RetrogeneDB ID: | retro_mdom_1441 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 5:71942087..71942557(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | AP1S2 | ||
| Ensembl ID: | ENSMODG00000017197 | ||
| Aliases: | None | ||
| Description: | adaptor-related protein complex 1, sigma 2 subunit [Source:HGNC Symbol;Acc:560] |
Retrocopy-Parental alignment summary:
>retro_mdom_1441
ATTCAGTTTATGTTGCTTTTTAGTCATCAGGGGAAGCTCCGACTTCAGAAATGGTATGTCCCACTATTGGACAAAGGAAA
GAAAAAAACCACAAGGGAACTTGTTCAAAGAGTTTTAACCCATAAACCTAAAATGTGCAGCTTTTTGGAGTGGTGAGATC
TCAAGATTGTCTACAAAAGATATGGAGCCTGCATTTCTGCTGTGCTATTGAAGATCAGGACAATGAACTAATTACCCTGG
AAATAATTCATCGTTACGTTGAACTACTTGACAAATATTTTGACAGCGTGTGTGAACTTGATATCATCTTTAATTTTGAG
AAGGCTTATTTAATTTTGGACGAGTTTCTTTTGGGAGGAGAAGTTCAGGAAACGTCCAAGAAAAATGTACTTAAAGCTAT
CGAGCAGCCAGATCTTCTACAAGAGGAAGCTGAAACCCCACGTAGTGTTCTTGAAGAAATTGGACTGACA
ORF - retro_mdom_1441 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.51 % |
| Parental protein coverage: | 99.37 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MQFMLLFSRQGKLRLQKWYVPLSDKEKKKITRELVQTVLARKPKMCSFLEWRDLKIVYKRYA-SLYFCCA |
| .QFMLLFS.QGKLRLQKWYVPL.DK.KKK.TRELVQ.VL..KPKMCSFLEW.DLKIVYKRY..SL.FCCA | |
| Retrocopy | IQFMLLFSHQGKLRLQKWYVPLLDKGKKKTTRELVQRVLTHKPKMCSFLEW*DLKIVYKRYG<SLHFCCA |
| Parental | IEDQDNELITLEIIHRYVELLDKYFGSVCELDIIFNFEKAYFILDEFLLGGEVQETSKKNVLKAIEQADL |
| IEDQDNELITLEIIHRYVELLDKYF.SVCELDIIFNFEKAY.ILDEFLLGGEVQETSKKNVLKAIEQ.DL | |
| Retrocopy | IEDQDNELITLEIIHRYVELLDKYFDSVCELDIIFNFEKAYLILDEFLLGGEVQETSKKNVLKAIEQPDL |
| Parental | LQEEAETPRSVLEEIGLT |
| LQEEAETPRSVLEEIGLT | |
| Retrocopy | LQEEAETPRSVLEEIGLT |
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_1441 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1441 was not experimentally validated.