RetrogeneDB ID: retro_mdom_197

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: Un:23882936..23883707(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000022798
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000010090
• Aliases: None
• Description: None

Sequence

>retro_mdom_197
ATGGCCAAGCAGCCCTCCAAGGTGCACGGTTTGCGAACCGAGGACTCTCTTATCGAAGGAGTCAGCGACCAGGTGCTCGT
GGCTGTGCTGCTCGGTTTTGCTTTCTTGGCCGCGGTGGGCTATGCCCTGCTAAGAAATGCCCAGCAGCACATCCACCCCA
ACAACCGGGAGCTGGTCCGGGTACTGAGAGAACAACTCCACAGGGAACAAGACCCCCCGGCTCCTAGACCGCAGTTCTAT
ACGGACCTGTCCTGCCCCATCTGTTTACATCATGCCTCTCTTCCTATCGAAACCAACTGTGGCCACCTCTTCTGCGGCAA
CTGCCTGATTGCTTACTGGCGTTACGGCTCCTGGCTTGGGATGGTCAGTTGTCCAATCTGCCGCCAAACAGTGACTTTGC
TGTTTCCTGTGTTTGGCGAAGATGTTCTCTCTGTGGATTCCAGGCGTTTGCACCAAGATATTCACGACTACAACCGAAGG
TTCTCTGGTCAGCCCCGGTCTCTCACCGACAGACTTATGGACCTCCCCACTCTACTAAGGCATGCATTCCGGGAACTGTT
TTCTGTGGGCGGACTTTTCTGGATGTTTCGCATCAGAATTGTCCTGTGCTTGGTGGGAGCCTTTTTCTACCTGATATCAC
CTCTGGATCTGGTTCCCGAAGGCTTGTTTGGGATTCTGGGGTTTCTGGACGATTTCTTTGTCATCTTTCTCTTGCTTATT
TACATCTCTATCATGTATAGGGAGGTAATAACACAAAGGCTAAACAGATGA

Alignment

ORF - retro_mdom_197 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.6 %
• Parental protein coverage: 98.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEYQSQIPSLKLDDSVIEGVSDQVLVAVVISFAFIASLIYILLRNAEQNIHPDNQELVRVLREQLQTEQ
          MA...S....L...DS.IEGVSDQVLVAV...FAF.A...Y.LLRNA.Q.IHP.N.ELVRVLREQL..EQ
Retrocopy MAKQPSKVHGLRTEDSLIEGVSDQVLVAVLLGFAFLAAVGYALLRNAQQHIHPNNRELVRVLREQLHREQ

Parental  DAPAVVRQQFYTDMSCPICLHQASLPIETNCGHLFCGTCIIAYWRYGSWLGAISCPICRQTVTLLLPVFV
          D.PA..R.QFYTD.SCPICLH.ASLPIETNCGHLFCG.C.IAYWRYGSWLG..SCPICRQTVTLL.PVF.
Retrocopy DPPAP-RPQFYTDLSCPICLHHASLPIETNCGHLFCGNCLIAYWRYGSWLGMVSCPICRQTVTLLFPVFG

Parental  EDNQTQDVLELRQDINDYNRRFSGQPRSIMERIMDLPTLLRHAFREMFSVGGLFWMFRIRILLCLLGAFF
          ED....D...L.QDI.DYNRRFSGQPRS...R.MDLPTLLRHAFRE.FSVGGLFWMFRIRI.LCL.GAFF
Retrocopy EDVLSVDSRRLHQDIHDYNRRFSGQPRSLTDRLMDLPTLLRHAFRELFSVGGLFWMFRIRIVLCLVGAFF

Parental  YLISPLDFVPEALFGILGFLDDFFVIFLLLIYISIMYREVITQRLNR
          YLISPLD.VPE.LFGILGFLDDFFVIFLLLIYISIMYREVITQRLNR
Retrocopy YLISPLDLVPEGLFGILGFLDDFFVIFLLLIYISIMYREVITQRLNR

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	68.54 RPM
SRP007412_cerebellum	0.00 RPM	44.07 RPM
SRP007412_heart	0.00 RPM	16.55 RPM
SRP007412_kidney	0.00 RPM	50.04 RPM
SRP007412_liver	0.00 RPM	28.70 RPM
SRP007412_testis	0.00 RPM	168.34 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_197 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_197 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000001127	1 retrocopy	retro_meug_862,
Monodelphis domestica	ENSMODG00000010090	1 retrocopy	retro_mdom_197 ,
Mus musculus	ENSMUSG00000013878	1 retrocopy	retro_mmus_2907,
Otolemur garnettii	ENSOGAG00000007925	1 retrocopy	retro_ogar_2905,
Pteropus vampyrus	ENSPVAG00000013497	1 retrocopy	retro_pvam_856,
Sorex araneus	ENSSARG00000006471	1 retrocopy	retro_sara_706,
Sarcophilus harrisii	ENSSHAG00000018446	1 retrocopy	retro_shar_118,