RetrogeneDB ID: | retro_cpor_1497 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_9:28591509..28591941(-) | ||
| Located in intron of: | ENSCPOG00000013843 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | C16ORF96 | ||
| Ensembl ID: | ENSCPOG00000023268 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_1497
CCACAGCTGATCACCATTCGTAAGAGTCTATCTACTGTTGAGGCTGGGGGCAGCCATTGCCAAACAGCTATGAGTACCTG
TAGTGTCAGCAGATGAGGGCATGTTAGCAGCTGCTGTTACAGGAGCTTGGCATCCCAGAGGAAAGCCTGTATGCCCTGGT
TCCCACCAGGATTGGCATGACAGCCTTGAAATGATGCCAGCATCAAGCTCCAGTCTTGTAATCTTTCAACTCTTTCCATT
TATGGGGATCCTCAGGTGATAGACTATGACACTACTAAGGTGGACAAGCTAGGGTGGATGGGCTGCAGTACAAAGATTGG
AACAACCAGATTGGGACTCAACCCTTGGCCGTTGAGGAAAGAGCTAGTTTTGAAGATTCCATGTCCCCAGGCTCAAAATA
CGTATGACCATGTGCCCTATAGTTCCTTAATT
ORF - retro_cpor_1497 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 54.25 % |
| Parental protein coverage: | 54.65 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | PQLITIR-RAHLLSRLRPASA-NSYEYLQRQQMREQHQLHFQHLSTTEDSFDPL-SSHQDWNDG-PRNDP |
| PQLITIR.R..LL.RL..A.A.NSYEYL..QQMR...QL..Q.L...E.S...L..SHQDW.D..P.ND. | |
| Retrocopy | PQLITIR>RVYLLLRLGAAIA>NSYEYL*CQQMRAC*QLLLQELGIPEESLYAL<GSHQDWHDS<P*NDA |
| Parental | NLKLKSYNLSTLYPYGDPQVIDYDTAEVDILG-VDGILYKGRMTNQTGTRLLATGEKEPAVMKIPCPPG- |
| ..KL.S.NLSTL..YGDPQVIDYDT..VD.LG.VDG..YK....NQ.GT..LA..E...A.......PG. | |
| Retrocopy | SIKLQSCNLSTLSIYGDPQVIDYDTTKVDKLG<VDGLQYKD-WNNQIGTQPLAVEER--ASFEDSMSPG> |
| Parental | QSLCDRVRSSALV |
| Q...D.V..S.L. | |
| Retrocopy | QNTYDHVPYSSLI |
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 .15 RPM |
| SRP017611_kidney | 0 .42 RPM | 0 .10 RPM |
| SRP017611_liver | 0 .13 RPM | 0 .09 RPM |
| SRP040447_lung | 0 .03 RPM | 1 .01 RPM |
| SRP040447_skeletal_muscle | 0 .03 RPM | 0 .18 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1497 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1497 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 | ENSCPOG00000023268 | 1 retrocopy |
retro_cpor_1497 ,
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