RetrogeneDB ID: | retro_mdom_1816 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 7:214572735..214573249(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSMODG00000011135 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_mdom_1816
GTCCAGCTGGTTGATGAGGAGTTGGACCATGCTCAGGAGCGAATGGCAACAGCTCTGTGGAACCTAGAAGTGGTAGAGAA
GGCAGCTGATGAGACAGAGAGCAATGAAAGCCATTGAAAATCAGGCCTGAAGAATGGAGAGAAAAGTGAGCTGCAAGAAA
CCCAGCTGAAAGTGATGAGTGTGCAGGGGAGGAAGGAGACAGGAAGGAAGAGGAGATGGCCAGCCAGTTGGTGATTATGG
AAACCTTCGAGTGTACAGGGGGGCCAGCCCAGCTGGCTGATCCCATTGCTGAGAGATGGGGGAGCAGAATAAATTGATGG
ACTAGAATGTTAAATTTCTGAATGCTAATGAAGAAAAGTATTCTCGAAAAGAAGACAAATATGAAGAGGAGATAAAGATT
CTTACTGAGAAACTCAAGGAGGCAGAGAAACACACCAAGTTTGCTGAGGGATTAGTGAAGCTGGAAAAGACAACTGAAGA
TTTGAAGGATGAGCTCTATGCCCCAAAACTGAAG
ORF - retro_mdom_1816 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 53.11 % |
| Parental protein coverage: | 61.62 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | IQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLK-EAKHIAEDADR |
| .QLV.EELD.AQER.ATAL..LE..EKAADE.E.......S...K..EK.E.QE.QLK.......E..DR | |
| Retrocopy | VQLVDEELDHAQERMATALWNLEVVEKAADETESNESH*KS-GLKNGEKSELQETQLK<SDECAGEEGDR |
| Parental | KYEEVARKLVIIESDLERAEERAELSE-GKCAELEEELKTVTNNLKSLEAQAEKYSQKEDKYEEEIKVLS |
| K.EE.A..LVI.E...E.....A.L.....C.E..E..K....N.K.L.A..EKYS.KEDKYEEEIK.L. | |
| Retrocopy | KEEEMASQLVIMET-FECTGGPAQLAD<SHC*EMGEQNKLMD*NVKFLNANEEKYSRKEDKYEEEIKILT |
| Parental | DKLKEAETRAEFAERSVTKLEKSIDDLEDELYAQKLK |
| .KLKEAE....FAE....KLEK...DL.DELYA.KLK | |
| Retrocopy | EKLKEAEKHTKFAE-GLVKLEKTTEDLKDELYAPKLK |
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 | 165 .09 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 117 .52 RPM |
| SRP007412_heart | 0 .00 RPM | 21805 .30 RPM |
| SRP007412_kidney | 0 .00 RPM | 235 .71 RPM |
| SRP007412_liver | 0 .00 RPM | 54 .88 RPM |
| SRP007412_testis | 0 .00 RPM | 106 .66 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_1816 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1816 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 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000011135 | 1 retrocopy |
retro_mdom_1816 ,
|
| Monodelphis domestica | ENSMODG00000014882 | 1 retrocopy |