RetrogeneDB ID: | retro_cpor_532 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_18:32096423..32096860(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | AIF1 | ||
| Ensembl ID: | ENSCPOG00000002068 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_532
GCCATGAGCCCAAACAGGGATTTACAGGGAGGAAAAGCCTGCAGACTGCTGAAGGCCCAGCAGAAAGACAGGCTGGAGGA
GATCAAGCAGCAACTCCTGGATGGTCCCTAATACAGCCCTGGTGAGGACCGGCCCTCCAAACTGGAAGCCTTCAAGAAGA
AATACGTGGAGTTCAACCTGAATGGAAATGGAGACATCGATATCATGTCCCTGAAGAGAATGCTGCAGAAATTTGGGGTC
CCCAAGACCCACTTAGAGCTAAAGAAATTAATTGGAGAGGTATCTGGTGGCTCTGGGGAGACGTTCAGCTACCTTGACTT
TCTCAGAATGATGCTGGGCAAGCGATCTGCCACCCTGAAAATGATCCTGATGTATGAAGAGAAAGAAAGAGAACAGGAGA
GGCCAACGGCCCCCCAGCCAAGAAAGCTACCTCTGAT
ORF - retro_cpor_532 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.63 % |
| Parental protein coverage: | 98.65 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | AMSQTRDFQGGKAFGLLKAQQEERLEEINKQFLDDPKYSTDEDLPSKLEAYKKKYMEFDLNGNGDIDIMS |
| AMS..RD.QGGKA..LLKAQQ..RLEEI..Q.LD.P.YS..ED.PSKLEA.KKKY.EF.LNGNGDIDIMS | |
| Retrocopy | AMSPNRDLQGGKACRLLKAQQKDRLEEIKQQLLDGP*YSPGEDRPSKLEAFKKKYVEFNLNGNGDIDIMS |
| Parental | LKRMLEKLGVPKTHLELKKLIGEVSGGSGETFSYPDFLRMMLGKRSAILKMILMYEEKAREQEKPT-GPP |
| LKRML.K.GVPKTHLELKKLIGEVSGGSGETFSY.DFLRMMLGKRSA.LKMILMYEEK.REQE.PT.GPP | |
| Retrocopy | LKRMLQKFGVPKTHLELKKLIGEVSGGSGETFSYLDFLRMMLGKRSATLKMILMYEEKEREQERPT<GPP |
| Parental | AKKAISE |
| AKKA.S. | |
| Retrocopy | AKKATSD |
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 .12 RPM | 7 .53 RPM |
| SRP017611_kidney | 0 .10 RPM | 18 .42 RPM |
| SRP017611_liver | 0 .04 RPM | 21 .46 RPM |
| SRP040447_lung | 0 .05 RPM | 24 .94 RPM |
| SRP040447_skeletal_muscle | 0 .03 RPM | 0 .87 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_532 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_532 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 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000002068 | 2 retrocopies |
retro_cpor_180, retro_cpor_532 ,
|