RetrogeneDB ID: retro_mdom_80

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:384796049..384797132(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000005764
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000011691
• Aliases: None
• Description: None

Sequence

>retro_mdom_80
ATGACTGTTACAAAACAAAAGATGAGCAAGAACAAAGAAGATGCTCCCCATGAGCTGGAAAGCCAGTTCATATTACGCTT
ACCCCCAGAATATGCTTCTACTGTGAGAAGGGCAATACAATCTGGAAGTGTTAATCTGAAAGATAAGTTGACCATTGAAT
TACATGCAGATGGACGTCATGGAATTGTCCGAGTGGATCGTGCCCCATTAGCTGCTAAGGTGGTTGACCTTCCCTGTGTT
ACTGAATCCATGAAAACCATAGATAAAAAAACCTTTTACAAGACAGCAGATATCTGCCAGATGCTTGTGTGCAGTGTCGA
TGGGGATCTTTACCCTCCTCCAGAAGAACCAGTTGCTACTACTGATCCAAAAGCAAGTAAGAAAAAAGATAAAGACAGGG
AGAGAAAATTCATCTGGAACCATGGTATCACTCTGCCACTAAAGAATGTCAGAAAGAGAAGGTTCCGTAAGACAGCCAAG
AAGAAATATATTGAATCACCAGATGTGGAAAAAGAAGTAAAAAGGCTTCTAAGTACAGATGCAGAAGCTGTCAGTACCCG
GTGGGAAGTAATTGCAGAAGATGAAACAAAGGAAGCAGACAACCAAGTTTCCCTGGCAGGCCTAGATATTTCCTCTCCAG
GAATGAGTGGCCATAAGCAGGGCCATGGCTCCTCAGAACATGATGAACTTCGAGAGATATTTAATGACATTAGCAGCAGT
AGTGAAGAGGAAGATGAGAGAGATCCTCATGATGATGAAGACATAAACATCATTGACACTGAGGAAGACCTAGAGAGGCA
GCTACAAGACAAGCTTGATGAATCTGATGAACAGCGCCAAGAAAACGAGCAAACAAATCAGATGGTTATGGGAATTCAGA
AGCAGATTGATATAATGAAAGGGAAACTCCAGGAGACTCAAGGGAGAGCAAAGCGACAGGAAGATCTCATTATCAAAGTT
GAAAATCTGGCACTCAAGACTCGTCTTCAGGCTGTCCTGGATGAGCTCAAACAACAGGAAGAACGAGAGAAGCAACAGCT
CAGTTCTTTGGAGGAACAGCTAGAATCACTCCTGGAAAAATAA

Alignment

ORF - retro_mdom_80 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.44 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSKNKEDPPHELENQFILRLPPEYASTVRRAIQSGNVNLKDKLTIELHPDGRHGIVRVDRVPLASKLVDL
          MSKNKED.PHELE.QFILRLPPEYASTVRRAIQSG.VNLKDKLTIELH.DGRHGIVRVDR.PLA.K.VDL
Retrocopy MSKNKEDAPHELESQFILRLPPEYASTVRRAIQSGSVNLKDKLTIELHADGRHGIVRVDRAPLAAKVVDL

Parental  PCVIGSLKTIDKKTFYKTADICQMLVSTVDGDLYPPLEEPAATNDPKLNKKKDRDREKKFIWNHGITLPL
          PCV..S.KTIDKKTFYKTADICQMLV..VDGDLYPP.EEP.AT.DPK..KKKD.DRE.KFIWNHGITLPL
Retrocopy PCVTESMKTIDKKTFYKTADICQMLVCSVDGDLYPPPEEPVATTDPKASKKKDKDRERKFIWNHGITLPL

Parental  KNVRKRRFRKTAKKKYIESPDVEKEVKRLLSTDAEAVSTRWEVIAEDETKDTDNHGSLTSLDI-SPGMSS
          KNVRKRRFRKTAKKKYIESPDVEKEVKRLLSTDAEAVSTRWEVIAEDETK..DN..SL..LDI.SPGMS.
Retrocopy KNVRKRRFRKTAKKKYIESPDVEKEVKRLLSTDAEAVSTRWEVIAEDETKEADNQVSLAGLDISSPGMSG

Parental  QKQGHSSSEHDELREIFNDISSSSDDDDEQDHHDDDDLNIIDIEEELERRSASAFDESDEQRQEDEKANH
          .KQGH.SSEHDELREIFNDISSSS...DE.D.HDD.D.NIID.EE.LER......DESDEQRQE.E..N.
Retrocopy HKQGHGSSEHDELREIFNDISSSSEEEDERDPHDDEDINIIDTEEDLERQLQDKLDESDEQRQENEQTNQ

Parental  LILGLRKQIDMMKGKHQETQDRAKRQEDLIFKVENLALKSRLQAVLDELKQQEEQEKEQLSSLQEQLDSL
          ...G..KQID.MKGK.QETQ.RAKRQEDLI.KVENLALK.RLQAVLDELKQQEE.EK.QLSSL.EQL.SL
Retrocopy MVMGIQKQIDIMKGKLQETQGRAKRQEDLIIKVENLALKTRLQAVLDELKQQEEREKQQLSSLEEQLESL

Parental  LEK
          LEK
Retrocopy LEK

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_80 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_80 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000011691	1 retrocopy	retro_mdom_80 ,