RetrogeneDB ID: | retro_cfam_390 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 10:46034540..46034947(-) | ||
| Located in intron of: | ENSCAFG00000002463 | ||
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_390
ATGGTGGCGGCTGGAGCTGGCCGTCTGAGGCAGGCAGCGTTGGCCTTGCTGCTCCGGAGCCCGCGCCTGCCTGCCTGGGA
ACTGTTGGCTCCGGCCCGGCTCTATCACAAGAAGGTTGTTGATCATTATGAAAATCCTAGAAACGTGGGTCCCTTGACAA
GACATCAAAAAATGTTGGAACTGGATTGGTGGGGGCTCCAGCATGTGGTGACGTAATGAAATTACAGATTCAAGTGGATG
AAAAGGGGAAGATTGTGGATGCCAGGTTTAAAACATTTGGCTGTGGGTCTGAAATTGCCTCCAGCTCCTTAGCCACTGAC
TGGGTAAAAGGCAAGACGGTGGAGGAAACCTTGACCATCAAGAACACGGACATCGCCAAGGAGCTCTGCCTTCCCCTCGT
GAAACTG
ORF - retro_cfam_390 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.7 % |
| Parental protein coverage: | 81.44 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAAAGAGRLRRAASALLLRSPRLPARELSAPARLYHKKVVDHYENPRNV-GSLDKTSKNVGTGLVGAPAC |
| M.AAGAGRLR.AA.ALLLRSPRLPA.EL.APARLYHKKVVDHYENPRNV.GSLDKTSKNVGTGLVGAPAC | |
| Retrocopy | MVAAGAGRLRQAALALLLRSPRLPAWELLAPARLYHKKVVDHYENPRNV<GSLDKTSKNVGTGLVGAPAC |
| Parental | GDVMKLQIQVDEKGKIVDARFKTFGCGSAIASSSLATEWVKGKTVEEALTIKNTDIAKELCLPPVKL |
| GDVMKLQIQVDEKGKIVDARFKTFGCGS.IASSSLAT.WVKGKTVEE.LTIKNTDIAKELCLP.VKL | |
| Retrocopy | GDVMKLQIQVDEKGKIVDARFKTFGCGSEIASSSLATDWVKGKTVEETLTIKNTDIAKELCLPLVKL |
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 | 0 .13 RPM | 47 .00 RPM |
| SRP017611_brain | 0 .08 RPM | 44 .38 RPM |
| SRP017611_kidney | 0 .07 RPM | 104 .07 RPM |
| SRP017611_liver | 0 .00 RPM | 29 .37 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_390 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_390 was not experimentally validated.