RetrogeneDB ID: | retro_mdom_1540 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 5:160226059..160226993(-) | ||
| 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_1540
AAATGCACCGTTATCAAAACCTATTTCTTGCAAGTGACGATTTTGTTGATGCAGAAAAGTTGAAGTCTGGAGACCTGGTG
AGAGAAAACAAAGCATCCTATCTGATCCTAGAGATTCTACCCACTGAGTATGAATCCCATGTGAAAGTCATGGAGGTGAA
TGAAAGACCCACAAAGCAATACAGCATTATTGGAGGGCTGGATAAACACACCCAGATACTCATAGAGGCTATTGGATTGC
TAATGAATGAACCATAAAGAGATATTGAGAATTTGGTTATTCAGTCTCCAAAGGGAGGATTTATATATGGAGCCTGAGGT
ATTGGAAAAAGTCTGCTAGCCCAGACTTGTGGTGCCCAGACCAAGGCCACCTTTCTGAAAGTGGCTGGCCCTCATTTGGT
AAGATGTTAACTGGGAATGGAGCAAAGTTTGTCTGAGATGCCTCTTACTGGCCAAAGGGAATGTGCCTTCCATTATATTC
ACTGATGAACTAGATGCCATTAGAACCAAGCACTTAGACAGTGAGTAGGCCCAGGATCAGAAGTTCAAAGAACTATACTG
AAAACTCCTAAACTATCAGGATGAATTTCAGCATAACACCCAAGGTAATATAATTACTGATATAAATAGGGTGGACCTTC
CTGGACCTTGCCTTGCTCCCTATATGGATCATAAGGTTGAATTCCCAAACTCTACAGAGGAAACCAGAGCCAGGAGCATG
CAGATTCATTCTTGAAAAATGAATGAGAGCCCTGTGAAGTATCAAGAGCTGGCATACTCCAGGAGCAAATTCAGAGGAGT
TCAGTGCAAGGCCATGTGCATTGAAGAAAGGAATGATCCAGCTCTGCCTGGAAGCCACTGAGCTCATACATAAAGACTAG
ATGGAGGGTATGCTTGGGGCTCCAGTCAAGAATAAAGCCAGTTTGCACTTCTAT
ORF - retro_mdom_1540 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 59.81 % |
| Parental protein coverage: | 69.93 % |
| Number of stop codons detected: | 6 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | KTSTRQTYFLPVIGL-VDAEKLKPGDLVGVNKDSYLILETLPTEYDSRVKAMEVDERPTEQYSDIGGLDK |
| K.....TYFL.V..L.VDAEKLK.GDLV..NK.SYLILE.LPTEY.S.VK.MEV.ERPT.QYS.IGGLDK | |
| Retrocopy | KCTVIKTYFLQVTIL<VDAEKLKSGDLVRENKASYLILEILPTEYESHVKVMEVNERPTKQYSIIGGLDK |
| Parental | QIQELVEAIVLPMNHK-EKFENLGIQPPKGVLMYGPPGTGKTLLARACAAQTKATFLKLAGPQLV-QMFI |
| ..Q.L.EAI.L.MN......ENL.IQ.PKG...YG..G.GK.LLA..C.AQTKATFLK.AGP.LV..M.. | |
| Retrocopy | HTQILIEAIGLLMNEP*RDIENLVIQSPKGGFIYGA*GIGKSLLAQTCGAQTKATFLKVAGPHLV<KMLT |
| Parental | GDGAKLVRDA-FALAKEKAPSIIFIDELDAIGTKRFDSEKAGDR-EVQRTML-ELLNQLDGFQPNTQVKV |
| G.GAK.V.DA...LAK...PSIIF.DELDAI.TK..DSE.A.D..EVQRT.L..LLN..D.FQ.NTQ... | |
| Retrocopy | GNGAKFV*DA<LLLAKGNVPSIIFTDELDAIRTKHLDSE*AQDQ<EVQRTIL>KLLNYQDEFQHNTQGNI |
| Parental | IAATNRVDILDPALLRSGRLDRKIEFPMPNEEARARIMQIHSRKMNVSPDVNYEELARCTDDFNGAQCKA |
| I...NRVD...P.L......D.K.EFP...EE.RAR.MQIHS.KMN.SP.V.Y.ELA.....F.G.QCKA | |
| Retrocopy | ITDINRVDLPGPCL--APYMDHKVEFPNSTEETRARSMQIHS*KMNESP-VKYQELAYSRSKFRGVQCKA |
| Parental | VCVE-AGMIALRRGATELTHEDYMEGILEVQAKKKANLQYY |
| .C.E..GMI.L...ATEL.H.D.MEG.L....K.KA.L..Y | |
| Retrocopy | MCIE>KGMIQLCLEATELIHKD*MEGMLGAPVKNKASLHFY |
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_1540 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1540 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 |