RetrogeneDB ID: retro_mdom_1539

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:157858993..157859897(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000020732
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: UPP1
• Ensembl ID: ENSMODG00000009417
• Aliases: None
• Description: uridine phosphorylase 1 [Source:HGNC Symbol;Acc:12576]

Sequence

>retro_mdom_1539
ACATGCAAAAATTCTTCAGGTGAACATTTAATTCACGTTTCAAACCCAAATATCTCAAAAATGAAAGAAGAGATGTTCTC
TATCATTTCAGTCTTGGAACTAAAACTCATGATTTGTCAACTATGTTTGGAAATGTGAAGTTCCTATGTGTTGGAGGAAG
TCCTTCCCTGATGAAAGCTTTTATTCACTTCATAGCTGAAGAACTGGGACTTGCAAAACCTGGCATGGACTATCCTAAAC
TTTGTGAAGGAACTGACCACTTTGCCATGTATAAGATTGGACCTGTATTAACAGTTAGTCATGGTATGGGCATTCCTTCC
ATTGGAATCATGTTACATGAATTTTCAAGTTACTATATCATGCCAAGTGTTCTAATGTTACCATCTTTGCATTGACACAT
CTGGTGGAATAGGTCTAGAGCCTGGTTCAGAAATGCTAAGTAAACAAGCTGTAGATTCTTGCTTCAAACTTGAATTTGAA
GTTTGTTTTGGGGAAAGGAGTAGTGCCATCTACAGATCTCTGTGCTGACCTAATTCAGGAATTATTGTCATGTACCAAGG
AAATTAATGAGTTTAATACTGTTATGGGAAATACCATGTATACTTTAGACTTCCAAGAAGGTCAAGGGTGGATGGATGGT
GCTTTCTGCTCATATATTGAGAAAGATAAGTTCCAGTATTTACAGGCTTCTCATGATGCTGGAATCAGAAACATTGATAT
GGAATCTACTATCATTGCAGCCATGTGCAGTGCCAGTGGCATCCCAGCTGTTGTTGTGTGTGTTATTCTTCTGAATCTTC
TCAAGGGAGATCAGAATACCAGTCCCCGTGATGTGCTTGTAGAGTACCAACAAAGACCACAGAAGTTGGTAGCATGTTTC
ATTAAGAAACATCTAGAAAAAGCA

Alignment

ORF - retro_mdom_1539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.13 %
• Parental protein coverage: 99.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  TTENSSGEHLVYISNPHISKM-EE-DVLYHFNLGTKTHDLPAIFGDVKFICVGGSPSRMKAFIRFIAEEL
          T..NSSGEHL...SNP.ISKM.EE.DVLYHF.LGTKTHDL...FG.VKF.CVGGSPS.MKAFI.FIAEEL
Retrocopy TCKNSSGEHLIHVSNPNISKMKEE<DVLYHFSLGTKTHDLSTMFGNVKFLCVGGSPSLMKAFIHFIAEEL

Parental  GLAKPDMDYPNLCEGTDRFAMYKIGPVLAVSHGMGVPSIGIMLHE-LFKLLYHAKCSDVTIFR-IGTSGG
          GLAKP.MDYP.LCEGTD.FAMYKIGPVL.VSHGMG.PSIGIMLHE..FKLLYHAKCS.VTIF..I.TSGG
Retrocopy GLAKPGMDYPKLCEGTDHFAMYKIGPVLTVSHGMGIPSIGIMLHE<IFKLLYHAKCSNVTIFA<IDTSGG

Parental  IGLEPGSVVLTKQAVDSCFKPEFEQFVLGKR-VVRSTDLCADLIEELLSCAKGMNEFNTVVGNTMCTLDF
          IGLEPGS..L.KQAVDSCFK.EFE....G.R.VV.STDLCADLI.ELLSC.K..NEFNTV.GNTM.TLDF
Retrocopy IGLEPGSEMLSKQAVDSCFKLEFE-VCFGER>VVPSTDLCADLIQELLSCTKEINEFNTVMGNTMYTLDF

Parental  YEGQGRLDGAFCSYTEKDKFEYLQAAHDAGVRNIEMESTIFAAMCRASGIPAAVVCVTLLNRLKGDQITS
          .EGQG..DGAFCSY.EKDKF.YLQA.HDAG.RNI.MESTI.AAMC.ASGIPA.VVCV.LLN.LKGDQ.TS
Retrocopy QEGQGWMDGAFCSYIEKDKFQYLQASHDAGIRNIDMESTIIAAMCSASGIPAVVVCVILLNLLKGDQNTS

Parental  PHDVLVEYQQRPQKLVACFIKKRLGKA
          P.DVLVEYQQRPQKLVACFIKK.L.KA
Retrocopy PRDVLVEYQQRPQKLVACFIKKHLEKA

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	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

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1539 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1539 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.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000013986	1 retrocopy	retro_etel_1829,
Monodelphis domestica	ENSMODG00000009417	1 retrocopy	retro_mdom_1539 ,