RetrogeneDB ID: | retro_mdom_997 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 3:159037839..159038317(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PPIL1 | ||
| Ensembl ID: | ENSMODG00000013502 | ||
| Aliases: | None | ||
| Description: | peptidylprolyl isomerase (cyclophilin)-like 1 [Source:HGNC Symbol;Acc:9260] |
Retrocopy-Parental alignment summary:
>retro_mdom_997
GATTCTGGGCAGCTTCCCAATTTCTTCCTAGAAAATAGTATGAAGACTATTGTACTAGAGTTGTATTGGAAACTTGCCCC
AAAGATCTGTTAGTATTTTGAAGAATTGGCTTGATGTAGTTAATGTAATAGCTCCAGATTTTATTGGTTCATCAAAGACT
TCATGATATGGGGTGGTGATGCAACAGGAACAGACAGAGGTTGTGCATCTACTTATGGGAAGTAATTTAAAGATGAACTT
CATCCAGAATAGAAATTCAAGGGAGCTGGAAAGTTTGCAAGAACCAATGCAGGGCCAGATATAAATGGCAGCCAATTCTT
TGTGACTTTGGCTCCCTTCCAGTGGCTTGATGGAAGCACACTATTTTTTTTGGCCAGGTGTTCCAGGGCATGTGCTTGGT
GAATTAAGTGGAAAGGCAGAAAGAAATGCCCAGAACCATCTTGTCGATGAAATGGAGATTATCAAGGCCTACCCCTCC
ORF - retro_mdom_997 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 64.2 % |
| Parental protein coverage: | 93.53 % |
| Number of stop codons detected: | 6 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | DSWQPPNVFLETSMGTVVLELYWKHAPKTCKNFAELARRGYYNGTKFHRIIKDFMVQGGDPTGTGRGGAS |
| DS.Q.PN.FLE.SM.T.VLELYWK.APK.C..F.ELA.....N...F...IKDFM..GGD.TGT.RG.AS | |
| Retrocopy | DSGQLPNFFLENSMKTIVLELYWKLAPKIC*YFEELA*CS*CNSSRFYWFIKDFMIWGGDATGTDRGCAS |
| Parental | IYGKQFEDELHPELKFTGAGILAMANAGPDTNGSQFFVTLAPTQWLDG-KHT-IFGRVCQGIGMVNRV-G |
| .YGK.F.DELHPE.KF.GAG..A..NAGPD.NGSQFFVTLAP.QWLDG.KHT...G.V.QG...VN.V.G | |
| Retrocopy | TYGK*FKDELHPE*KFKGAGKFARTNAGPDINGSQFFVTLAPFQWLDG<KHTXXXGQVFQGMCLVN*V<G |
| Parental | MVETNAQDRPVDDVKIIKAYPS |
| ..E.NAQ...VD...IIKAYPS | |
| Retrocopy | KAERNAQNHLVDEMEIIKAYPS |
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 |
|---|---|---|
| SRP007412_brain | 0 .00 RPM | 0 .00 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 0 .00 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .00 RPM |
| SRP007412_kidney | 0 .00 RPM | 0 .00 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .00 RPM |
| SRP007412_testis | 0 .00 RPM | 0 .00 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_997 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_997 was not experimentally validated.