RetrogeneDB ID: | retro_mdom_1035 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 3:305758560..305759679(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PSMC3 | ||
| Ensembl ID: | ENSMODG00000019911 | ||
| Aliases: | None | ||
| Description: | proteasome (prosome, macropain) 26S subunit, ATPase, 3 [Source:HGNC Symbol;Acc:9549] |
Retrocopy-Parental alignment summary:
>retro_mdom_1035
GCTATGAAGGATAAAATCAAAGAGAACACGCTGTAGAAAATTAAAGTGAACAAGACGCTGCCCTACCTTGTTTCCAACGT
TATCGAGCTGCTAGATGTTGACCCCAATGACCAAGAAGAAGATGGTGCAAACATTGACCTTGACTCTCAGAGAAAGGGCA
AATGTGCTGTGATCAAAACCTCTACCCGACAGACCTATTTCCTGCCAGTTATTGGTTTGGTTGATGCAGAGAAATTGAAG
CCGGGAGACCTGGTGGGAGTAAACAAAGATTCCTATCTGATCTTAGAGACCCTGCCCATCGAATATGATTCCCGAGTGAA
GACCATGGAGGTGGATGAGAGGCCCACAGAGCAATACAGTGACATTGGAGGACTGGACAAACAAATCCAGGAACTGGTAG
AGGCTATTGTATTGCCAATGAACCATAAAGAGAAATTTGAGAATTTGGGTATTCAGCTTCCAAAGGGAGTATTGATGTAT
GGACCCCCAGGTACTGGAAAAACCCTGCTAGCCCGTGCATGTGCTGCTCAGACCAAGGCCACCTTTCTGAAATTGGCTGG
ACCCCAGCTGGTACAAATGTTCATTGGGGATGGAGCAAAGCTTGTCCGAGATGCCTTTGCATTGGCTAAAGAGAAAGCTC
CCTCCATTATCTTCATTGATGAGCTGGATGCTATTGGAACCAAACGCTTTGACAGTGAGAAAGCAGGAGATCGTGAAGTT
CAGAGGACAATGCTGGAGCTCTTGAACCAGCTGGATGGATTTCAGCCTAACACTCAAGTCAAGGTGATTGCTGCCACAAA
TAGGGTGGACATCCTAGACCCTGCTTTGCTCCGCTCTGGTCGTCTGGACCGCAAGATTGAATTTCCAATGCCGAATGAGG
AAGCTAGAGCCAGGATCATGCAGATACATTCCCGAAAAATGAATGTGAGCTCTGACGTGAACTATGAGGAGCTAGCACGC
TGTACCAATGATTTCAATGGCGCCCAGTGTAAAGCTGTGTGTGTGGAAGCCGGAATGATCGCCCTCCGGGGTGGAGCCAC
TGAACTCACCCATGAAGACTACATGGAGGGCATCCTGGAGGTTCAGGCCAAGAAGAAAGCCAATTTGCAGTACTATGCT
ORF - retro_mdom_1035 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 97.59 % |
| Parental protein coverage: | 82.85 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | AMKDKIKENSE-KIKVNKTLPYLVSNVIELLDVDPNDQEEDGANIDLDSQRKGKCAVIKTSTRQTYFLPV |
| AMKDKIKEN...KIKVNKTLPYLVSNVIELLDVDPNDQEEDGANIDLDSQRKGKCAVIKTSTRQTYFLPV | |
| Retrocopy | AMKDKIKENTL*KIKVNKTLPYLVSNVIELLDVDPNDQEEDGANIDLDSQRKGKCAVIKTSTRQTYFLPV |
| Parental | IGLVDAEKLKPGDLVGVNKDSYLILETLPTEYDSRVKAMEVDERPTEQYSDIGGLDKQIQELVEAIVLPM |
| IGLVDAEKLKPGDLVGVNKDSYLILETLP.EYDSRVK.MEVDERPTEQYSDIGGLDKQIQELVEAIVLPM | |
| Retrocopy | IGLVDAEKLKPGDLVGVNKDSYLILETLPIEYDSRVKTMEVDERPTEQYSDIGGLDKQIQELVEAIVLPM |
| Parental | NHKEKFENLGIQPPKGVLMYGPPGTGKTLLARACAAQTKATFLKLAGPQLVQMFIGDGAKLVRDAFALAK |
| NHKEKFENLGIQ.PKGVLMYGPPGTGKTLLARACAAQTKATFLKLAGPQLVQMFIGDGAKLVRDAFALAK | |
| Retrocopy | NHKEKFENLGIQLPKGVLMYGPPGTGKTLLARACAAQTKATFLKLAGPQLVQMFIGDGAKLVRDAFALAK |
| Parental | EKAPSIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFQPNTQVKVIAATNRVDILDPALLRSG |
| EKAPSIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFQPNTQVKVIAATNRVDILDPALLRSG | |
| Retrocopy | EKAPSIIFIDELDAIGTKRFDSEKAGDREVQRTMLELLNQLDGFQPNTQVKVIAATNRVDILDPALLRSG |
| Parental | RLDRKIEFPMPNEEARARIMQIHSRKMNVSPDVNYEELARCTDDFNGAQCKAVCVEAGMIALRRGATELT |
| RLDRKIEFPMPNEEARARIMQIHSRKMNVS.DVNYEELARCT.DFNGAQCKAVCVEAGMIALR.GATELT | |
| Retrocopy | RLDRKIEFPMPNEEARARIMQIHSRKMNVSSDVNYEELARCTNDFNGAQCKAVCVEAGMIALRGGATELT |
| Parental | HEDYMEGILEVQAKKKANLQYYA |
| HEDYMEGILEVQAKKKANLQYYA | |
| Retrocopy | HEDYMEGILEVQAKKKANLQYYA |
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_1035 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1035 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 | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000008701 | 1 retrocopy | |
| Monodelphis domestica | ENSMODG00000019911 | 2 retrocopies |
retro_mdom_1035 , retro_mdom_1540,
|
| Mustela putorius furo | ENSMPUG00000003992 | 1 retrocopy |