RetrogeneDB ID: | retro_mdom_921 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 2:450539194..450540201(-) | ||
| Located in intron of: | ENSMODG00000006241 | ||
Retrocopy information | Ensembl ID: | ENSMODG00000006251 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SNX16 | ||
| Ensembl ID: | ENSMODG00000006200 | ||
| Aliases: | None | ||
| Description: | sorting nexin 16 [Source:HGNC Symbol;Acc:14980] |
Retrocopy-Parental alignment summary:
>retro_mdom_921
ATGGCAACTCCATATATCCCTGTGCCTATTCCTGTAGGAAATTCTTCATCAAATTTTACAACAAACAGAAGCCAAAGAAG
TTCTTCTTTTGGGAGTATTTCAACAAGTTCAAATTCTTCCAAAGGCCAACCAGAAGACTCTAATGTGGGTAGTTACAAAA
AGACAACTATGCCTGATCAGATGGATAACAATTCATCTATGTGTAGCAGCCCTCTAATTAGGACTAAATTTACAGGTATA
GAATCTTCCATTGAATATTCTACTAGGCCAGTAGAAAATGAAGACCAAAGTACAGAATCTGTGAACTGGGAAGAAAGACC
TTCTACACCTACTATATTGGGTTATGAGGTGATGGAAGAAAGGGCTAAATTTACTGTATATAAAGTGCTAATAAGAAGAA
GCCCAGAAGAAAGCTGGGTTGTTTTCAGAAGGTATACTGATTTCTCTAGGCTGAATGACAAATTAAAGGACATGTTTCCA
GGCTTTCGGCTGGCCCTTCCACCAAAACACTGGTTCAAAGACAATTATAATGCTGATTTCTTAGAAGATAGACAGCTGGG
ACTTCAGGCATTCCTACAGAATTTAGTAGCTCATAAAGACATTGCTAACTGCCTTGCAGTAAGAGAATTTCTTTGGATGA
TCCACCAGGTCCATTTGATAGCTTAGAAGAAAGCAGGGCTTTCTGTGAAACTCTAGAAGAAACAAACTATCAATTACAAA
AAGAGCTACTTGAAAAACAAAAAGAGGTGGAATCACTGAAGAAATTGCTAAATGAGAAACAACTGCATATAGACACTATA
GAGAACAGAATTATGTTATTGTCCTTAGAACATGAAGAAACACTTAGAATTTCAAGAGAAGGTGAATGTATCCGAAAGAT
AGAGTCTTCTGCAATTGAAGCAGATCAAGATAGCTTGGATGAAAAAAACAGGTCTGATAAGGTTCCCAAGAGTGGCTGGA
CTGATTGTGAATCTGAAAAATCAATAACTGAAGTGGAGGTAGCTGAA
ORF - retro_mdom_921 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.04 % |
| Parental protein coverage: | 97.12 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MATPYVPVPIPVGNSSSNFTTNRSQRSSSFGSISTSSNSSKGQPEDSNVGSYKKTSMPDQMDNNSSMCSS |
| MATPY.PVPIPVGNSSSNFTTNRSQRSSSFGSISTSSNSSKGQPEDSNVGSYKKT.MPDQMDNNSSMCSS | |
| Retrocopy | MATPYIPVPIPVGNSSSNFTTNRSQRSSSFGSISTSSNSSKGQPEDSNVGSYKKTTMPDQMDNNSSMCSS |
| Parental | PLIRTKFTGIESSIEYSTRPVENEDQSTESVNWEERPSTPTILGYEVMEERAKFTVYKVLIRRSPEESWV |
| PLIRTKFTGIESSIEYSTRPVENEDQSTESVNWEERPSTPTILGYEVMEERAKFTVYKVLIRRSPEESWV | |
| Retrocopy | PLIRTKFTGIESSIEYSTRPVENEDQSTESVNWEERPSTPTILGYEVMEERAKFTVYKVLIRRSPEESWV |
| Parental | VFRRYTDFSRLNDKLKDMFPGFRLALPPKRWFKDNYNADFLEDRQLGLQAFLQNLVAHKDIANCLAVREF |
| VFRRYTDFSRLNDKLKDMFPGFRLALPPK.WFKDNYNADFLEDRQLGLQAFLQNLVAHKDIANCLAVREF | |
| Retrocopy | VFRRYTDFSRLNDKLKDMFPGFRLALPPKHWFKDNYNADFLEDRQLGLQAFLQNLVAHKDIANCLAVREF |
| Parental | LCL-DDPPGPFDSLEESRAFCETLEETNYRLQKELLEKQKEVESLKKLLNEKQLHIDTIENRIRLLSLEH |
| L...D.P.GPFDSLEESRAFCETLEETNY.LQKELLEKQKEVESLKKLLNEKQLHIDTIENRI.LLSLEH | |
| Retrocopy | LWM<DPP-GPFDSLEESRAFCETLEETNYQLQKELLEKQKEVESLKKLLNEKQLHIDTIENRIMLLSLEH |
| Parental | EETLRISREGECIRKIESSAIEADQDSLDEKNRSDKVPKSGWTDCESEKSITEVEVAE |
| EETLRISREGECIRKIESSAIEADQDSLDEKNRSDKVPKSGWTDCESEKSITEVEVAE | |
| Retrocopy | EETLRISREGECIRKIESSAIEADQDSLDEKNRSDKVPKSGWTDCESEKSITEVEVAE |
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_921 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_921 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 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000006200 | 1 retrocopy |
retro_mdom_921 ,
|