RetrogeneDB ID: | retro_mdom_1987 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | Un:84905549..84906020(-) | ||
| 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_1987
ATGCAGTTTATGTTGCTTTTTAGTCGTCAGGGGAAGCTCCGACTTCAGAAATGGTATGTCCCACTATTGGACAAAGAAAA
GAAAAAAATCACAAGGGAACTTGTTCAAACAGTTTTAGCCCATAAACCCAAAATGTGCAGCTTTTTGGAGTGGTGAGATC
TCAAGATTGTCTACAAAAGATATGCTAGCCTGTATTTCTGCTGTGCTATTGAAGATCAGGACAATGAACTAATTACCCTG
GAAATAATTCAGCGTTATGTTGAACTACTTGACAAATATTTTGGCAGCGTGTGTGAACTTGATATCATCTTTAATTTTGA
GAAGGCTTATTTTATTTTGGACGAGTTTCTTTTGGGAGGAGAAGTTCAGGAAACGTCCAAGAAAAATGTACTTAAAGCCA
TCGAGCAGGCAGATCTGCTACAAGAGGAAGCTGAAACCCCACATAGTGTTCTTGAAGAAATTGGACTGACA
ORF - retro_mdom_1987 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 96.82 % |
| Parental protein coverage: | 99.37 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MQFMLLFSRQGKLRLQKWYVPLSDKEKKKITRELVQTVLARKPKMCSFLEWRDLKIVYKRYASLYFCCAI |
| MQFMLLFSRQGKLRLQKWYVPL.DKEKKKITRELVQTVLA.KPKMCSFLEW.DLKIVYKRYASLYFCCAI | |
| Retrocopy | MQFMLLFSRQGKLRLQKWYVPLLDKEKKKITRELVQTVLAHKPKMCSFLEW*DLKIVYKRYASLYFCCAI |
| Parental | EDQDNELITLEIIHRYVELLDKYFGSVCELDIIFNFEKAYFILDEFLLGGEVQETSKKNVLKAIEQADLL |
| EDQDNELITLEII.RYVELLDKYFGSVCELDIIFNFEKAYFILDEFLLGGEVQETSKKNVLKAIEQADLL | |
| Retrocopy | EDQDNELITLEIIQRYVELLDKYFGSVCELDIIFNFEKAYFILDEFLLGGEVQETSKKNVLKAIEQADLL |
| Parental | QEEAETPRSVLEEIGLT |
| QEEAETP.SVLEEIGLT | |
| Retrocopy | QEEAETPHSVLEEIGLT |
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_1987 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1987 was not experimentally validated.