RetrogeneDB - Retrocopy retro_mdom

						
>retro_mdom_60
ATGGCAATGGCAAAATTAGCTGAAAACCTCAAGGAAGAGCTGACTTGTCCTGTGTACATGGACTACTTCAGCCACCCAGT

GAATTTAGGCTGTGGCCATAGCTTTTGCCAACCTTGCCTCCTTAGGACCTGGAGAGAAGTTGACAAATCCTGCCCCTGTC

CTGAATGCAGAAGAGCCTTCCAGATAAAAGACTTGGAGTCCAACCATTGCTTGGGAAAGCTGTCTAGCTTAGCTAGAAAC

ATTAGACCCTACTTATTGCAGCTGAGGATGGAAAGAGCAATATGTGAGAGACACCAGGAAGAACAAAAGTTATTCTGTGA

GGAGGATCAAACCCTCCACTGTGTATCCTGTTTTGAAAGCCAGGAGCATAGCAGGCATACAGTGCACCTTATAGAAATGG

CTGCAGAGGATTCTAGAGACAAGCTCCAGAAAACTTTGGATCTTCTCTGGAAAGAAGTGGAGATGATTCAAAACATGCTG

ACTGAAGAGAGACAGAAAATGGAGACTTGGAATGAACAGGCAGATGCTTGGAGGGAGAGCATTAGAGCAGAATATAAGAG

ATTATATGAGTTCCTAAAGTGTGAGGAAAAGTGGCACCTTCAAAACTTGAGCAGAGATGAAAGTAAGAACATTAAGAATC

TTAGAGAAAGTGAGACCAGGCTTTCTCAACATCTTCAGAGCTTAAAGGAGATCATTATAGATCTTGAGCAAAATGGCCAG

AAACCAGATCTCCAGCTTCTGAAGGTAGGAGGAGGTACACTGAAGAGGATCAAGTCCCTTTTAAGTCATCGTCCAGAAGC

TACCATTATTCAAGTGTCCATGGCTCCAATCACTGGAATCTGGGAAATGATGAAACACTTCAGAGTGAATGTGACACTGG

ATCCTGAAAGTGCCTGTCCTTATCTCATTGTGTCTGAAAATATGAAGACTGTAACCCATAGAGGATATCAGCAGTATATA

CCAGTTGCTCCGCACCAATTTGAAGATAGTATCATTTTGGGGGCTCAAGTCTTTACCTTTGGAATGCACTACTGGGAAGT

AAATGTGGGAGAAAGTAGGAAATGGGCAGTTGGGGTATGTAAGGCATCATTAAGTAGGAATGCAAGTGTTTCTCTTTCTA

CTGGGGATGTATTTCTCCTTACACATTTTCAGAAGCGAAATACTTATTCTATGATGACCACACCTTTCTGCATAGAATAT

CATTCAAATTCACCAATCCAAAAAGTAGGAATTTTTCTAGGTTATGATCAAGGATCCATTTCATTTTATGATGCTTTGAA

GAATTCTTTAATATTTCGTTTCCCTGCCTTCCCCTTCTCTGACCCCCTGAAACCTATATTTTGTCCTTGTCCCCCCAGGG

GAGAAGAGAATGGGATTCCAATGACTATAGATCCTTGA

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:

									ParentalENFKEELTCPVCLDYFSRPVTLGCGHNFCRLCLLKKWGEVDQPCPCPECRRSFLIRDFEINHRLSRLSKM
		EN.KEELTCPV..DYFS.PV.LGCGH.FC..CLL..W.EVD..CPCPECRR.F.I.D.E.NH.L..LS..
RetrocopyENLKEELTCPVYMDYFSHPVNLGCGHSFCQPCLLRTWREVDKSCPCPECRRAFQIKDLESNHCLGKLSSL
ParentalARKIRPYLLQLKKESAVCERHQEEQKLFCKEDQTLLCVSCVQTQDHSKHTVCPIEKAAEYSRDKLQKTLE
		AR.IRPYLLQL..E.A.CERHQEEQKLFC.EDQTL.CVSC...Q.HS.HTV..IE.AAE.SRDKLQKTL.
RetrocopyARNIRPYLLQLRMERAICERHQEEQKLFCEEDQTLHCVSCFESQEHSRHTVHLIEMAAEDSRDKLQKTLD
ParentalLLWKKVELIQNMLTEEREKMLTWNEQADAWRESTRIQYKRFCEFLKYEEKWHLHLLKMDESKNMKNLRAS
		LLWK.VE.IQNMLTEER.KM.TWNEQADAWRES.R..YKR..EFLK.EEKWHL..L..DESKN.KNLR.S
RetrocopyLLWKEVEMIQNMLTEERQKMETWNEQADAWRESIRAEYKRLYEFLKCEEKWHLQNLSRDESKNIKNLRES
ParentalEARLSQYLQNLKKVIIELEQNDQKTDLQLLQVRLGKISKYSETIA
		E.RLSQ.LQ.LK..II.LEQN.QK.DLQLL.V..G..........
RetrocopyETRLSQHLQSLKEIIIDLEQNGQKPDLQLLKVGGGTLKRIKSLLS

							

							Legend:
							
								*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide

						

RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

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 - click to see more details

Monodelphis domestica was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mdom_60 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_60 was not experimentally validated.

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,

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

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

*	Stop codon
>	Forward frameshift by one nucleotide
<	Reverse frameshift by one nucleotide

RetrogeneDB ID:

retro_mdom_60