RetrogeneDB ID: | retro_btau_282 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | 1:131748086..131748432(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PPP1R14A | ||
| Ensembl ID: | ENSBTAG00000023472 | ||
| Aliases: | None | ||
| Description: | protein phosphatase 1 regulatory subunit 14A [Source:RefSeq peptide;Acc:NP_001179999] |
Retrocopy-Parental alignment summary:
>retro_btau_282
CTGCAAAAGTGACGCGTGCGCGTCACCGGCAAGTATGACCGGCTGGAGCTGCAGCTAAGCCTGGAGGTGGAGAAGTGGAT
CGACGGGCGCTTGGAGGAGTTGTTCAGCGCAGGGAGGCAGACAATGAGGTCAACATCGTGAATTGTTGAAACTAGAGAGC
GAAGAGGAGAGAAGCCAGAACAGCCAGGGATCTTCTAAAGTCCTGCACAAACCCCACAGAGGGCTTCATCCAGGAACTGC
TGGTGAAGCCCCGAGGCCTCCACAAGCAGCCAACTTTCTGCCAGCCCAGCTCCTTCGGCGGCGGCAGCCTGAGCCCCTCC
AGGACCGAGCCCGGAAGGCGCCGCCT
ORF - retro_btau_282 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 71.31 % |
| Parental protein coverage: | 80.27 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | LQKRHARVTVKYDRRELQRRLDVEKWIDGRLEELYRG-READMPDEVNI-DELLELESEEERSRKIQG-L |
| LQK...RVT.KYDR.ELQ..L.VEKWIDGRLEEL....READ...EVNI..ELL.LESEEERS...QG.L | |
| Retrocopy | LQK*RVRVTGKYDRLELQLSLEVEKWIDGRLEELFSA<READ--NEVNI<RELLKLESEEERSQNSQG>L |
| Parental | LKSCTNPTEDFVQELLAKLRGLHKQPGLRQPSPSGDGSLSPR-QDRARTAPP |
| LKSCTNPTE.F.QELL.K.RGLHKQP...QPS..G.GSLSP..QDRAR.APP | |
| Retrocopy | LKSCTNPTEGFIQELLVKPRGLHKQPTFCQPSSFGGGSLSPS<QDRARKAPP |
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 | 0 .65 RPM |
| ERP005899_muscle | 0 .00 RPM | 5 .28 RPM |
| SRP017611_brain | 0 .00 RPM | 38 .37 RPM |
| SRP017611_kidney | 0 .00 RPM | 4 .21 RPM |
| SRP017611_liver | 0 .00 RPM | 1 .89 RPM |
| SRP030211_testis | 0 .01 RPM | 15 .10 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_282 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_282 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_282 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000023472 | 1 retrocopy |
retro_btau_282 ,
|
| Bos taurus | ENSBTAG00000026586 | 2 retrocopies | |
| Rattus norvegicus | ENSRNOG00000020676 | 1 retrocopy |