RetrogeneDB ID: | retro_cpor_1112 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_47:10442858..10443332(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TROAP | ||
| Ensembl ID: | ENSCPOG00000014679 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_1112
ATCAGTTCTAAGAGATGCCTGCCTTTCCCTACAGTCAGACTGAGTGTCCAGGACCAGCAGTAACAAGACCCAAGAAGGCG
GTGCAGAAGCTGCCACTCAGGATTCAGTGTTCTGTCAACTCAACAGGCTCCAGGTGGAAAGTCATGCACCAAAAAGAGAT
ATCAAATGGTTAATGGGGATCACGCAGTTCCAAAACCCATCAGAGGAGCTCAGGCCTAGTACCAGGGGGCAAAACATGGG
GTTTGGTTGCCTCCCTAGAAAGAAGCTCTATAGTCCAGAGTTTGTAGCTGACCCTGCTGCCCTGGTCAGCATCCCGTCAG
GCGAGAGAGTGACGTGCTGCCAACAGGGTGCTGGTGCAGTCTGGCTCAGAGAGTGCTGGTTTGACAGAGCCTGGGCAGCG
CCATCTAGAGAGGCCAGGGTGCTCTGACCTCTGCATATATGGACCCCAGAACCCCCATCCATCAAGTGAGCCCA
ORF - retro_cpor_1112 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 51.22 % |
| Parental protein coverage: | 56.69 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | VRSRRRPPFLTVKPSAQDQENQDPRT-LMEKSQLSIQRNFVDSAGPSSKATHQTEKSQR-SMAITQLRNP |
| ..S.R..PF.TV..S.QDQ..QDPR.....K..L.IQ...V.S.G...K..HQ.E.S....M.ITQ..NP | |
| Retrocopy | ISSKRCLPFPTVRLSVQDQQ*QDPRR<AVQKLPLRIQCS-VNSTGSRWKVMHQKEISNG<LMGITQFQNP |
| Parental | LEELRPSPGEQNSGLGPPPQTEAPGPIEFVADPVALATILSGEGVKSC-PMGRQSSLAQRVLVRESQGGT |
| .EELRPS...QN.G.G..P......P.EFVADP.AL..I.SGE.V..C.P.G...SLAQRVLV..S.G.. | |
| Retrocopy | SEELRPSTRGQNMGFGCLPRKKLYSP-EFVADPAALVSIPSGERVTCC<PTGCWCSLAQRVLV*QSLGSA |
| Parental | IRRGQVSRASAYLAPRTPMHQLGP |
| I.RGQ....SAY..PRTP.HQ..P | |
| Retrocopy | I*RGQGALTSAYMDPRTPIHQVSP |
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 | 0 .40 RPM |
| SRP017611_kidney | 0 .00 RPM | 0 .63 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .44 RPM |
| SRP040447_lung | 0 .03 RPM | 2 .47 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 0 .26 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1112 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1112 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 | ENSCPOG00000014679 | 1 retrocopy |
retro_cpor_1112 ,
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