RetrogeneDB ID: | retro_cpor_29 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_8:5010023..5010446(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCPOG00000008817 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NXT2 | ||
| Ensembl ID: | ENSCPOG00000003310 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_29
ATGGCATCTGTGGATTTCAAGACCTATGTGGACCAGGCCTGCAGAGCAGCCGAGGAGTTTGTCAACGTCTACTACACCAC
CATGGATAAGCGGCGGCGCCTGCTGTCCCGCCTCTACATGGGCACAGCCACCTTGGTATGGAATGGAAACGCCGTTTCAG
GACAGGAGTCCCTGAGTGAGTTCTTTGAAATGTTGCCCTCCAGCGAGTTCCAGATCAATGTGGTTGACTGCCAACCTGTC
CACGATGAGGCCACACCTAGTCAGACCACAGTCCTGGTTGTTATCTGTGGGTCTGTGAAGTTTGAGGGCAACAAACAGCG
GGACTTCAACCAGAATTTCATCCTCACCGCCCAGGCCTCCCCTACCAACACGGTATGGAGGATCGCAAGTGACTGTTTCC
GTTTCCAGGACTGGGCCAACTAG
ORF - retro_cpor_29 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 73.53 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | DFKTYVDQACKAAEEFINIYYETMDKRRRALIRLYLDKATLVWNGNVVTGLDALNNFFEMLPSSEFQVNM |
| DFKTYVDQAC.AAEEF.N.YY.TMDKRRR.L.RLY...ATLVWNGN.V.G...L..FFEMLPSSEFQ.N. | |
| Retrocopy | DFKTYVDQACRAAEEFVNVYYTTMDKRRRLLSRLYMGTATLVWNGNAVSGQESLSEFFEMLPSSEFQINV |
| Parental | LDCQPVHEQATQSQSTVLVVTSGTVKFDGNRQHYFNQNFLLTAQVSHNSTVWKIASDCFRFQDWAN |
| .DCQPVH..AT.SQ.TVLVV..G.VKF.GN.Q..FNQNF.LTAQ.S...TVW.IASDCFRFQDWAN | |
| Retrocopy | VDCQPVHDEATPSQTTVLVVICGSVKFEGNKQRDFNQNFILTAQASPTNTVWRIASDCFRFQDWAN |
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 | 3 .39 RPM | 0 .06 RPM |
| SRP017611_kidney | 4 .29 RPM | 0 .31 RPM |
| SRP017611_liver | 1 .96 RPM | 0 .57 RPM |
| SRP040447_lung | 7 .89 RPM | 0 .45 RPM |
| SRP040447_skeletal_muscle | 3 .38 RPM | 0 .20 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_29 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_29 was not experimentally validated.