RetrogeneDB ID: | retro_cfam_80 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | X:89171984..89172845(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCAFG00000018270 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCAFG00000013855 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cfam_80
ATGAATGCCGTCTTCTCCCTGCCACGCTGGCGGCGGCGGCTGTGGCTCTGGCTGTGGCGGCGGCGGAGGAACCCGCCACG
CACCAGCCTTGCTCCCGCCCCACTCGGAGCCGAAGCTGCAGCCGGGCGGGGGCCTTGGGGCCTGAGGACGGAGGTGGAGG
CAGCGGGGCCACCGCTGGAGCCGGGAGACTTTGTGCAGCTGCCCGTGCCCATCATCCAGCAGCTCTCCCACTGGGACTGC
GGCCTGGCCTGCTCCAAGATGGTGCTGCGGTACCTGGGCCAGGTGGACGACAATGAGTTTGAGAGTGCCCTGCGGGAGCT
GCAGCTAACCAGGAACATCTGGACCATTGATCTGGCCTACCTGATGCGCCACTTTGGTGTGAGGCACCGCTTCTGCACAC
AGACCCTGGGTGTTGACAAGGGCTACAAGAACCAGTCCTTCTACAGGAAGCACTTTGACACAGAGGAGACCCGGGTGAAC
CAGTTGTTTGCACAAGCCAAGGCTTGCAAGGTGCTCGTGGAGAAATGCACAGTGAGCGTGCAGGACATCCAGGAGCACCT
GGCACAGGGCCACGTGGCCATCGTGCTGGTGAACTCTGGGGTACTGCACTGCGACCTTTGCTCCAGTCCTGTCAAGTACT
CCTGCTTTGCCCCCAGTGGCCACCGCTGCTTCTGTGGCACCCCTGACTACCAGGGCCACTTCATCGTGCTGTGCGGCTAC
AGCCGGGCCACGGGCTGCATCTTCTACAACAATCCAGCCTACGCCGACCGAATGTGCAGCACCAGCATCAGTAACTTCGA
GGGAGCCAGAACCAGTTACGGCACAGATGAGGACATCCTCTTAGTCTACCTGGATAGCTGA
ORF - retro_cfam_80 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.54 % |
| Parental protein coverage: | 94.82 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MRTEAEAAGPPLEPEDFVQLPVPIIQQLYHWDCGLACSKMVLRYLGQVDDNEFESALQELRLTRSIWTID |
| .RTE.EAAGPPLEP.DFVQLPVPIIQQL.HWDCGLACSKMVLRYLGQVDDNEFESAL.EL.LTR.IWTID | |
| Retrocopy | LRTEVEAAGPPLEPGDFVQLPVPIIQQLSHWDCGLACSKMVLRYLGQVDDNEFESALRELQLTRNIWTID |
| Parental | LAYLMRHFGVRHRFCTQTLGVDKGYKNQSFYRKHFDTEETRVNQLFAQAKACKVLVEKCTVSVQDIQEHL |
| LAYLMRHFGVRHRFCTQTLGVDKGYKNQSFYRKHFDTEETRVNQLFAQAKACKVLVEKCTVSVQDIQEHL | |
| Retrocopy | LAYLMRHFGVRHRFCTQTLGVDKGYKNQSFYRKHFDTEETRVNQLFAQAKACKVLVEKCTVSVQDIQEHL |
| Parental | AQGHVAIVLVNSGVLHCDLCSSPVKYCCFAPSGHRCFCRTPDYQGHFIVLRGYNRATGCIFYNNPAYADR |
| AQGHVAIVLVNSGVLHCDLCSSPVKY.CFAPSGHRCFC.TPDYQGHFIVL.GY.RATGCIFYNNPAYADR | |
| Retrocopy | AQGHVAIVLVNSGVLHCDLCSSPVKYSCFAPSGHRCFCGTPDYQGHFIVLCGYSRATGCIFYNNPAYADR |
| Parental | MCSTSISNFEEARTSYGTDEDILFVYLD |
| MCSTSISNFE.ARTSYGTDEDIL.VYLD | |
| Retrocopy | MCSTSISNFEGARTSYGTDEDILLVYLD |
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 | 16 .25 RPM |
| SRP017611_brain | 0 .00 RPM | 7 .07 RPM |
| SRP017611_kidney | 0 .07 RPM | 92 .72 RPM |
| SRP017611_liver | 0 .00 RPM | 74 .11 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_80 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_80 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_80 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000013855 | 1 retrocopy |
retro_cfam_80 ,
|
| Felis catus | ENSFCAG00000001511 | 1 retrocopy |