RetrogeneDB ID: | retro_cfam_838 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 19:7921212..7921474(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PDCD5 | ||
| Ensembl ID: | ENSCAFG00000007555 | ||
| Aliases: | None | ||
| Description: | programmed cell death 5 [Source:HGNC Symbol;Acc:8764] |
Retrocopy-Parental alignment summary:
>retro_cfam_838
ATGAGAAACAGTATCTTAGCCCAAGTCCTGGATCAGTCAGCCCAGGGCCCGTTTAAGTAACTTAGCACTTGTAAAGTCTG
AAAAAACTAAAGCAGTAGAGAATTACCTCATATAGATGGCAAGATACGGACAACTCAGTGGGGAGGTATCAGAACAAGGT
TTAATAGAAATCCTTGAGAAAGTAAGCCAACAAACAGAAAAGAAAACCACAGTTAAATTCAACAGAAGAAAAGTCATGGA
CTCTGATGAAGAGGATGATTAT
ORF - retro_cfam_838 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.45 % |
| Parental protein coverage: | 78.38 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MRNSILAQVLDQSA-RARLSNLALVKPEKTKAVENYLIQMARYGQLSGKVSEQGLIEILEKVSQQTEKKT |
| MRNSILAQVLDQSA.RARLSNLALVK.EKTKAVENYLI.MARYGQLSG.VSEQGLIEILEKVSQQTEKKT | |
| Retrocopy | MRNSILAQVLDQSA>RARLSNLALVKSEKTKAVENYLI*MARYGQLSGEVSEQGLIEILEKVSQQTEKKT |
| Parental | TVKFNRRKVMDSDEEDDY |
| TVKFNRRKVMDSDEEDDY | |
| Retrocopy | TVKFNRRKVMDSDEEDDY |
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 | 41 .37 RPM |
| SRP017611_brain | 0 .00 RPM | 24 .85 RPM |
| SRP017611_kidney | 0 .00 RPM | 24 .43 RPM |
| SRP017611_liver | 0 .00 RPM | 9 .72 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_838 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_838 was not experimentally validated.