RetrogeneDB ID: | retro_cfam_1228 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 27:29538084..29538353(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCAFG00000012600 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | DBI | ||
| Ensembl ID: | ENSCAFG00000004895 | ||
| Aliases: | DBI, ACBP, EP | ||
| Description: | Canis lupus familiaris diazepam binding inhibitor (GABA receptor modulator, acyl-CoA binding protein) (DBI), mRNA. [Source:RefSeq mRNA;Acc:NM_001197047] |
Retrocopy-Parental alignment summary:
>retro_cfam_1228
CCCGCCAGCATGTTTCAGGCTGAGTTTGACAAAGCTGCCGAGGATGTTAAGTACTTCAAGACCAAGCCAGCAGATGATGA
GATGTTGTTCATCTACAGCCACTACAAGCAAGCAACTGTACGTCACGTAAACACAGAATGGCCTTGGCTGTTGAATCTCA
GAGGCAAGGCCAAGTGGGATGCCTGGAATCAGCTGAAAGGGACTTCCAAGGAAGATGCCATAAAACCTTACGTCAACAAG
TAGAAGATCTAAAGAAAAAATATGGAATA
ORF - retro_cfam_1228 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.42 % |
| Parental protein coverage: | 65.69 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | PADRLEAEFDKAAEDVKHLKTKPADDEMLYIYSHYKQATVGDINTERPGLLDLRGKAKWDAWNQLKGTSK |
| PA....AEFDKAAEDVK..KTKPADDEML.IYSHYKQATV...NTE.P.LL.LRGKAKWDAWNQLKGTSK | |
| Retrocopy | PASMFQAEFDKAAEDVKYFKTKPADDEMLFIYSHYKQATVRHVNTEWPWLLNLRGKAKWDAWNQLKGTSK |
| Parental | EDAMKAYVNK-VEDLKKKYGI |
| EDA.K.YVNK.VEDLKKKYGI | |
| Retrocopy | EDAIKPYVNK<VEDLKKKYGI |
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 .00 RPM | 333 .22 RPM |
| SRP017611_brain | 0 .00 RPM | 73 .28 RPM |
| SRP017611_kidney | 0 .00 RPM | 701 .51 RPM |
| SRP017611_liver | 0 .00 RPM | 196 .51 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1228 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1228 was not experimentally validated.