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 symbol: PSMD5
• Ensembl ID: ENSMODG00000019635
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 5 [Source:HGNC Symbol;Acc:9563]

Sequence

>retro_mdom_1523
AGTGACATCAAATAACATACGGTCTTTGAGCCGATTGCGGAGATTTCCTCTGTGGCACCAGAGTCCTTAAAACACTGTAC
TGACAGAGGATTAGTAATTTGTCTCATGAGAGAGCTGGCTGGTGATACTGTGCTAGTCAATGTCACCTGGATAGACATGG
TGACATCACAGGCATACACTCATCAAGGATGACCAATACCTTGCCCAAGAAGGAGTAATTGATCATATTTCTAATATCAT
CATTGGGGCAGATTCGGATCCTTTCTCCAGTTTCTATTTCCTGGGATTTGTCCATTTTTTGACAACCTGGCAATAGTGGA
GATCCCTGAACAGATCTGTGAATGATACCCAATCTTTGTAGAAATCTTTGAAATGGCAGAAGATCAGGACCCTACCATGC
TAGGAGTAGCAATGGACATTCCAGGGATCCTGGGCTCAAATGTTGAAGGAAAACAGGTTTTGTAGAAAAAGGAAGTTAAT
TTGAACATCTGCTAAAGAGTATTGGACACCATGCAAAGAATGCTTCAGTACAACTAAAGATTAGTTGTTTGGATGTGATT
TCACCTCTTCTTCATCTCTCATATGATCAACAGATTGAAGATCTTCTAAGAACGGTAGAATTCTGGTTCTCTTCTTTAAC
TCAGGACCCATTGGAACATTTTAGAGGGATCAGCACCCAGCCTTTCCCAGAGCTGCATTGTGCTTGCATTAAAAGTGTTC
ATAGCCATTGCAAACCAATCCTGAGCTCAGAACCTTATGCTTAACAACCCACGGTTTGTGGATTATGTTATGGATTGATC
TGTGCAACATGACAAAGCTTTAAAAGATACAAAATAGGAACTCATGAAAGCCCTAGCAAACTCAAGAACAATCACAGAAA
TCTTCAGAAACCAATATTATTTAAGACTAAGACCTTGTTTGAGTGAAGGTCCATACTTTGTGAAGTCTGTTTCAGCTACA
GCTGTGGAAGGA

Alignment

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

Expression

RNA-Seq

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

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1523 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1523 was not experimentally validated.

Homology

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	retro_vpac_127,