RetrogeneDB ID: retro_mdom_1092

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:66844828..66845522(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000003400
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000002508
• Aliases: None
• Description: None

Sequence

>retro_mdom_1092
ATGGCTGGGGATGCCAGAGGTCACAGTTGCCCAGGCTCAGAGATTCTCCTGCACCCTGAGCTGCTGACCCAAGAGTTCCT
GCTACTCCTGCTCCTGCTGGAGTGGAAGAATATAGTTGTTGAAGAGGACATAAAGATCGACAAAGATGACTTTACTGACC
TCTATGTTCAATATGCCATACCACTGTCTCAAAGGAATTACCAAAAAGTAGATGGAGGAAAATGATGGAAAAGAAAAGAG
GGCAAAATGAATTGAAAAATGAGCATAAAAGGGGTATGAGTGTGGAAGGTTTACATAAAAGGCCCCTCATTGTCTTTGAT
GGAAATTCAACAAGTACAAGCATAAAAGTGAGAAAGACTGAAAATGGAACTAAAGATCTTCTGAAACCTTCTCCATCAGT
ACACATTACTAACAATACCTTTAGGAAGTTTCTACATGCAAACACTTCCTCCCTTATCCTGCCTTTTACCTTACCTACAG
ACCTTAAAGTGGAAAGCAGTAATAACACTAAACTGAACCACGTGTTAATGACTAGTAGGTGTACACTGGCCAATGTAAAA
TCGCCACCATTATCTCTTGTTGAGGGAACTACTGTTGTGAAATTAAAGAAAACTGCTCCAAAAGAAGAAGCAGAATCAGT
GAGTGAATTAAAGCCCACAGAAGCAAAGAGAAGATCCAACATGTTACATGGCCG

Alignment

ORF - retro_mdom_1092 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAGDAGGRGCPGSEMLLHPELLSQEFLLLTL--EQKNIVVEEEIKINKDDLTDFYVQHAIPLPQR-ELPK
          MAGDA.G..CPGSE.LLHPELL.QEFLLL.L..E.KNIVVEE.IKI.KDD.TD.YVQ.AIPL.QR.ELPK
Retrocopy MAGDARGHSCPGSEILLHPELLTQEFLLLLLLLEWKNIVVEEDIKIDKDDFTDLYVQYAIPLSQR<ELPK

Parental  SRWGKMMEKKRGQNELKNEHKRNMSVESLRKRPLIVFDGNSTSTSIKVRKTENGTNDRLKPPPSVGVTNN
          SRW....................MSVE.L.KRPLIVFDGNSTSTSIKVRKTENGT.D.LKP.PSV..TNN
Retrocopy SRWXXXXXXXXXXXXXXXXXXXGMSVEGLHKRPLIVFDGNSTSTSIKVRKTENGTKDLLKPSPSVHITNN

Parental  TFRKLPHSNTSSLILPSTLPTDIKVESNNDTKQNHVLMTSRSTLANVKSPPLSPVGGTTVVKLKRTAPKE
          TFRK..H.NTSSLILP.TLPTD.KVES.N.TK.NHVLMTSR.TLANVKSPPLS.V.GTTVVKLK.TAPKE
Retrocopy TFRKFLHANTSSLILPFTLPTDLKVESSNNTKLNHVLMTSRCTLANVKSPPLSLVEGTTVVKLKKTAPKE

Parental  EAESVSDCKPTEAKR-KIQHVTWP
          EAESVS..KPTEAKR.KIQHVTWP
Retrocopy EAESVSELKPTEAKR<KIQHVTWP

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_1092 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1092 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000002508	3 retrocopies	retro_mdom_1092 , retro_mdom_1870, retro_mdom_41,