RetrogeneDB ID: | retro_cpor_1518 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_91:6192523..6193255(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PRKAR2B | ||
| Ensembl ID: | ENSCPOG00000002372 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_1518
TCAGTATGTACAAAAGCATATAACCCTGATGAAGAAGATGTTGCAGAGTCCAGGATTACACATCCAAAAATCAATGATCA
AAGAAATAGATTGCAAGAAGCTTACAAAGACATCCTGCTCTTTAAGAACATGGATCCAGAACAGATGTCTCAAGTATTAG
ATGCCATGTTTGAAAAACTGGTCAAAAAATGGAACCATGTAATTGATCAAGGAGATGACAGTGACAACTTTTATGTAACT
GATAGATGAACTTTTGATATTTATATAAAATGTGATGGTGTTGGAAGATGAGTTGGTAATTGTGACAATTGTGGGAGTTT
GGGTGAACAGGCTTTAATGTACAACACACCCAGAGCAGCTACACTCACAGCTAACTCTCCTGGTGCTTTGTGTGGTTTGG
ACAGGGTAACTTCAGGAGAATAATTGTAAAAAACAATATCAAAAGAGAAAAATGCATGAAAGCTTTATTGAGTCTCTGCC
ATTCCTTAAATCTCTGAAGTCCCTGAAGGCCTAAAACTGGTAGATCTGATAGGCACCAAAGTATAGAACAATGGAGAACA
AATCATTTCTCAGGGAGATTTGGCTGATTCTTTTTTCATTGTAGTATTTGGAGAAGTAAAAATTACTATGAATAGAAAGG
GAAAATCAGAAGTGGAAGAGAACGGTGCAATAGAAATTGGTCAATGTTCCTGGGAATAGTACTTTAGAGAGCTTGCCAAC
AAACCTCGAGCC
ORF - retro_cpor_1518 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 79.76 % |
| Parental protein coverage: | 69.17 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | SVCAEAYNPDEEEDDAESRIIHPKTDDQRNRLQEACKDILLFKNLDPEQMSQVLDAMFEKLVKEGEHVID |
| SVC..AYNPDEE.D.AESRI.HPK..DQRNRLQEA.KDILLFKN.DPEQMSQVLDAMFEKLVK...HVID | |
| Retrocopy | SVCTKAYNPDEE-DVAESRITHPKINDQRNRLQEAYKDILLFKNMDPEQMSQVLDAMFEKLVKKWNHVID |
| Parental | QGDDGDNFYVIDRGTFDIYVKCDGVGRCVGNYDNRGSFGELALMYNTPRAATITATSPGALWGLDRVT-F |
| QGDD.DNFYV.DR.TFDIY.KCDGVGR.VGN.DN.GS.GE.ALMYNTPRAAT.TA.SPGAL.GLDRVT.F | |
| Retrocopy | QGDDSDNFYVTDR*TFDIYIKCDGVGR*VGNCDNCGSLGEQALMYNTPRAATLTANSPGALCGLDRVT<F |
| Parental | RRIIVKNNAK-KRKMYESFIESLPFLKSL-EVSERLKVVDVIGTKVYSDGEQIIAQGDLADSFFIVESGE |
| RRIIVKNN.K.KRKM.ESFIESLPFLKSL.EV.E.LK.VD.IGTKV...GEQII.QGDLADSFFIV..GE | |
| Retrocopy | RRIIVKNNIK<KRKMHESFIESLPFLKSL<EVPEGLKLVDLIGTKV*NNGEQIISQGDLADSFFIVVFGE |
| Parental | VKITMKRKGKSEAEENGAVEIARCSRGQYFGELALVTNKPRA |
| VKITM.RKGKSE.EENGA.EI..CS...YF.ELA...NKPRA | |
| Retrocopy | VKITMNRKGKSEVEENGAIEIGQCSWE*YFRELA---NKPRA |
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 | 50 .04 RPM |
| SRP017611_kidney | 0 .00 RPM | 42 .61 RPM |
| SRP017611_liver | 0 .00 RPM | 19 .06 RPM |
| SRP040447_lung | 0 .03 RPM | 51 .58 RPM |
| SRP040447_skeletal_muscle | 0 .00 RPM | 3 .88 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_1518 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_1518 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 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000002372 | 1 retrocopy |
retro_cpor_1518 ,
|
| Oryctolagus cuniculus | ENSOCUG00000012747 | 1 retrocopy |