RetrogeneDB ID: | retro_mdom_1870 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 8:165086049..165086737(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMODG00000015979 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSMODG00000002508 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_mdom_1870
ATGGCTGGGGATGCGGGAGGTCGTGGTTGCCCAGGCTCGGAGATGCTCCTGCACCCGGAGCTGCTCTCCCAGGACTTCCT
GCTGCTCACGCTGGAGCAGAAGAATATAGTTGTTGAAGAGGAAATAAAGATCAACAAAGATGACCTTACCGATTTCTGTG
TTCAACATGCCATACCATTGCCTCAAAGGGAATTACCAAAAAGTAGATGGGGGAAAATGATGGAAAAGAAAAGAGGGCAA
AATGAATTGAAAAATGAGCATAAAAGGGATATGAGTGTGGAAAGTTTACGGAAAAGACCCCTCGTTGTCTGATGGAAATT
CAACAAGTACAAGCATAAAAGTGAGAAAGACTGAAAATGGAACTAATGATCTTCTAAAACCTCCTCCATCAGTAGGCATT
ACTAACAATACCTTTAGGAAGTTACCACATTCAAACACTTCCTCCCTTATTCTGCCTTCTACCTTGCCTACAGACATTAA
AGTGGAAAGCAATAATGACACTAAACAGAACTATGTGTTAATGACTAGTAGGAGTACACTGGCCAATGTAAAATCACCAC
CATTATCTCCTGTTGGGGGAACTACTGTTGTGAAATTAAAGAGAACTGCTCCAAAAGAAGAAGCAGAATCAGTGAGTGAC
TTCAAGCCCACAGAAGCAAAAAGGAAGATCCAGCATGTTACATGGCCG
ORF - retro_mdom_1870 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.37 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAGDAGGRGCPGSEMLLHPELLSQEFLLLTLEQKNIVVEEEIKINKDDLTDFYVQHAIPLPQRELPKSRW |
| MAGDAGGRGCPGSEMLLHPELLSQ.FLLLTLEQKNIVVEEEIKINKDDLTDF.VQHAIPLPQRELPKSRW | |
| Retrocopy | MAGDAGGRGCPGSEMLLHPELLSQDFLLLTLEQKNIVVEEEIKINKDDLTDFCVQHAIPLPQRELPKSRW |
| Parental | GKMMEKKRGQNELKNEHKRNMSVESLR-KRPLIVFDGNSTSTSIKVRKTENGTNDRLKPPPSVGVTNNTF |
| GKMMEKKRGQNELKNEHKR.MSVESLR.K.P....DGNSTSTSIKVRKTENGTND.LKPPPSVG.TNNTF | |
| Retrocopy | GKMMEKKRGQNELKNEHKRDMSVESLR>KDPSLS-DGNSTSTSIKVRKTENGTNDLLKPPPSVGITNNTF |
| Parental | RKLPHSNTSSLILPSTLPTDIKVESNNDTKQNHVLMTSRSTLANVKSPPLSPVGGTTVVKLKRTAPKEEA |
| RKLPHSNTSSLILPSTLPTDIKVESNNDTKQN.VLMTSRSTLANVKSPPLSPVGGTTVVKLKRTAPKEEA | |
| Retrocopy | RKLPHSNTSSLILPSTLPTDIKVESNNDTKQNYVLMTSRSTLANVKSPPLSPVGGTTVVKLKRTAPKEEA |
| Parental | ESVSDCKPTEAKRKIQHVTWP |
| ESVSD.KPTEAKRKIQHVTWP | |
| Retrocopy | ESVSDFKPTEAKRKIQHVTWP |
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_1870 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1870 was not experimentally validated.
Retrocopy orthology:
Monodelphis domestica 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 1 parental gene, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000002508 | 3 retrocopies |
retro_mdom_1092, retro_mdom_1870 , retro_mdom_41,
|