RetrogeneDB ID: | retro_ecab_47 | ||
Retrocopy location | Organism: | Horse (Equus caballus) | |
| Coordinates: | 16:53653367..53655314(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSECAG00000005116 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSECAG00000011807 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ecab_47
ATGGAGCACATACAGGGGGCCTGGAAGACGATCAGCAGTGGTTTTGGATTCAAAGACGCGGTGTTTGATGGCCCCAGCTG
TATCTGCCCTACAATAGTTCAGCAGTTTGGCTATCAGCGTCGGGCGTCAGATGATGGCAAACTTACGGACTCTTCTAAGA
CAAGCAACACTATCTGTGTTTTCTTGCCAAATAAGCAAAGAACGGTGGTCAGTGTGCGAAATGGAGTGAGCTTGCATGAC
TGCCTTATGAAAGCACTCAAGGTGAGGGGCCTGCAACCGGAGTGCTGTGCAGTGTTCAGACTTCTCCACGAACACAAAGG
TAAAAAAGCACGTTTAGATTGGAATACTGATGCTGCCTCATTGATTGGAGAAGAACTTCAAGTAGATTTCCTGGATCATG
TTCCTCTCACAACACACAGCTTTGCTCGGAAGACCTTTCTGAAGCTTGCCTCTTGTGACATCTGTCAGAAGTTCTTGCTA
AATGGATTTCGATGTCAGACTTGTGGCTACAAATTTCATGAGCACTGTAGCACCAAAGTACCTACGATGTGTGTGGACTG
GAGTAATATCAGACAACTCTTATTGTTTCCAAATTCCACTTTTGGTGATAGTGGAGTCCCAGCACTGCCTTCCTTGACAA
TGCGTCGGATGCGAGAGTCTGTTTCCCGGATGCCTGTTAGTTCCCAGCACAGATACTCCACGCTCCACGCCTTCACACTC
AACATCTCCAGTTCCTGCTCTGAAGGTTCCCTCTCCCAGAGGCAGAGGTCAACGTCCACACCTAATGTCCACATGGTCAG
CACCACCCTGCCTGTGGACAGCAGGGTGATTGAGGATGCAATTCGAAGTCACAGTGAATCAGCTTCACCTTCAGCCTTGT
CTAGCAGCCCCAACAATCTGAGCCCAACGGGCTGGTCACAGCCTAAAACCCCTGTGCCAGCACAGAGAGAGCGGGCACCA
GGATCCGGGACCCAGGAGAAAAACAAAATTAGACCTCGTGGTCAGAGAGATTCAAGCTGTTACTGGGAAATAGAAGCCAG
TGAAGTGATGCTCTCCACTCGGATTGGGTCAGGCTCCTTTGGAACTGTGTATAAGGGCAAATGGCACGGAGACGTTGCAG
TGAAAATCTTAAAGGTTGTTGACCCCACATCAGAGCACTTCCAGGCATTCAGGAACAAGGTGGCTGTCCTGCATAAAACA
CGGCACGTGAACGTCCTGCTCTTCATGGGGTACATGACGAAGGATAACCTGGCAATTGTGACCCAGTGGTGTGAGGGCAG
CAGCCTCTACAAACACTTGCATGTCCAGGAGACCAAGTTCCAGATGTTCCAGTTGATTGACATCACCCGGCAGACAGCTC
AGGGAATGGACTATTTGCATGCAAAAAACATCATCCACAGAGATATGAAGTCCAAAAATATATTTCTCCACGAAGGCCTG
ACGGTGAAAATTGGAGACTTTGGTTTGGCAACAGTCAAGTCGCGCTGGAGTGGTTCTCAGCAGGTTGAACAACCCACTGG
CTCTGTCCTGTGGTTGGCCCCAGAGGTGATCCGAATGCAGGATAATAACCCGTTCAGCTTCCAGTCCGATGTCTACTCCT
ATGGCATTGTACTGTATGAGCTCATGACAGGGGAACTGCCTTACTCCCACATCAACAACCGAGATCAGATCCTCTTCATG
GTGGGCCGAGGATATGCCTCCCCAGACCTTAGTAAGCTATACAAGAACTGCCCCAAAGCAGTGAAGAGGCTTGTGGCTGA
CTGCGTGAAGAAAGTTAAGGAGGAGAGGCCTCTTTTTCCCCAGATCTTGTCTCCCGTTGAGTTGCTCCAACACTCTCTAC
CGAAAATCAACCGGAGTGCTTCTGAGCCATCCCTGCATCGGGCGGCCCACACCAAGGACATCAATGCCTGCACGTTGACC
ACGTCCCCTAGACTACCTGTCTTCTAG
ORF - retro_ecab_47 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.07 % |
| Parental protein coverage: | 55.54 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LSSSPNNLSPTGWSQPKTPVPAQRERAPGSGTQEKNKIRPRGQRDSSYYWEIEASEVMLSTRIGSGSFGT |
| LSSSPNNLSPTGWSQPKTPVPAQRERAPGSGTQEKNKIRPRGQRDSS.YWEIEASEVMLSTRIGSGSFGT | |
| Retrocopy | LSSSPNNLSPTGWSQPKTPVPAQRERAPGSGTQEKNKIRPRGQRDSSCYWEIEASEVMLSTRIGSGSFGT |
| Parental | VYKGKWHGDVAVKILKVVDPTPEQFQAFRNEVAVLRKTRHVNILLFMGYMTKDNLAIVTQWCEGSSLYKH |
| VYKGKWHGDVAVKILKVVDPT.E.FQAFRN.VAVL.KTRHVN.LLFMGYMTKDNLAIVTQWCEGSSLYKH | |
| Retrocopy | VYKGKWHGDVAVKILKVVDPTSEHFQAFRNKVAVLHKTRHVNVLLFMGYMTKDNLAIVTQWCEGSSLYKH |
| Parental | LHVQETKFQMFQLIDIARQTAQGMDYLHAKNIIHRDMKSNNIFLHEGLTVKIGDFGLATVKSRWSGSQQV |
| LHVQETKFQMFQLIDI.RQTAQGMDYLHAKNIIHRDMKS.NIFLHEGLTVKIGDFGLATVKSRWSGSQQV | |
| Retrocopy | LHVQETKFQMFQLIDITRQTAQGMDYLHAKNIIHRDMKSKNIFLHEGLTVKIGDFGLATVKSRWSGSQQV |
| Parental | EQPTGSVLWMAPEVIRMQDNNPFSFQSDVYSYGIVLYELMTGELPYSHINNRDQIIFMVGRGYASPDLSK |
| EQPTGSVLW.APEVIRMQDNNPFSFQSDVYSYGIVLYELMTGELPYSHINNRDQI.FMVGRGYASPDLSK | |
| Retrocopy | EQPTGSVLWLAPEVIRMQDNNPFSFQSDVYSYGIVLYELMTGELPYSHINNRDQILFMVGRGYASPDLSK |
| Parental | LYKNCPKAMKRLVADCVKKVKEERPLFPQILSSIELLQHSLPKINRSASEPSLHRAAHTEDINACTLTTS |
| LYKNCPKA.KRLVADCVKKVKEERPLFPQILS..ELLQHSLPKINRSASEPSLHRAAHT.DINACTLTTS | |
| Retrocopy | LYKNCPKAVKRLVADCVKKVKEERPLFPQILSPVELLQHSLPKINRSASEPSLHRAAHTKDINACTLTTS |
| Parental | PRLPVF |
| PRLPVF | |
| Retrocopy | PRLPVF |
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 |
|---|---|---|
| SRP021940_articular_cartilage | 0 .35 RPM | 25 .97 RPM |
| SRP021940_cerebellum | 0 .10 RPM | 21 .50 RPM |
| SRP021940_embryo | 0 .87 RPM | 46 .62 RPM |
| SRP021940_placental_villous | 0 .38 RPM | 26 .03 RPM |
| SRP021940_synovial_membrane | 0 .77 RPM | 31 .13 RPM |
| SRP021940_testis | 0 .58 RPM | 22 .64 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_47 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_47 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_ecab_47 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Equus caballus | ENSECAG00000011807 | 1 retrocopy |
retro_ecab_47 ,
|
| Macaca mulatta | ENSMMUG00000007450 | 1 retrocopy | |
| Tarsius syrichta | ENSTSYG00000007438 | 1 retrocopy |