RetrogeneDB ID: retro_mdom_1097

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:98631849..98632595(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: DUS1L
• Ensembl ID: ENSMODG00000003351
• Aliases: None
• Description: dihydrouridine synthase 1-like (S. cerevisiae) [Source:HGNC Symbol;Acc:30086]

Sequence

>retro_mdom_1097
AAAGTGGCTTGGAGTCTAGTAAGCCGTCGCCATGGAGCTCAGTTGTGCTACGCACCTATGTTTCATGCTCAGGTTTTTGT
TTGAGATGCCAACTATCAAAAGGAGAATCAGTATTGTGATGTGTGTCCTGAGGATAGCCCCCGTATCCTACAGTTCTGGG
CCAATGATCCTGAGGTGTTTATCAAAGCGGCTCTTCTGGCCCCAGATGATTGTGATGCTATAGATTTGAATTTGGGCTGT
CCTCAAATGATTGCCAAGAGAGGTCATTACAGAGCCTTCTTACAAGACGAGTGGGATCTGCTCCAGAGAATGATTCTATT
GGCAAAGGAGAAACTCTCTGTTCCAGTCACCTGCAAAATCCCTGTCTTCCCAGAAATTGACAGGGCTGTGAGATGTGCTC
AGTTGCTGGAGAAAGCAGATGCCAATTCTTAACACTTCATGGACATACCAAGGAACTGAAGAGTCTGCTATCTGCAATTG
CATCTTGGGAGTATATAAAGGCTATGGGGAAGGCAGTGAATATTCCTGTATTTGCAAATGGGAACATCCAATATCTCCAT
GATGTGGACAAATGCATCCAGGAAACGGGAGTTCATGGGGTGATGAGTGCAAAGGATAACCTACACAACCCAGTCTTGTT
TGAGGGTTGAAATCCACTGTTGTAGGAGATGGCTGAAGAATATCTGGAGATTGTACAGCAGCACCCCTGCCTTCTGTCCT
ATGCCCCACTTCATCTCAAGAATCTT

Alignment

ORF - retro_mdom_1097 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.4 %
• Parental protein coverage: 51.77 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYRKENLYCDVCPEDRPLIVQFCANDPEVFVKAALLAQDY
          ..AW.L.SRRHGAQLCY.PM.HAQVFV.DANY.KEN.YCDVCPED.P.I.QF.ANDPEVF.KAALLA.D.
Retrocopy KVAWSLVSRRHGAQLCYAPMFHAQVFV*DANYQKENQYCDVCPEDSPRILQFWANDPEVFIKAALLAPDD

Parental  CDAIDLNLGCPQMIAKRGHYGAFLQEEWDLLQRMILLAHEKLSVPVTCKIRVFPEIDKTVKYAQLLEKAG
          CDAIDLNLGCPQMIAKRGHY.AFLQ.EWDLLQRMILLA.EKLSVPVTCKI.VFPEID..V..AQLLEKA.
Retrocopy CDAIDLNLGCPQMIAKRGHYRAFLQDEWDLLQRMILLAKEKLSVPVTCKIPVFPEIDRAVRCAQLLEKAD

Parental  -CQLLTVHGRTKEQKGPLSGIASWEHIKAVRKAVNIPVFANGNIQYLHDVEKCIQETGVHGVMSAEGNLH
          .CQ.LT.HG.TKE.K..LS.IASWE.IKA..KAVNIPVFANGNIQYLHDV.KCIQETGVHGVMSA..NLH
Retrocopy <CQFLTLHGHTKELKSLLSAIASWEYIKAMGKAVNIPVFANGNIQYLHDVDKCIQETGVHGVMSAKDNLH

Parental  NPALFEGRNPLVWEMAEEYLEIVQQHPCPLSYVRAHLFKL
          NP.LFEG.NPL..EMAEEYLEIVQQHPC.LSY...HL..L
Retrocopy NPVLFEG*NPLL*EMAEEYLEIVQQHPCLLSYAPLHLKNL

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_1097 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1097 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 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018104	5 retrocopies	retro_cjac_1422, retro_cjac_1887, retro_cjac_3451, retro_cjac_4002, retro_cjac_4018,
Monodelphis domestica	ENSMODG00000003351	1 retrocopy	retro_mdom_1097 ,
Pan troglodytes	ENSPTRG00000009790	1 retrocopy	retro_ptro_883,