RetrogeneDB ID: | retro_mdom_1314 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 4:412492659..412493077(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MED22 | ||
| Ensembl ID: | ENSMODG00000012748 | ||
| Aliases: | None | ||
| Description: | mediator complex subunit 22 [Source:HGNC Symbol;Acc:11477] |
Retrocopy-Parental alignment summary:
>retro_mdom_1314
ATGGCCCAACAAAGAGTTCTCCCCCCAGAGCAAAGAGACCCTCCTTCAGTCCTACAATAAGAGGCTGAAAGATGACGTTA
AGTGGATTATGGATAATTTCACTTAGATCATAAAGACAGCAAAGATTGAAAATGAAACTCAGGTCTCCCGGGCAACTCAG
GGAGAGCAGGACAATTATGAGATGCATGTGAGAGCTGCCAATATTGTCCATGCTGGGGAATCTCCGATGAAGCTTGTGTC
TGACCTCAAGCAATTTCTCATCCTCAATGACTTTCCCTCGATGAATGAAGCCATTGATCAGAGTAACCAGCAGCTTCAAA
GCTTGCAGGATGAATGTGACAAGAAGCTCATTTCCCTGCAGGATGAGATATCCATTGACTTATATGAGCTAGAGGAGGAG
TATTACTCGTCCAGGTAC
ORF - retro_mdom_1314 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.43 % |
| Parental protein coverage: | 68.47 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MAQQRVLP-QSKETLLQSYNKRLKDDIKSIMDNFTEIIKTAKIEDETQVSRATQGEQDNYEMHVRAANIV |
| MAQQRVLP.QSKETLLQSYNKRLKDD.K.IMDNFT.IIKTAKIE.ETQVSRATQGEQDNYEMHVRAANIV | |
| Retrocopy | MAQQRVLP>QSKETLLQSYNKRLKDDVKWIMDNFT*IIKTAKIENETQVSRATQGEQDNYEMHVRAANIV |
| Parental | RAGESLMKLVSDLKQFLILNDFPSVNEAIDQRNQQLRSLQDECDKKLISLRDEISIDLYELEEEYYSSSY |
| .AGES.MKLVSDLKQFLILNDFPS.NEAIDQ.NQQL.SLQDECDKKLISL.DEISIDLYELEEEYYSS.Y | |
| Retrocopy | HAGESPMKLVSDLKQFLILNDFPSMNEAIDQSNQQLQSLQDECDKKLISLQDEISIDLYELEEEYYSSRY |
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 | 41 .84 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 59 .74 RPM |
| SRP007412_heart | 0 .00 RPM | 68 .98 RPM |
| SRP007412_kidney | 0 .00 RPM | 121 .15 RPM |
| SRP007412_liver | 0 .00 RPM | 86 .10 RPM |
| SRP007412_testis | 0 .00 RPM | 54 .41 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_1314 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1314 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 | |
|---|---|---|---|
| Myotis lucifugus | ENSMLUG00000004674 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000012748 | 1 retrocopy |
retro_mdom_1314 ,
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