RetrogeneDB ID: | retro_cfam_1267 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 28:15632793..15633196(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCAFG00000004339 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCAFG00000019677 | ||
| Aliases: | None | ||
| Description: | Nucleoside diphosphate kinase [Source:UniProtKB/TrEMBL;Acc:F1PEZ2] |
Retrocopy-Parental alignment summary:
>retro_cfam_1267
CAGCGGCCCGCGGGCCGGGGTCATGGGCGGCGTCTTGGGGCGCGTCGCGCTGCCGGGGCTGCTGAGTGGCCCGCGGGCCC
CCGGGCCGAGGCTACTCGCGCGCCCCAACTCGGGAGGGTCCTCCTGGACTCGAGAGCGGACCCTGGTTGCAGTGAAGCCG
GATGGGGTGCAGCGGCGGCTTGTGGGGAATGCGATCCAGCGCTTTGAGAGGAGCGTCTTCAAGCTGGTGGGGATGAAGAT
GCTGCAGGCGCCAGAGAGAGTCCTTGTTGAGCACTACCATGACCTGCGGAGGAAGCCCTTCTACCCAGCGCTCATCAGCT
ACAGGACCTCCGGCCCCGTGGTGGCCATGGTCTGGGAAGGCCCCAATGTGGTCTGCTCCTCAAGGACCATGGTCACACCC
ACT
ORF - retro_cfam_1267 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.15 % |
| Parental protein coverage: | 68.37 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | QRPAGRGHGRRLGARRAAG-LMRGPRAPGPCLLARSNSGGSSWTRERTLVAVKPDGVQRRLVGDVIQRFE |
| QRPAGRGHGRRLGARRAAG.L..GPRAPGP.LLAR.NSGGSSWTRERTLVAVKPDGVQRRLVG..IQRFE | |
| Retrocopy | QRPAGRGHGRRLGARRAAG>LLSGPRAPGPRLLARPNSGGSSWTRERTLVAVKPDGVQRRLVGNAIQRFE |
| Parental | RRGFKLVGMKMLQAPERVLAEHYHDLQRKPFYPSLISYMTSGPVVAMVWEGPNVVCSSRTMIGHT |
| R..FKLVGMKMLQAPERVL.EHYHDL.RKPFYP.LISY.TSGPVVAMVWEGPNVVCSSRTM...T | |
| Retrocopy | RSVFKLVGMKMLQAPERVLVEHYHDLRRKPFYPALISYRTSGPVVAMVWEGPNVVCSSRTMVTPT |
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 .59 RPM | 14 .53 RPM |
| SRP017611_brain | 0 .08 RPM | 8 .73 RPM |
| SRP017611_kidney | 0 .40 RPM | 60 .69 RPM |
| SRP017611_liver | 0 .07 RPM | 21 .32 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1267 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1267 was not experimentally validated.