RetrogeneDB ID: | retro_cpor_1003 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_4:5924797..5925263(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | CFL2 | ||
| Ensembl ID: | ENSCPOG00000008996 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_1003
TCTGGAGTTACAGTGAATGATGAAGTCAAAGTTTTTAATGATATGAAAGTAAAGAAATCACAAAAGGAGATCAAAATGCA
AAAGAAAGCATTGTGTCTTGGTTTCTTCTGTTTATGATGACAAAAGACAATTGTAGAGAAAACAGCACATCTTGGAGGAT
GACATTGGTGATACTGTAGAAGACCCCCGCACATCTCTTGTGAAGCTGCCTCTGAATAACTGCTGATATACTTTGTATGA
TGCCCCTACAAAACGAAAGACTCTGAAGGAAGACTACCTAGTATTTATGTTCTGGGCTTGTGAAAGTGCACCGTTATAAA
GCAAGATGACTCATGGTTGCTCTAATGATGCCATTAAAAGGAAATTTACAAGTATTAAACAGAAATATTCAGGCTTGGAT
GACATTAAGGACCATTCAACACTTGGAAAGAAATTGAGGTGCAATGTAGTAGTTTCACCTGAAGGA
ORF - retro_cpor_1003 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 59.88 % |
| Parental protein coverage: | 96.99 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | SGVTVNDEVIKVFNDMKVRKSSTQEEIKKRKKAVLF-CLSDDKRQIIVEEAKQILVGDIGDTVEDPYTSF |
| SGVTVNDEV.KVFNDMKV.KS.......K......F....DDKRQ........IL..DIGDTVEDP.TS. | |
| Retrocopy | SGVTVNDEV-KVFNDMKVKKSQKEIKMQKKALCLGF>SVYDDKRQL*RKQ--HILEDDIGDTVEDPRTSL |
| Parental | VKLLPLNDCRYALYDATYETKESKKEDLVFIFWAPESAPLKSKMIYASSKDAIKKKFTGIKHEWQVNGLD |
| VKL.PLN.C.Y.LYDA....K..K...LVF.FWA.ESAPL.SKM....S.DAIK.KFT.IK......GLD | |
| Retrocopy | VKL-PLNNC*YTLYDAPTKRKTLKEDYLVFMFWACESAPL*SKMTHGCSNDAIKRKFTSIKQKY--SGLD |
| Parental | DIKDRSTLGEKLGGNVVVSLEG |
| DIKD.STLG.KL..NVVVS.EG | |
| Retrocopy | DIKDHSTLGKKLRCNVVVSPEG |
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 |
|---|---|---|
| SRP017611_brain | 0 .00 RPM | 14 .90 RPM |
| SRP017611_kidney | 0 .00 RPM | 7 .96 RPM |
| SRP017611_liver | 0 .00 RPM | 9 .49 RPM |
| SRP040447_lung | 0 .00 RPM | 7 .72 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 352 .98 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1003 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1003 was not experimentally validated.