RetrogeneDB ID: | retro_mdom_640 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 1:643331972..643332710(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PCMTD1 | ||
| Ensembl ID: | ENSMODG00000009645 | ||
| Aliases: | None | ||
| Description: | protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1 [Source:HGNC Symbol;Acc:30483] |
Retrocopy-Parental alignment summary:
>retro_mdom_640
GAACTTCACTCAGATGTGGTGGAATATGCCAAGGAAAAACTCGAGATCTTCATCAAAAATAGTGATAGTTATGACAAATT
TGAGTTCTCTGAACCAGCATTTGTGGCAGGTAACTGCCTAGAGATAGCATCCGATAGCCATCAGTATGACCGGATTTATT
GTGGAGCTGGTGTCCAGAAAGACCATGAAAACTACATGAAAATATTATTGAAAGTGGGAGGTATTCTAGTCATGCCTATA
GAAGATCAGTTAACTCAAATTATGCAAACTGGACAGAATACTTGGGAAAGGAAAAGCATCCTTGCTGTTTCTTTCACTCC
ATTAATACAACCAAATAGAAATGACAATAGCAAACCAGATTCAGTGGGATTACCTCCTTGTGCTGTCAGGAATCTTCAAG
GCTTGGTTTGGATTTATATTCTACATACACTTAGAAACTTCATAAATGATGAGATGCAAGCCAAGGGTATTTCTCAGAGG
GCTCCTCCCAAAAGAAAAAGGAAGAGCGTTAAACAAAGAATCAATGCATATGTGTTTGTAGGCAATCAACTTATTCCTCA
GCCTCTAGACAGTGAGGATGATGAAAAAATGGAAGAAGACCACAAAGAAGAGGAAGAGAAAGACCAGGGTGAAACCTTGA
AGCCAGAGGAACCCCCTCAGAATCTATTGAGAGGGAAAATCATGTGAATACCCCTGCCAGAGTCTTTAAAAGTGTATTTG
ACCTATTTTAGAGATAAA
ORF - retro_mdom_640 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.28 % |
| Parental protein coverage: | 68.91 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ELHSDVVEYAKEKLESFIKNSDSFDKFEFCEPAFVVGNCLEIASDSHQYDRIYCGAGVQKDHENYMKILL |
| ELHSDVVEYAKEKLE.FIKNSDS.DKFEF.EPAFV.GNCLEIASDSHQYDRIYCGAGVQKDHENYMKILL | |
| Retrocopy | ELHSDVVEYAKEKLEIFIKNSDSYDKFEFSEPAFVAGNCLEIASDSHQYDRIYCGAGVQKDHENYMKILL |
| Parental | KVGGILVMPIEDQLTQIMRTGQNTWESKNILAVSFAPLIQPNRNDNSKPDSVGLPPCAVRNLQDLARIYI |
| KVGGILVMPIEDQLTQIM.TGQNTWE.K.ILAVSF.PLIQPNRNDNSKPDSVGLPPCAVRNLQ.L..IYI | |
| Retrocopy | KVGGILVMPIEDQLTQIMQTGQNTWERKSILAVSFTPLIQPNRNDNSKPDSVGLPPCAVRNLQGLVWIYI |
| Parental | RRTLRNFINDEMQAKGISQRAPPKRKRKRVKQRINTYVFVGNQLIPQPLDSEDDEKMEEDHKEEEEKDQG |
| ..TLRNFINDEMQAKGISQRAPPKRKRK.VKQRIN.YVFVGNQLIPQPLDSEDDEKMEEDHKEEEEKDQG | |
| Retrocopy | LHTLRNFINDEMQAKGISQRAPPKRKRKSVKQRINAYVFVGNQLIPQPLDSEDDEKMEEDHKEEEEKDQG |
| Parental | ETLKPEEPPQNLLREKIMRLPLPESLKAYLTYFRDK |
| ETLKPEEPPQNLLR.KIM..PLPESLK.YLTYFRDK | |
| Retrocopy | ETLKPEEPPQNLLRGKIM*IPLPESLKVYLTYFRDK |
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_640 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_640 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 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Cavia porcellus | ENSCPOG00000006593 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000009645 | 1 retrocopy |
retro_mdom_640 ,
|
| Oryctolagus cuniculus | ENSOCUG00000016958 | 2 retrocopies |