RetrogeneDB ID: retro_mdom_357

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:274004395..274005670(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX39A
• Ensembl ID: ENSMODG00000002448
• Aliases: None
• Description: DEAD (Asp-Glu-Ala-Asp) box polypeptide 39A [Source:HGNC Symbol;Acc:17821]

Sequence

>retro_mdom_357
ATGGCAGAGAATGATGTGGACAATGAACTCCTGGATTATGAAGATGAAGTAGAGACAGCAGCTGGGGGTGATGGTGCTGA
GGCCCCTGCAAAGGGAAGATGTCAAAGGTTCCTATGTCTCCATCCACAGCTCTGGCTTCCATGACTTTCTACTTAAGCCA
GAGCTCCTCCAGGTCATTGTAGATTGTGACTTTGAGCATCCATCTGAAGTTCAGCATGAGTGTATTCCTCAGGCCATCTT
GGGAATGGATGTCTTGTGCCAGGCCAAGTCAGACATGGGAAAGACAGCTGTGTTTGTGCTGGCCACACTGCAACAGCTGG
AGTCAGTCACTGGTGGGGTTTCTGTGCTGGTAATGTGTCATACTCAGGAGTTGGCCTTTCAAATCAGTAAGGATTTGAGC
ACTTCTCCAAATACATGCCTAATGTCAAGGGGGTGGTATTTTTTGGTGGGCTTTCAATAAGGAAGGATGAAGAGGTGCTG
AAGAACTGCCCACACATTGTCGTGGGGACTCCAGGCCGTATCCTGGCTCTGACCCAAAATAAGAGCCTCAATCTCAAACA
CATTAAACATTTTATCTTGGATGAGTGTGACAAAATGCTCGAACAACTCGACATGCATCGAGATGTTCAGGAAATTTTCC
ACATGACCCCCCATGAGAAGCAGGTCATGATGTTCCGTGCCACCCTGAGCAAAGAGATCCGCCCTGTCTGCCACAAGTTC
ATGCAAGACCCAATGGAGATCTTCATGGATGATGAGATGAAGCTGACGCTGCATGGCCTGCAGCAGTACTAAGTGAAGCT
GAAGGACAATGAGAAGAACTGAAAACTCTTTGACCTCCTGGATGTTTTGGAGTTCAACCAGGTGGTGATCTTTGTGAAAT
CTGTGCAGCTCTGCATTGCCTTGGCCCAGCTCTTAGTGGAACAGAACTTCCCAGTCATTGCCATCCATCATGGGATGCCC
CAAGAGGAGAGGCTGTCCCTGTATCAGCAGTTTAAGGACTTCCAGCGTCGTATCCTTGCGACTACTAACCTCTTTGGCCA
GGGCATGGATATTGAACAAGTAAACATTGCTTTCAACTATGACATGCCAGAGGACTCAGATACCTACTTACATCGGGTGG
CTAGGGCAGGCTGGTTTGGTACAAAGGGTTTGTCTATCACATTCATGTCAGATGAAAATGATGCCAAAATACTCAGTGAT
GTCCAGGATCACTTCGATGTCAATATCAGTGAACTGCCTGATGAGATAGACATTTCTTCCTACATGGAGCAGACT

Alignment

ORF - retro_mdom_357 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.31 %
• Parental protein coverage: 87.47 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEQDVENELLDYEEDEEPQPLTESTPTPAK-KDVKGSYVSIHSSGFRDFLLKPELLRAIVDCGFEHPSE
          MAE.DV.NELLDYE...E..........PAK..DVKGSYVSIHSSGF.DFLLKPELL..IVDC.FEHPSE
Retrocopy MAENDVDNELLDYEDEVETAAGGDGAEAPAK>EDVKGSYVSIHSSGFHDFLLKPELLQVIVDCDFEHPSE

Parental  VQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEPVDGQVTVLVMCHTRELAFQISKE-YERFSKY
          VQHECIPQAILGMDVLCQAKS.MGKTAVFVLATLQQ.E.V.G.V.VLVMCHT.ELAFQISK...E.FSKY
Retrocopy VQHECIPQAILGMDVLCQAKSDMGKTAVFVLATLQQLESVTGGVSVLVMCHTQELAFQISKD<FEHFSKY

Parental  MPNVKVSVFFGGLSIKKDEDVLKKNCPHVVVGTPGRILALVRNKSLNLKNVKHFVLDECDKMLEQLDMRR
          MPNVK..VFFGGLSI.KDE.VLK.NCPH.VVGTPGRILAL..NKSLNLK..KHF.LDECDKMLEQLDM.R
Retrocopy MPNVKGVVFFGGLSIRKDEEVLK-NCPHIVVGTPGRILALTQNKSLNLKHIKHFILDECDKMLEQLDMHR

Parental  DVQEIFRLTPHEKQCMMFSATLSKEIRPVCRKFMQDPMEVFVDDETKLTLHGLQQYYVKLKDSEKNRKLF
          DVQEIF..TPHEKQ.MMF.ATLSKEIRPVC.KFMQDPME.F.DDE.KLTLHGLQQY.VKLKD.EKN.KLF
Retrocopy DVQEIFHMTPHEKQVMMFRATLSKEIRPVCHKFMQDPMEIFMDDEMKLTLHGLQQY*VKLKDNEKN*KLF

Parental  DLLDVLEFNQVVIFVKSVQRCVALAQLLVEQNFPAIAIHRGMAQEERLSRYQQFKDFQRRILVATNLFGR
          DLLDVLEFNQVVIFVKSVQ.C.ALAQLLVEQNFP.IAIH.GM.QEERLS.YQQFKDFQRRIL..TNLFG.
Retrocopy DLLDVLEFNQVVIFVKSVQLCIALAQLLVEQNFPVIAIHHGMPQEERLSLYQQFKDFQRRILATTNLFGQ

Parental  GMDIERVNIVFNYDMPEDSDTYLHRVARAGRFGTKGLAITFVSDEGDAKILNDVQDRFEVNVAELPEEID
          GMDIE.VNI.FNYDMPEDSDTYLHRVARAG.FGTKGL.ITF.SDE.DAKIL.DVQD.F.VN..ELP.EID
Retrocopy GMDIEQVNIAFNYDMPEDSDTYLHRVARAGWFGTKGLSITFMSDENDAKILSDVQDHFDVNISELPDEID

Parental  ISTYIEKS
          IS.Y.E..
Retrocopy ISSYMEQT

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	7.87 RPM	0.00 RPM
SRP007412_cerebellum	11.10 RPM	0.00 RPM
SRP007412_heart	4.59 RPM	0.00 RPM
SRP007412_kidney	15.80 RPM	0.00 RPM
SRP007412_liver	11.58 RPM	0.00 RPM
SRP007412_testis	8.25 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_357 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_357 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000002448	1 retrocopy	retro_mdom_357 ,
Otolemur garnettii	ENSOGAG00000010280	2 retrocopies	retro_ogar_147, retro_ogar_155,