RetrogeneDB ID: | retro_mdom_1375 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 4:177698704..177699365(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMODG00000007590 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | METTL22 | ||
| Ensembl ID: | ENSMODG00000005792 | ||
| Aliases: | None | ||
| Description: | methyltransferase like 22 [Source:HGNC Symbol;Acc:28368] |
Retrocopy-Parental alignment summary:
>retro_mdom_1375
AAATAGGTGTGGAGAGGAGCTTTCCTTCTGGCTGATTACATCCTGTTCCAACGTGACCTGTTCAAAAGTTGCACTGTGCT
CAAACTTGGGGCAGGCACTGGGATTGCCAGCATCATCACAGCAACAGTTGCTAAGACTGTTTACTGCACAGATGTGGGTG
AAGATCTCCTCACTATATCTGAACAGAATGTTGCCCTGAACAGGCACCTGACTTCAACAGGAGGTGGTCTAGTTATGGTT
AAAGAATTGGATTGGCTAAAAGATGACTTGTGTACTGATCCTCAAGTTCCTTTCAGTTGGTCTGAAGATGAGATTTCTGA
CTTATATGCTCATACTACTATCATAATGGCAGCTGATGTTTTTTATGATGATGACCTCACAGATGCTTTATTTAAAACAC
TACAGAATTACTCACAGTTTGAAAAATGCTTCTACAATCTTCTTATCAATAGAAAAAAAACGAAACTTCACACTTAGACA
ATTGGACATTACATGTGAAGCTTACAATCATTTTTGATTTTCCCTAAATGATCTAGAGAAACTCAGAGATGGCAAAATGA
AGTTTATTGTAGAGCCAATTGAAGCTACTTTCCCCCAGTTCCTTGTTTATGAACATATAGAGCCGTTGGAACTCTGGAAG
ATTATTGCTGCACCAATAAGT
ORF - retro_mdom_1375 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.19 % |
| Parental protein coverage: | 54.7 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | KQVWRGAFLLADYILFQRDLFKSCTVLELGAGTGIASIITATVAKTVYCTDVGEDLLTMCERNVALNKHL |
| K.VWRGAFLLADYILFQRDLFKSCTVL.LGAGTGIASIITATVAKTVYCTDVGEDLLT..E.NVALN.HL | |
| Retrocopy | K*VWRGAFLLADYILFQRDLFKSCTVLKLGAGTGIASIITATVAKTVYCTDVGEDLLTISEQNVALNRHL |
| Parental | TSTGGGVVMVKELDWLKDDLCTDPQVPFSWSEDEISDLYAHTTIIMAADVFYDDD-LTDALFKTLYRITH |
| TSTGGG.VMVKELDWLKDDLCTDPQVPFSWSEDEISDLYAHTTIIMAADVFY.DD.....L....YRITH | |
| Retrocopy | TSTGGGLVMVKELDWLKDDLCTDPQVPFSWSEDEISDLYAHTTIIMAADVFY-DD>TSQMLYLKHYRITH |
| Parental | SLKNASTIFLSIEKRLNFTLRQLDITCEAYNHFRFSLNDLEKLRDGKMKFIVEPIEATFPQFLVYERIEQ |
| SLKNASTIFLSI....NFTLRQLDITCEAYNHF.FSLNDLEKLRDGKMKFIVEPIEATFPQFLVYE.IE. | |
| Retrocopy | SLKNASTIFLSIXXXRNFTLRQLDITCEAYNHF*FSLNDLEKLRDGKMKFIVEPIEATFPQFLVYEHIEP |
| Parental | LELWKIIAAPIS |
| LELWKIIAAPIS | |
| Retrocopy | LELWKIIAAPIS |
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_1375 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1375 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 | ENSMODG00000005792 | 1 retrocopy |
retro_mdom_1375 ,
|
| Sarcophilus harrisii | ENSSHAG00000000726 | 1 retrocopy |