RetrogeneDB ID: | retro_cpor_670 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_22:10340229..10340587(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | EMP1 | ||
| Ensembl ID: | ENSCPOG00000012346 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_670
AATGCACCTATAGGTTTTTGGAAAAACTGAACCAGTGGTGATGGCTATAACTTGTCATATGAGAATGAAGATGCCCTTAA
GACAGTGCAGGTCTTTATGATCCTGCTCATCATATCCTTTGGGGTCTTTATGTTCCAGCTCTTTGCCATGGATAAGGGAA
ACCTGTTCTTCCTGGGAGCCACCCTGCTGGTGTGCTGGTTGTGTGTTATGAATCAGAGTGTCCATCTACATTCTTTATGC
CAACAGCAGGGAAAATTCTGGCACAGGCACCTACCATGGCTATTGCTTCATCCTGATCTAGATCTGCTTCTGCTTGAGGT
TCATCACTGACATTTTATATGTGCCCCTGAGAAAGAAA
ORF - retro_cpor_670 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 51.18 % |
| Parental protein coverage: | 76.83 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | NGSAGLWKNCSDGNCGDLLYGHEGALKSSQAFMILSIIFSVVALMVFIFQLFTMEKGNRFFLSGASMLVC |
| N...G.WKN...G....L.Y..E.ALK..Q.FM....I.......VF.FQLF.M.KGN.FFL.GA..LVC | |
| Retrocopy | NAPIGFWKN*TSGDGYNLSYENEDALKTVQVFM----ILLIISFGVFMFQLFAMDKGNLFFL-GATLLVC |
| Parental | WLCIL-IGVSIYTNRYTNAEATFPSSTIHHGYCFILAWICFCFSFIIGILYLVLRKK |
| WLC...I.VSIY...Y.N........T..HGYCFIL..ICFC..FI..ILY..LRKK | |
| Retrocopy | WLCVM>IRVSIYI-LYANSRENSGTGT-YHGYCFILI*ICFCLRFITDILYVPLRKK |
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 | 1 .67 RPM |
| SRP017611_kidney | 0 .00 RPM | 22 .51 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .04 RPM |
| SRP040447_lung | 0 .00 RPM | 14 .07 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 6 .45 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_670 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_670 was not experimentally validated.
Retrocopy orthology:
Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000012346 | 1 retrocopy |
retro_cpor_670 ,
|