RetrogeneDB ID: | retro_cpor_1411 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_8:1475194..1475737(-) | ||
| Located in intron of: | ENSCPOG00000011675 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MCTS1 | ||
| Ensembl ID: | ENSCPOG00000005502 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_1411
ATGTTCAAGAAATTTGACGAAAAGGAAAATGTGTCCAATTGCATCCAGTTGAAAACTTCAGTTATAAAGGGTATGAAGAA
CCAACTGATAGAGCAGTTTCCAGATATTGAGCCATGGCTTAACCAAATCATGCCTAAGAAAGAGCCTGTCAAAATGGTCC
GATGCCATGAACATACGGAAATCCTTACGGTAAATGGAGAATTAATTTTTTTTAGACAAAGGAAAGGACCTTTTTATCCA
ACTCTAAGGTTACTTCACAAATACCCTTTTATCCTGCCACACCAGCAAGTTGATAAAGGAGCCATCAAATTTGTGCTAAG
CGGTGCGAATATCATGTGCCCAGGTTTAACTTCTCCAGGAGCAAAGCTTTACCCTGCCGCAGTCGATACGATTGTTGCAG
TCATGGCGGAAGGAAAACAGCACGCGCTGTGTATTGGAGTCATGAAGATGTCTGGAGGAGACATTGGGAAAATTAACAAA
GGAATCGGCATTGAGAATATCCATTATTTAAATGATGGGCTGTGGCACATGAAGACATATAAA
ORF - retro_cpor_1411 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.16 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MFKKFDEKENVSNCIQLKTSVIKGIKNQLIEQFPGIEPWLNQIMPKKDPVKIVRCHEHIEILTVNGELLF |
| MFKKFDEKENVSNCIQLKTSVIKG.KNQLIEQFP.IEPWLNQIMPKK.PVK.VRCHEH.EILTVNGEL.. | |
| Retrocopy | MFKKFDEKENVSNCIQLKTSVIKGMKNQLIEQFPDIEPWLNQIMPKKEPVKMVRCHEHTEILTVNGELXX |
| Parental | FRQREGPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAAADTIVAIMAEGKQ |
| .RQR.GPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAA.DTIVA.MAEGKQ | |
| Retrocopy | XRQRKGPFYPTLRLLHKYPFILPHQQVDKGAIKFVLSGANIMCPGLTSPGAKLYPAAVDTIVAVMAEGKQ |
| Parental | HALCVGVMKMSAEDIEKVNKGIGIENIHYLNDGLWHMKTYK |
| HALC.GVMKMS..DI.K.NKGIGIENIHYLNDGLWHMKTYK | |
| Retrocopy | HALCIGVMKMSGGDIGKINKGIGIENIHYLNDGLWHMKTYK |
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 | 5 .35 RPM | 14 .49 RPM |
| SRP017611_kidney | 4 .19 RPM | 11 .41 RPM |
| SRP017611_liver | 1 .96 RPM | 13 .67 RPM |
| SRP040447_lung | 5 .57 RPM | 8 .98 RPM |
| SRP040447_skeletal_muscle | 1 .22 RPM | 7 .92 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1411 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1411 was not experimentally validated.