RetrogeneDB ID: | retro_cfam_1960 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 8:43087648..43087897(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GCHFR | ||
| Ensembl ID: | ENSCAFG00000029586 | ||
| Aliases: | None | ||
| Description: | GTP cyclohydrolase I feedback regulator [Source:HGNC Symbol;Acc:4194] |
Retrocopy-Parental alignment summary:
>retro_cfam_1960
ATGCCCTATCTCCTCATCAGCACCCACATCCACACAGAAGTGCGCCCCACCCTGGTGGGCGGTAAGTACTCAGATCTAGA
GCAGGTTCAGTATCTGGGGGCCTCAAAGAGAAGTGTCTTGGGAAACAACTTTTGTTAGCACTTTATTAATAACCCTCCTC
GCATAGTCCTAGATGAGCTGAAATGCAAAGGCTTCCTTGTGCTGAGCATGACTGAGATGGGCCAGACACTGGTGTGGTGG
CTGCACAAG
ORF - retro_cfam_1960 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 68.67 % |
| Parental protein coverage: | 98.81 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MPYVLISTQTRMEVGPTMVGDEHSDPELMRYLGASKRSVLGNNFYEYFVNDPPRIVLDKLERKGFRVLSM |
| MPY.LIST....EV.PT.VG...SD.E...YLGASKRSVLGNNF...F.N.PPRIVLD.L..KGF.VLSM | |
| Retrocopy | MPYLLISTHIHTEVRPTLVGGKYSDLEQVQYLGASKRSVLGNNFC*HFINNPPRIVLDELKCKGFLVLSM |
| Parental | TGVGQTLVWCLHK |
| T..GQTLVW.LHK | |
| Retrocopy | TEMGQTLVWWLHK |
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 | 3 .19 RPM | 0 .67 RPM |
| SRP017611_brain | 3 .10 RPM | 0 .56 RPM |
| SRP017611_kidney | 0 .26 RPM | 1 .92 RPM |
| SRP017611_liver | 0 .51 RPM | 1 .31 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1960 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1960 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1960 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ailuropoda melanoleuca | ENSAMEG00000016929 | 1 retrocopy | |
| Canis familiaris | ENSCAFG00000029586 | 1 retrocopy |
retro_cfam_1960 ,
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