RetrogeneDB ID: | retro_cpor_687 | ||
Retrocopy location | Organism: | Guinea Pig (Cavia porcellus) | |
| Coordinates: | scaffold_23:472856..473425(-) | ||
| Located in intron of: | ENSCPOG00000006976 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | GNB2L1 | ||
| Ensembl ID: | ENSCPOG00000008724 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cpor_687
AAAACCATAAAATTATGGAATACACTGGGTGTATGCAAATACACTGTCCAGGATGAGAGTCACTCAGAGTGGGTGTCTTG
CGTCCGTTTCTTGCCCAACAGCAGCAACCCTATCATTGTCTCCTATGGCTGGAACAAGCTGGTCAAGGTATGGAATTTGG
CAAACTGCAAGGTAAAGACCAACCACATTGGCCATACTGGCTATCTGAACACTGTGACCGCTTCTCCAGATGGATTCATG
TGTGCTTCTGGAGGCAAGGATGGCCAGGCTATGCTGTGGGATCTCAATGAAGGCAAACATCTTTATATATTAGATGGAGA
AGACATCATCAATGTCCTGTGCTTCAGCCCTAACCGCTATTGGCTCTGTACTGCCACTTGCCTCAGCATCAAGATCTAGG
ACTTGGAGGGCAAGATAATCATGGATGAACTGAAGCAAGAAGTTATAAGTACCAGCATCAAGGCAGAGCCCCTCAACGCA
CCTCTCTGGCCTGGTCTTCTGGTGGCCAGACTCTGTTTGCTGGCTACACAGATAACCTGGTGCGAGTGTGGCAGGTGACT
ATTGGCACT
ORF - retro_cpor_687 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.53 % |
| Parental protein coverage: | 55.23 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | KTIKLWNTLGVCKYTVQDESHSEWVSCVRFSPNSSNPIIVSCGWDKLVKVWNLANCKLKTNHIGHTGYLN |
| KTIKLWNTLGVCKYTVQDESHSEWVSCVRF.PNSSNPIIVS.GW.KLVKVWNLANCK.KTNHIGHTGYLN | |
| Retrocopy | KTIKLWNTLGVCKYTVQDESHSEWVSCVRFLPNSSNPIIVSYGWNKLVKVWNLANCKVKTNHIGHTGYLN |
| Parental | TVTVSPDGSLCASGGKDGQAMLWDLNEGKHLYTLDGGDIINALCFSPNRYWLCAATGPSIKIWDLEGKII |
| TVT.SPDG..CASGGKDGQAMLWDLNEGKHLY.LDG.DIIN.LCFSPNRYWLC.AT..SIKI.DLEGKII | |
| Retrocopy | TVTASPDGFMCASGGKDGQAMLWDLNEGKHLYILDGEDIINVLCFSPNRYWLCTATCLSIKI*DLEGKII |
| Parental | VDELKQEVISTSSKAEP-PQCTSLAWSADGQTLFAGYTDNLVRVWQVTIGT |
| .DELKQEVISTS.KAEP.PQ.TSLAWS..GQTLFAGYTDNLVRVWQVTIGT | |
| Retrocopy | MDELKQEVISTSIKAEP<PQRTSLAWSSGGQTLFAGYTDNLVRVWQVTIGT |
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 | 121 .76 RPM |
| SRP017611_kidney | 0 .00 RPM | 255 .65 RPM |
| SRP017611_liver | 0 .00 RPM | 200 .83 RPM |
| SRP040447_lung | 0 .00 RPM | 402 .02 RPM |
| SRP040447_skeletal_muscle | 0 .03 RPM | 507 .50 RPM |
Cavia porcellus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cpor_687 retrocopy.
Cavia porcellus was not studied using FANTOM5 data.
retro_cpor_687 was not experimentally validated.