RetrogeneDB ID: | retro_ecab_682 | ||
Retrocopylocation | Organism: | Horse (Equus caballus) | |
| Coordinates: | 27:25445060..25445392(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSECAG00000016499 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ecab_682
ATGGCCAGGCCAGGGGCTGCTTTCCGTCACCTGGGCCCCTTATCCAGAGCTGGGGCCTTGGGCTCGGCCTGCTGCGGGGC
ACATGGCGCCCAGTTCCTGGACGCCTATGGGAAGGAGCTCTTTGGCAAGGCCAACAAACCGTCCTTCCACAGCCTGGCCC
TAATGTTAGGGGGGTCCCGTTACAGAAAGTCCCTGTGGGTCGAGTTACTACCAGCCTCTGGAAGCACCTTATTGTGCACC
AGCTTTTACTGCCAGGCTGAGTGGAGACCCAGTGCCCAGATTGTGGCCCCAGTGGAAGGAGCCTGCCACTCCTGTGCTGG
CTTGCCTTTGCT
ATGGCCAGGCCAGGGGCTGCTTTCCGTCACCTGGGCCCCTTATCCAGAGCTGGGGCCTTGGGCTCGGCCTGCTGCGGGGC
ACATGGCGCCCAGTTCCTGGACGCCTATGGGAAGGAGCTCTTTGGCAAGGCCAACAAACCGTCCTTCCACAGCCTGGCCC
TAATGTTAGGGGGGTCCCGTTACAGAAAGTCCCTGTGGGTCGAGTTACTACCAGCCTCTGGAAGCACCTTATTGTGCACC
AGCTTTTACTGCCAGGCTGAGTGGAGACCCAGTGCCCAGATTGTGGCCCCAGTGGAAGGAGCCTGCCACTCCTGTGCTGG
CTTGCCTTTGCT
ORF - retro_ecab_682 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.91 % |
| Parental protein coverage: | 99.12 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAGLGATFRRLGALSGAGALGLATYGAHGAQFPDAYGKELFDRVNKHHFLHSLAL-LGVPHCRKPLWAGL |
| MA..GA.FR.LG.LS.AGALG.A..GAHGAQF.DAYGKELF...NK..F.HSLAL.LG....RK.LW..L | |
| Retrocopy | MARPGAAFRHLGPLSRAGALGSACCGAHGAQFLDAYGKELFGKANKPSF-HSLALMLGGSRYRKSLWVEL |
| Parental | LLASGTTLFCTSFYYQALSGDPSIQTLAPV-GGSLLLLGWLALA |
| L.ASG.TL.CTSFY.QA....PS.Q..APV.G.SL.LL.WLA.A | |
| Retrocopy | LPASGSTLLCTSFYCQA-EWRPSAQIVAPV<GRSLPLLCWLAFA |
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 .00 RPM | 6 .97 RPM |
| SRP021940_cerebellum | 0 .00 RPM | 4 .52 RPM |
| SRP021940_embryo | 0 .00 RPM | 5 .52 RPM |
| SRP021940_placental_villous | 0 .00 RPM | 11 .64 RPM |
| SRP021940_synovial_membrane | 0 .00 RPM | 7 .55 RPM |
| SRP021940_testis | 0 .00 RPM | 4 .22 RPM |
Equus caballus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ecab_682 retrocopy.
Equus caballus was not studied using FANTOM5 data.
retro_ecab_682 was not experimentally validated.