RetrogeneDB ID: | retro_mdom_1092 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 3:66844828..66845522(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMODG00000003400 | |
| 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_1092
ATGGCTGGGGATGCCAGAGGTCACAGTTGCCCAGGCTCAGAGATTCTCCTGCACCCTGAGCTGCTGACCCAAGAGTTCCT
GCTACTCCTGCTCCTGCTGGAGTGGAAGAATATAGTTGTTGAAGAGGACATAAAGATCGACAAAGATGACTTTACTGACC
TCTATGTTCAATATGCCATACCACTGTCTCAAAGGAATTACCAAAAAGTAGATGGAGGAAAATGATGGAAAAGAAAAGAG
GGCAAAATGAATTGAAAAATGAGCATAAAAGGGGTATGAGTGTGGAAGGTTTACATAAAAGGCCCCTCATTGTCTTTGAT
GGAAATTCAACAAGTACAAGCATAAAAGTGAGAAAGACTGAAAATGGAACTAAAGATCTTCTGAAACCTTCTCCATCAGT
ACACATTACTAACAATACCTTTAGGAAGTTTCTACATGCAAACACTTCCTCCCTTATCCTGCCTTTTACCTTACCTACAG
ACCTTAAAGTGGAAAGCAGTAATAACACTAAACTGAACCACGTGTTAATGACTAGTAGGTGTACACTGGCCAATGTAAAA
TCGCCACCATTATCTCTTGTTGAGGGAACTACTGTTGTGAAATTAAAGAAAACTGCTCCAAAAGAAGAAGCAGAATCAGT
GAGTGAATTAAAGCCCACAGAAGCAAAGAGAAGATCCAACATGTTACATGGCCG
ORF - retro_mdom_1092 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.21 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MAGDAGGRGCPGSEMLLHPELLSQEFLLLTL--EQKNIVVEEEIKINKDDLTDFYVQHAIPLPQR-ELPK |
| MAGDA.G..CPGSE.LLHPELL.QEFLLL.L..E.KNIVVEE.IKI.KDD.TD.YVQ.AIPL.QR.ELPK | |
| Retrocopy | MAGDARGHSCPGSEILLHPELLTQEFLLLLLLLEWKNIVVEEDIKIDKDDFTDLYVQYAIPLSQR<ELPK |
| Parental | SRWGKMMEKKRGQNELKNEHKRNMSVESLRKRPLIVFDGNSTSTSIKVRKTENGTNDRLKPPPSVGVTNN |
| SRW....................MSVE.L.KRPLIVFDGNSTSTSIKVRKTENGT.D.LKP.PSV..TNN | |
| Retrocopy | SRWXXXXXXXXXXXXXXXXXXXGMSVEGLHKRPLIVFDGNSTSTSIKVRKTENGTKDLLKPSPSVHITNN |
| Parental | TFRKLPHSNTSSLILPSTLPTDIKVESNNDTKQNHVLMTSRSTLANVKSPPLSPVGGTTVVKLKRTAPKE |
| TFRK..H.NTSSLILP.TLPTD.KVES.N.TK.NHVLMTSR.TLANVKSPPLS.V.GTTVVKLK.TAPKE | |
| Retrocopy | TFRKFLHANTSSLILPFTLPTDLKVESSNNTKLNHVLMTSRCTLANVKSPPLSLVEGTTVVKLKKTAPKE |
| Parental | EAESVSDCKPTEAKR-KIQHVTWP |
| EAESVS..KPTEAKR.KIQHVTWP | |
| Retrocopy | EAESVSELKPTEAKR<KIQHVTWP |
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_1092 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1092 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,
|