RetrogeneDB ID: retro_mdom_60

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:424156126..424157524(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000019818
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000001670
• Aliases: None
• Description: None

Sequence

>retro_mdom_60
ATGGCAATGGCAAAATTAGCTGAAAACCTCAAGGAAGAGCTGACTTGTCCTGTGTACATGGACTACTTCAGCCACCCAGT
GAATTTAGGCTGTGGCCATAGCTTTTGCCAACCTTGCCTCCTTAGGACCTGGAGAGAAGTTGACAAATCCTGCCCCTGTC
CTGAATGCAGAAGAGCCTTCCAGATAAAAGACTTGGAGTCCAACCATTGCTTGGGAAAGCTGTCTAGCTTAGCTAGAAAC
ATTAGACCCTACTTATTGCAGCTGAGGATGGAAAGAGCAATATGTGAGAGACACCAGGAAGAACAAAAGTTATTCTGTGA
GGAGGATCAAACCCTCCACTGTGTATCCTGTTTTGAAAGCCAGGAGCATAGCAGGCATACAGTGCACCTTATAGAAATGG
CTGCAGAGGATTCTAGAGACAAGCTCCAGAAAACTTTGGATCTTCTCTGGAAAGAAGTGGAGATGATTCAAAACATGCTG
ACTGAAGAGAGACAGAAAATGGAGACTTGGAATGAACAGGCAGATGCTTGGAGGGAGAGCATTAGAGCAGAATATAAGAG
ATTATATGAGTTCCTAAAGTGTGAGGAAAAGTGGCACCTTCAAAACTTGAGCAGAGATGAAAGTAAGAACATTAAGAATC
TTAGAGAAAGTGAGACCAGGCTTTCTCAACATCTTCAGAGCTTAAAGGAGATCATTATAGATCTTGAGCAAAATGGCCAG
AAACCAGATCTCCAGCTTCTGAAGGTAGGAGGAGGTACACTGAAGAGGATCAAGTCCCTTTTAAGTCATCGTCCAGAAGC
TACCATTATTCAAGTGTCCATGGCTCCAATCACTGGAATCTGGGAAATGATGAAACACTTCAGAGTGAATGTGACACTGG
ATCCTGAAAGTGCCTGTCCTTATCTCATTGTGTCTGAAAATATGAAGACTGTAACCCATAGAGGATATCAGCAGTATATA
CCAGTTGCTCCGCACCAATTTGAAGATAGTATCATTTTGGGGGCTCAAGTCTTTACCTTTGGAATGCACTACTGGGAAGT
AAATGTGGGAGAAAGTAGGAAATGGGCAGTTGGGGTATGTAAGGCATCATTAAGTAGGAATGCAAGTGTTTCTCTTTCTA
CTGGGGATGTATTTCTCCTTACACATTTTCAGAAGCGAAATACTTATTCTATGATGACCACACCTTTCTGCATAGAATAT
CATTCAAATTCACCAATCCAAAAAGTAGGAATTTTTCTAGGTTATGATCAAGGATCCATTTCATTTTATGATGCTTTGAA
GAATTCTTTAATATTTCGTTTCCCTGCCTTCCCCTTCTCTGACCCCCTGAAACCTATATTTTGTCCTTGTCCCCCCAGGG
GAGAAGAGAATGGGATTCCAATGACTATAGATCCTTGA

Alignment

ORF - retro_mdom_60 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.8 %
• Parental protein coverage: 51.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ENFKEELTCPVCLDYFSRPVTLGCGHNFCRLCLLKKWGEVDQPCPCPECRRSFLIRDFEINHRLSRLSKM
          EN.KEELTCPV..DYFS.PV.LGCGH.FC..CLL..W.EVD..CPCPECRR.F.I.D.E.NH.L..LS..
Retrocopy ENLKEELTCPVYMDYFSHPVNLGCGHSFCQPCLLRTWREVDKSCPCPECRRAFQIKDLESNHCLGKLSSL

Parental  ARKIRPYLLQLKKESAVCERHQEEQKLFCKEDQTLLCVSCVQTQDHSKHTVCPIEKAAEYSRDKLQKTLE
          AR.IRPYLLQL..E.A.CERHQEEQKLFC.EDQTL.CVSC...Q.HS.HTV..IE.AAE.SRDKLQKTL.
Retrocopy ARNIRPYLLQLRMERAICERHQEEQKLFCEEDQTLHCVSCFESQEHSRHTVHLIEMAAEDSRDKLQKTLD

Parental  LLWKKVELIQNMLTEEREKMLTWNEQADAWRESTRIQYKRFCEFLKYEEKWHLHLLKMDESKNMKNLRAS
          LLWK.VE.IQNMLTEER.KM.TWNEQADAWRES.R..YKR..EFLK.EEKWHL..L..DESKN.KNLR.S
Retrocopy LLWKEVEMIQNMLTEERQKMETWNEQADAWRESIRAEYKRLYEFLKCEEKWHLQNLSRDESKNIKNLRES

Parental  EARLSQYLQNLKKVIIELEQNDQKTDLQLLQVRLGKISKYSETIA
          E.RLSQ.LQ.LK..II.LEQN.QK.DLQLL.V..G..........
Retrocopy ETRLSQHLQSLKEIIIDLEQNGQKPDLQLLKVGGGTLKRIKSLLS

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	2.50 RPM	0.00 RPM
SRP007412_cerebellum	1.63 RPM	0.00 RPM
SRP007412_heart	1.20 RPM	0.00 RPM
SRP007412_kidney	1.32 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	250.26 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_60 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_60 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000018518	1 retrocopy	retro_fcat_71,
Monodelphis domestica	ENSMODG00000001670	1 retrocopy	retro_mdom_60 ,
Monodelphis domestica	ENSMODG00000022818	2 retrocopies	retro_mdom_129, retro_mdom_1836,