RetrogeneDB ID: | retro_mdom_646 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 1:669301730..669302414(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TXNDC15 | ||
| Ensembl ID: | ENSMODG00000014348 | ||
| Aliases: | None | ||
| Description: | thioredoxin domain containing 15 [Source:HGNC Symbol;Acc:20652] |
Retrocopy-Parental alignment summary:
>retro_mdom_646
CTAACTTCTTCTGGAACCAATATTCCTAATAATGGAGAAGAATATAATTTGGTTCTTGAAGCTGTGCCCACAAACCCATC
ATCTAAAGAAGACTCTAATAGTACAGCCAATGTAAAGACTCCACAGGTGAATTGTGAGGAGAGAAATGTTATGGGCTTAG
AAAGTTTCACTTTATAAATTCTAAATGTTTCACAGGACCTGATGGAATTTTTAAACCCAAACAGTAGTGATTGTACATTA
GACTTATTTTATACTCCTTGGTGTCGTTTCGCTGCCAGTCTGGCCCCACATTTTAATTCTTTACTATGAACATTTCCATC
TCTTCATTTTTTGGCATTGAATGCTTCTCAGCACAGCAGTCTGTCTACCCGGTTTGGTACTGTGGCTGTTCCCAACATCT
TGCTATTTCAACGAGCTAAACCAATGGCAAGATTTAATCATACAGATCGGACTCTGGAAACTCTAAAAGCCTTCACTTTT
AATCAGACAGGGATAGAAGCCAGAAATTATGTGGTAGTGACTGAAGATGACCAAAGAGGCCCTCTTTCCAGCACCTTGGT
GAAAAGTGTGGATTGGTTGCTTGTATTTTCTTTATTCTTTTTAATTAGTTTTATTATGTATGCTACTGTTTGGACTGAAA
GTATTCGATGGCTCATTCCAGGACAAGAACATGGACATACTGAA
ORF - retro_mdom_646 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.35 % |
| Parental protein coverage: | 67.26 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LTTSGTNIPDKGEEYNLVLEAVPTSPSSKEDSNSTDNVKTPKVNCEERNVTGLESFTLQILNVSQDLMEF |
| LT.SGTNIP..GEEYNLVLEAVPT.PSSKEDSNST.NVKTP.VNCEERNV.GLESFTL.ILNVSQDLMEF | |
| Retrocopy | LTSSGTNIPNNGEEYNLVLEAVPTNPSSKEDSNSTANVKTPQVNCEERNVMGLESFTL*ILNVSQDLMEF |
| Parental | LNPNSSDCTLVLFYTPWCRFSASLAPHFNSLPRAFPSLHFLALDASQHSSLSTRFGTVAVPNILLFQGAK |
| LNPNSSDCTL.LFYTPWCRF.ASLAPHFNSL...FPSLHFLAL.ASQHSSLSTRFGTVAVPNILLFQ.AK | |
| Retrocopy | LNPNSSDCTLDLFYTPWCRFAASLAPHFNSLL*TFPSLHFLALNASQHSSLSTRFGTVAVPNILLFQRAK |
| Parental | PMARFNHTDRTLETLKAFIFNQTGIEARNDVVVTEDDQIGPLPSTLVKSVDWLLVFSLFFLISFIMYATV |
| PMARFNHTDRTLETLKAF.FNQTGIEARN.VVVTEDDQ.GPL.STLVKSVDWLLVFSLFFLISFIMYATV | |
| Retrocopy | PMARFNHTDRTLETLKAFTFNQTGIEARNYVVVTEDDQRGPLSSTLVKSVDWLLVFSLFFLISFIMYATV |
| Parental | RTESIRWLIPGQEHEHPE |
| .TESIRWLIPGQEH.H.E | |
| Retrocopy | WTESIRWLIPGQEHGHTE |
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 | 193 .46 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 119 .16 RPM |
| SRP007412_heart | 0 .00 RPM | 153 .70 RPM |
| SRP007412_kidney | 0 .00 RPM | 161 .97 RPM |
| SRP007412_liver | 0 .00 RPM | 194 .85 RPM |
| SRP007412_testis | 0 .00 RPM | 83 .29 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_646 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_646 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 2 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000014348 | 3 retrocopies |
retro_mdom_1644, retro_mdom_646 , retro_mdom_759,
|
| Tupaia belangeri | ENSTBEG00000015609 | 1 retrocopy |