKLHC |
| GD..MKLQIQVDEK.KIVDARFKTFGCGS.IASSSLAT.WVKGKTVEEALTIKNTDIAKELC.P.V...C | |
| Retrocopy | GD<LMKLQIQVDEKEKIVDARFKTFGCGSEIASSSLATDWVKGKTVEEALTIKNTDIAKELCPPSVR-NC |
| Parental | SMLAEDAIKAAL |
| ..L........L | |
| Retrocopy | TALCWPKMQSRL |
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 |
|---|---|---|
| SRP012049_cerebellum | 2 .23 RPM | 47 .00 RPM |
| SRP017611_brain | 1 .51 RPM | 44 .38 RPM |
| SRP017611_kidney | 2 .77 RPM | 104 .07 RPM |
| SRP017611_liver | 0 .80 RPM | 29 .37 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_388 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_388 was not experimentally validated.