RetrogeneDB ID: | retro_mdom_1523 | ||
Retrocopy location | Organism: | Opossum (Monodelphis domestica) | |
| Coordinates: | 5:107628392..107629364(-) | ||
| Located in intron of: | ENSMODG00000002334 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PSMD5 | ||
| Ensembl ID: | ENSMODG00000019635 | ||
| Aliases: | None | ||
| Description: | proteasome (prosome, macropain) 26S subunit, non-ATPase, 5 [Source:HGNC Symbol;Acc:9563] |
Retrocopy-Parental alignment summary:
>retro_mdom_1523
AGTGACATCAAATAACATACGGTCTTTGAGCCGATTGCGGAGATTTCCTCTGTGGCACCAGAGTCCTTAAAACACTGTAC
TGACAGAGGATTAGTAATTTGTCTCATGAGAGAGCTGGCTGGTGATACTGTGCTAGTCAATGTCACCTGGATAGACATGG
TGACATCACAGGCATACACTCATCAAGGATGACCAATACCTTGCCCAAGAAGGAGTAATTGATCATATTTCTAATATCAT
CATTGGGGCAGATTCGGATCCTTTCTCCAGTTTCTATTTCCTGGGATTTGTCCATTTTTTGACAACCTGGCAATAGTGGA
GATCCCTGAACAGATCTGTGAATGATACCCAATCTTTGTAGAAATCTTTGAAATGGCAGAAGATCAGGACCCTACCATGC
TAGGAGTAGCAATGGACATTCCAGGGATCCTGGGCTCAAATGTTGAAGGAAAACAGGTTTTGTAGAAAAAGGAAGTTAAT
TTGAACATCTGCTAAAGAGTATTGGACACCATGCAAAGAATGCTTCAGTACAACTAAAGATTAGTTGTTTGGATGTGATT
TCACCTCTTCTTCATCTCTCATATGATCAACAGATTGAAGATCTTCTAAGAACGGTAGAATTCTGGTTCTCTTCTTTAAC
TCAGGACCCATTGGAACATTTTAGAGGGATCAGCACCCAGCCTTTCCCAGAGCTGCATTGTGCTTGCATTAAAAGTGTTC
ATAGCCATTGCAAACCAATCCTGAGCTCAGAACCTTATGCTTAACAACCCACGGTTTGTGGATTATGTTATGGATTGATC
TGTGCAACATGACAAAGCTTTAAAAGATACAAAATAGGAACTCATGAAAGCCCTAGCAAACTCAAGAACAATCACAGAAA
TCTTCAGAAACCAATATTATTTAAGACTAAGACCTTGTTTGAGTGAAGGTCCATACTTTGTGAAGTCTGTTTCAGCTACA
GCTGTGGAAGGA
ORF - retro_mdom_1523 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 74.47 % |
| Parental protein coverage: | 64.48 % |
| Number of stop codons detected: | 7 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | SDIVRYRVYELIVEISSVSPESLKYCTDSGLVTQLIRELTGDDVLVRATCIEMVTSLAHTHHG-RQYLAQ |
| SDI....V.E.I.EISSV.PESLK.CTD.GLV..L.REL.GD.VLV..T.I.MVTS.A.TH.G..QYLAQ | |
| Retrocopy | SDIK*HTVFEPIAEISSVAPESLKHCTDRGLVICLMRELAGDTVLVNVTWIDMVTSQAYTHQG>DQYLAQ |
| Parental | EGIIDQISNIIVGADLDPFSSFYLPGFVKF-FGNLAIVDSPQQICERYPIFVEKVFEMAEGQDPTMIGVA |
| EG.ID.ISNII.GAD.DPFSSFY..GFV.F.F.NLAIV..P.QICE.YPIFVE..FEMAE.QDPTM.GVA | |
| Retrocopy | EGVIDHISNIIIGADSDPFSSFYFLGFVHF<FDNLAIVEIPEQICE*YPIFVE-IFEMAEDQDPTMLGVA |
| Parental | VDTLGILGSNVEGKQVLQKT-GSRFEHLLKRIGHQAKNASTELKIRCLDAISSLLHLPHDQQTEDLLRMT |
| .D..GILGSNVEGKQVL.K..GS.FEHLLK.IGH.AKNAS..LKI.CLD.IS.LLHL..DQQ.EDLLR.. | |
| Retrocopy | MDIPGILGSNVEGKQVL*KK<GS*FEHLLKSIGHHAKNASVQLKISCLDVISPLLHLSYDQQIEDLLRTV |
| Parental | ECWFSSLTRDPLEHFRGISTQPFSELHCA-ALKVFTAIANQPWAQKLMLNSPGFVEYVMDRSVERDKASK |
| E.WFSSLT.DPLEHFRGISTQPF.ELHCA.ALKVF.AIANQ..AQ.LMLN.P.FV.YVMD.SV..DKA.K | |
| Retrocopy | EFWFSSLTQDPLEHFRGISTQPFPELHCA>ALKVFIAIANQS*AQNLMLNNPRFVDYVMD*SVQHDKALK |
| Parental | DAKYELVKALANSKTIAEIFGNQYYLRLRAYLSEGPYFVKSVSTTAVEG |
| D.K.EL.KALANS.TI.EIF.NQYYLRLR..LSEGPYFVKSVS.TAVEG | |
| Retrocopy | DTK*ELMKALANSRTITEIFRNQYYLRLRPCLSEGPYFVKSVSATAVEG |
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 | 96 .55 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 87 .82 RPM |
| SRP007412_heart | 0 .00 RPM | 25 .52 RPM |
| SRP007412_kidney | 0 .00 RPM | 81 .64 RPM |
| SRP007412_liver | 0 .00 RPM | 70 .49 RPM |
| SRP007412_testis | 0 .00 RPM | 40 .66 RPM |
Monodelphis domestica was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mdom_1523 retrocopy.
Monodelphis domestica was not studied using FANTOM5 data.
retro_mdom_1523 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 | ENSMODG00000019635 | 1 retrocopy |
retro_mdom_1523 ,
|
| Vicugna pacos | ENSVPAG00000012577 | 1 retrocopy |