RetrogeneDB ID: | retro_btau_1315 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 4:31832604..31833005(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | COPS8 | ||
| Ensembl ID: | ENSBTAG00000005854 | ||
| Aliases: | None | ||
| Description: | COP9 signalosome complex subunit 8 [Source:RefSeq peptide;Acc:NP_001076966] |
Retrocopy-Parental alignment summary:
>retro_btau_1315
TGGTCAGTAGGACAAAGAATTTGGCAGAGAGATTTCCCCAGAATCTATTTCACCATCAAAGCTCACCAGTGGTCTGAGAT
GGTCCAGCCAATCGTGAAAGTGCTTAGAGATGCAACCTGGAGAGGAGCCTTCTCCCTGATCTCTCAAACATATACATCTA
TCGTCATCACCTGCTATTTTGCAACCTTTGTTGGACTTCCAGTGGAAGAGGCTGTGAAAGGTATACTAGAGAAGGATGGT
AGGCTGATTCTACCACAAGGATGGTCATGCCCACAAAGCCACTTGCAGGGGCCCTGGATATTTCCTCTAACAGGTTTATT
GCTTTATCACAGCCTGCCCCTGTTCCACCCATTCCCAGTGGGCAGCAGTTAGCCTGACTCACCGACTATGTGGCTTTCCT
T
ORF - retro_btau_1315 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.04 % |
| Parental protein coverage: | 63.64 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | WSVGQRIWQRDFPGVYSTINAHQWSEAVQPIMEALRDATRRRAFALVSQAYTSIIADD-FAAFVGLPVEE |
| WSVGQRIWQRDFP..Y.TI.AHQWSE.VQPI...LRDAT.R.AF.L.SQ.YTSI.....FA.FVGLPVEE | |
| Retrocopy | WSVGQRIWQRDFPRIYFTIKAHQWSEMVQPIVKVLRDATWRGAFSLISQTYTSIVITCYFATFVGLPVEE |
| Parental | AVKGILE-QGWQADSTTRMVMPKKPVAGALDVSFNRFIPLSEPAPVPPIPNEQQLARLTDYVAFL |
| AVKGILE..GW.ADSTTRMVMP.KP.AGALD.S.NRFI.LS.PAPVPPIP..QQLA.LTDYVAFL | |
| Retrocopy | AVKGILE<EGW*ADSTTRMVMPTKPLAGALDISSNRFIALSQPAPVPPIPSGQQLA*LTDYVAFL |
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 |
|---|---|---|
| ERP005899_liver | 0 .00 RPM | 28 .19 RPM |
| ERP005899_muscle | 0 .00 RPM | 25 .71 RPM |
| SRP017611_brain | 0 .00 RPM | 51 .98 RPM |
| SRP017611_kidney | 0 .00 RPM | 37 .64 RPM |
| SRP017611_liver | 0 .00 RPM | 16 .99 RPM |
| SRP030211_testis | 0 .00 RPM | 85 .71 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1315 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1315 was not experimentally validated.