RetrogeneDB ID: retro_mdom_1038

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:309732562..309733409(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UXS1
• Ensembl ID: ENSMODG00000002607
• Aliases: None
• Description: UDP-glucuronate decarboxylase 1 [Source:HGNC Symbol;Acc:17729]

Sequence

>retro_mdom_1038
GAAAGAAATAGGGAACTTTGGATTGATTATGAAAACTTTGAGATAATTAACCATGATGTAGAGCCCCTCTCCATTGAAGA
GAACCAGATTTATCATCTATCGTCTCCAAACTACATGTACAGCCCTATTAAGACATTAGAGACCAACATAATTGCTACAT
TAAATATGTTAAACTTGGCAAAATGTGTTGAAGCACATCTTCTAGTCTCTACCTCTGAAGTATATGGAGATTCAGAAGTC
CCCTCTTAATGAGAAGATTATTGGGGCCATGTGAATCCAAAAGGACCTAGAGTGTCTTATGATGAAGCAAAGTATGTGGC
AGAGACCCTGTGTTATACCTTACATGAAGCAGAGAGGGGTTGAAGTGAGAATTGCTTGAATCTTCAATAGTTTTGGACCA
TGAATGTATATGAATGCTGGCTGAGTTATGTTGTAACCTCTCCAAGGGAAGCCTCTCACAGTTTATGATTCTGGAACTCA
GACTTGAGCATTCCAATATGTCAGTGACCTAGTAAATGGACTGTTGGTCTTACTAAAAGCAATGTTAGTAGCCCTGTCAG
TTTGGGGAACCCAGAACACAATTCTAGAATTTGTTCTGTTAGTAAAAACTTTGTTGGTAGCAGTAATGAAATCCAGTTTC
TCTCAGAAGCACAACCCACAGAGAAGAAAACTGGACATCCAAAAAGCTAACCTAATGCTTGTGTGGTAGCTTGTGACCCT
TTTGCAAGAAGTCTTAAATAAGGCAATTCACTATTTCCATAAAGAACTCAAATACCAAGGAAATAATCACTACATCCCCA
AAGTGAAACCTGCTAAGATTAAAAAAAAAGGCCAAACATGACATGAC

Alignment

ORF - retro_mdom_1038 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.89 %
• Parental protein coverage: 70.07 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KRNVEHWIGHENFELINHDVVEPLYIEVDQIYHLASPASPPNYMYNPIKTLKTNTIGTLNMLGLAKRVGA
          .RN.E.WI..ENFE.INHDV.EPL.IE..QIYHL.S....PNYMY.PIKTL.TN.I.TLNML.LAK.V.A
Retrocopy ERNRELWIDYENFEIINHDV-EPLSIEENQIYHLSS----PNYMYSPIKTLETNIIATLNMLNLAKCVEA

Parental  RLLLASTSEVYGDPEVHPQSEDYWGHVNPIGPRACYDEGKRVAETMCYA-YMKQEGVEVRVARIFNTFGP
          .LL..STSEVYGD.EV....EDYWGHVNP.GPR..YDE.K.VAET.CY..YMKQ.GVEVR.A.IFN.FGP
Retrocopy HLLV-STSEVYGDSEVPS**EDYWGHVNPKGPRVSYDEAKYVAETLCYT>YMKQRGVEVRIA*IFNSFGP

Parental  RMHMNDGRVVSNFILQALQGEPLTVYGSGTQTRAFQYVSDLVNGL-VALMNSNVSSPVNLGNPEEHTILE
          .M.MN.G.V.....L..LQG.PLTVY.SGTQT.AFQYVSDLVNGL.V.L..SNVSSPV.LGNPE......
Retrocopy *MYMNAG*V----ML*PLQGKPLTVYDSGTQT*AFQYVSDLVNGL<VGLTKSNVSSPVSLGNPEHNS--R

Parental  FAQLIKNLVGSGSEIQFLSEAQDDPQRRKP-DIQKAKLMLGWEPVVPLEEGLNKAIHYFRKELEYQANNQ
          .....KN.VGS..EIQFLSEAQ..P...K..DIQKA.LML.W..V..L.E.LNKAIHYF.KEL.YQ.NN.
Retrocopy ICSVSKNFVGSSNEIQFLSEAQ--PTEKKT>DIQKANLMLVW*LVTLLQEVLNKAIHYFHKELKYQGNNH

Parental  YIPKPKPARI-KKGRTRHN
          YIPK.KPA.I...G.T.H.
Retrocopy YIPKVKPAKIXXXGQT*HD

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_1038 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1038 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
Monodelphis domestica	ENSMODG00000002607	1 retrocopy	retro_mdom_1038 ,
Monodelphis domestica	ENSMODG00000009373	1 retrocopy	retro_mdom_1562,