RetrogeneDB ID: | retro_cfam_2115 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | X:97988606..97988957(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCAFG00000018653 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | COA1 | ||
| Ensembl ID: | ENSCAFG00000031110 | ||
| Aliases: | None | ||
| Description: | cytochrome c oxidase assembly factor 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:21868] |
Retrocopy-Parental alignment summary:
>retro_cfam_2115
GGTAGCCAGTGGGAGCTGTACCCTTTTATATTACCTCATACAAAAAAGACTTCTTATTACCATCTGGCATTGAAGCAGCT
ACACAGCCACCCCAAGGCCCTGGAGGCTCTGTGCATTTCTCTCAATGTCTACTATTTCCAATTCTCCAACAAGTACAACT
TTGTCGCCAATGACCAGTTGAAGATTCTTGTCTTTGGATCCAAGTCAGAGAGCCATCTCTATGTCAGCTCAACCAGAGAT
GCCCCCTTTCAGTGGTGGCAACTTCAGGAGGTCTTCTTAAAGCTCAAGGTCAGTCAGCAGATACCTGTATTCAAGTTCAG
TGGCGATACTGGGGATGAAGTGAAAAAGGAG
ORF - retro_cfam_2115 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 63.03 % |
| Parental protein coverage: | 87.5 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | GSCTLIYYLIQKAFSKASYYQLALEQLHSRPEALEALGPPLHIHYLHLTDKYNFVDIADAQLKIPVSGSK |
| GS....Y..I.....K.SYY.LAL.QLHS.P.ALEAL...L...Y.....KYNFV..A..QLKI.V.GSK | |
| Retrocopy | GSQWELYPFILPHTKKTSYYHLALKQLHSHPKALEALCISLNVYYFQFSNKYNFV--ANDQLKILVFGSK |
| Parental | SEGHLYVSSSRDAPFQRWHLQEVFLKLKDGQQIPVFKHSGNSGHEVKEE |
| SE.HLYVSS.RDAPFQ.W.LQEVFLKLK..QQIPVFK.SG..G.EVK.E | |
| Retrocopy | SESHLYVSSTRDAPFQWWQLQEVFLKLKVSQQIPVFKFSGDTGDEVKKE |
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 | 20 .87 RPM |
| SRP017611_brain | 0 .00 RPM | 13 .58 RPM |
| SRP017611_kidney | 0 .00 RPM | 46 .23 RPM |
| SRP017611_liver | 0 .00 RPM | 8 .41 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_2115 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_2115 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_2115 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 10 parental genes, and 10 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ailuropoda melanoleuca | ENSAMEG00000009377 | 1 retrocopy | |
| Canis familiaris | ENSCAFG00000031110 | 1 retrocopy |
retro_cfam_2115 ,
|
| Callithrix jacchus | ENSCJAG00000007826 | 1 retrocopy | |
| Homo sapiens | ENSG00000106603 | 1 retrocopy | |
| Gorilla gorilla | ENSGGOG00000034928 | 1 retrocopy | |
| Macaca mulatta | ENSMMUG00000019023 | 1 retrocopy | |
| Mustela putorius furo | ENSMPUG00000018149 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000003316 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000017606 | 1 retrocopy | |
| Pan troglodytes | ENSPTRG00000019125 | 1 retrocopy |