RetrogeneDB ID: | retro_cfam_1469 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 32:16703319..16703558(+) | ||
| Located in intron of: | ENSCAFG00000024991 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | C1D | ||
| Ensembl ID: | ENSCAFG00000030099 | ||
| Aliases: | None | ||
| Description: | C1D nuclear receptor corepressor [Source:HGNC Symbol;Acc:29911] |
Retrocopy-Parental alignment summary:
>retro_cfam_1469
ATGACAGGTAAAGAAATTAATGAAGACTATCCAGTAGAAATTCATGAGTATTTATCAACATTTGAGAATTCCATTGGTAC
TGTGGATGAGATGCTGAAGACCATGATGTCTATTTCTAGAAATGAGCTGCAGAAATAGGATGTCCTTGAACAAGCCAAAG
TGGATTTAGTTTTTGCTTACACTTAAATTCAATGTTTTGGGTTTATTTGGCAACTCAAGGAGTTAATTCTAAGGAACAT
ORF - retro_cfam_1469 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.59 % |
| Parental protein coverage: | 57.45 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MASEEINEDYPVEIHEYLSTFENSIGAVDEMLKTMMSVSRNELLQKLDPLEQAKVDLVSAYT-LNSMFWV |
| M...EINEDYPVEIHEYLSTFENSIG.VDEMLKTMMS.SRNE.LQK.D.LEQAKVDLV.AYT.LNSMFWV | |
| Retrocopy | MTGKEINEDYPVEIHEYLSTFENSIGTVDEMLKTMMSISRNE-LQK*DVLEQAKVDLVFAYT<LNSMFWV |
| Parental | YLATQGVNPKEH |
| YLATQGVN.KEH | |
| Retrocopy | YLATQGVNSKEH |
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 .17 RPM | 24 .99 RPM |
| SRP017611_brain | 0 .00 RPM | 15 .72 RPM |
| SRP017611_kidney | 0 .00 RPM | 59 .43 RPM |
| SRP017611_liver | 0 .00 RPM | 6 .09 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1469 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1469 was not experimentally validated.