RetrogeneDB - Retrocopy retro_mdom

                        
>retro_mdom_7
ATGACCTTGGAGAGGGACAGACTGCCAGGCCAGGAGGCAGTGAAATTCAAGGATGTGGCTGTGGACTTCACTTGGGAAGA

GTGGCGCCTCTTGTCCCTTCCACAGAAGGAGCTATATAAGGAGGTGATGCTGGAGAATAGCAGGAATCTGCTCTCTGTGG

AAGGAGAGATCAGACCAGAAATGAAGGGGAATCCAACAGAGGAGGTGTTGACATTCAAAGATGTAGCTGTGGACTTCACC

CGGGAGGAGTGGCACCTCTTATCCCCTCTCAAGAAGGAGCTGTACAAGGAGGTGATGCTGGAGAATACCAGGAACCTGCT

CTCTATGGGTCTTCTAGCTCACCCAGAAGCCTTGCTCTTTTATTTGGAGCAGAGAGAAGCCCCACAGATGCTGGAGGAAG

AAGACCTGAGGAGCTGCTGCCCAGGAGGAGAGATCAGACCTGAAATGAAGGTTAATTCAACAGAGGTGAGCCTTCCTGTG

GAAGAAATGGACCTACAAAGATTCATGAGTGATGGTTCTGATAACTTTTATTTCCGAGAATTTGGTGCTGCAACTCAAAG

TTCATCTCATATTGAACATCAAAGAATCCACACTAAGGAAAAATCTAGTGAAAGTAATCATTGTAAAAAGACTTTTATGC

CCAGGGTCAGTTTTGTTAGACATCAGAGCATCAATACTGGTGAGAGATCTTATGAATTCAAGCAGTGTGGAAAGACATTC

AGTCAGAGCTCCCATCTTGCTGTACATCAGAAAATCCATGCTGGTGGGAAAGTTTATGAATGCACTCAATGTGGAACAAT

ATTCATAAATAACTCCAGTCTTTCTGTACATCAGAGAATCCACACTGGGGAGAAACCTTATGAATGCAAGCAGTATGGAA

AGACATTCAGTCAGAGCTCCCATCTTGCTGTACATCAGAGAATCCACACTGGGGAGAAACCTTATGAATGCAAGCAGTAT

GGAAAGACATTCAGTCAGAGCTCCCATCTTGCTGTACATCAGAGAATCCACACTGGGGAGAAACCTTATGAATGCAAGCA

ATGTGGAAAGGCATTCCGACAGAGCTCCCATCTTGCTGTACATCAGAGAGTCCACACTAGAGAGAAAACTTATCAATGCA

AACAATGTGGAAAGGCATTCCGACAGAGCTCCAATCTTTCTAGTCATTAG

ORF - retro_mdom_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	70.3 %
Parental protein coverage:	51.0 %
Number of stop codons detected:	0
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalERDGLPAQEVVSFKDVAVDFTREEWRLLSPPQKELYKEVMLENARNLLSVGLSAPPEDMFSSLEQREAPW
E..G.P..EV..FKDVAVDFTREEW.LLSP..KELYKEVMLEN.RNLLS.GL.A.PE.....LEQREAP.
RetrocopyEMKGNPTEEVLTFKDVAVDFTREEWHLLSPLKKELYKEVMLENTRNLLSMGLLAHPEALLFYLEQREAPQ
ParentalMLEKDDLRSCCPEGKMRPEMKTNSTEVSFSVEELDLEKFMSHGPNNFAFREFCVVPKNSSHIENQRMHTE
MLE..DLRSCCP.G..RPEMK.NSTEVS..VEE.DL..FMS.G..NF.FREF......SSHIE.QR.HT.
RetrocopyMLEEEDLRSCCPGGEIRPEMKVNSTEVSLPVEEMDLQRFMSDGSDNFYFREFGAATQSSSHIEHQRIHTK
ParentalEKSSVNNKCGKTFMPRESLYRYQRIYTTDKPFECHQCGKAFSRSSNLAVHQRIHTGEKPYECQQCGKAFS
EKSS..N.C.KTFMPR.S..R.Q.I.T.....E..QCGK.FS.SS.LAVHQ.IH.G.K.YEC.QCG..F.
RetrocopyEKSSESNHCKKTFMPRVSFVRHQSINTGERSYEFKQCGKTFSQSSHLAVHQKIHAGGKVYECTQCGTIFI
ParentalCSHSLAVHQRIHTGEKPYECKQCEKSFSCSSNLAVHQRIHTGEKPYGCKQCGKTFSRNSHLALHQRIHTG
...SL.VHQRIHTGEKPYECKQ..K.FS.SS.LAVHQRIHTGEKPY.CKQ.GKTFS..SHLA.HQRIHTG
RetrocopyNNSSLSVHQRIHTGEKPYECKQYGKTFSQSSHLAVHQRIHTGEKPYECKQYGKTFSQSSHLAVHQRIHTG
ParentalEKPYECKQCGKAFSCSSTLAVHQRIHTGEKPYECKQCGKAFSCSSTLAEH
EKPYECKQCGKAF..SS.LAVHQR.HT.EK.Y.CKQCGKAF..SS.L..H
RetrocopyEKPYECKQCGKAFRQSSHLAVHQRVHTREKTYQCKQCGKAFRQSSNLSSH

                            

                            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	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 - 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_7 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_7 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000026260	1 retrocopy	retro_acar_18,
Cavia porcellus	ENSCPOG00000004610	1 retrocopy	retro_cpor_99,
Monodelphis domestica	ENSMODG00000023632	1 retrocopy	retro_mdom_7 ,

	RetrogeneDB ID:	retro_mdom_7
Retrocopy location	Organism:	*Opossum (Monodelphis domestica)*
	Coordinates:	5:243067983..243069153(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSMODG00000024617
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	None
	Ensembl ID:	ENSMODG00000023632
	Aliases:	None
	Description:	None

Parental	ERDGLPAQEVVSFKDVAVDFTREEWRLLSPPQKELYKEVMLENARNLLSVGLSAPPEDMFSSLEQREAPW
	E..G.P..EV..FKDVAVDFTREEW.LLSP..KELYKEVMLEN.RNLLS.GL.A.PE.....LEQREAP.
Retrocopy	EMKGNPTEEVLTFKDVAVDFTREEWHLLSPLKKELYKEVMLENTRNLLSMGLLAHPEALLFYLEQREAPQ

Parental	MLEKDDLRSCCPEGKMRPEMKTNSTEVSFSVEELDLEKFMSHGPNNFAFREFCVVPKNSSHIENQRMHTE
	MLE..DLRSCCP.G..RPEMK.NSTEVS..VEE.DL..FMS.G..NF.FREF......SSHIE.QR.HT.
Retrocopy	MLEEEDLRSCCPGGEIRPEMKVNSTEVSLPVEEMDLQRFMSDGSDNFYFREFGAATQSSSHIEHQRIHTK

Parental	EKSSVNNKCGKTFMPRESLYRYQRIYTTDKPFECHQCGKAFSRSSNLAVHQRIHTGEKPYECQQCGKAFS
	EKSS..N.C.KTFMPR.S..R.Q.I.T.....E..QCGK.FS.SS.LAVHQ.IH.G.K.YEC.QCG..F.
Retrocopy	EKSSESNHCKKTFMPRVSFVRHQSINTGERSYEFKQCGKTFSQSSHLAVHQKIHAGGKVYECTQCGTIFI

Parental	CSHSLAVHQRIHTGEKPYECKQCEKSFSCSSNLAVHQRIHTGEKPYGCKQCGKTFSRNSHLALHQRIHTG
	...SL.VHQRIHTGEKPYECKQ..K.FS.SS.LAVHQRIHTGEKPY.CKQ.GKTFS..SHLA.HQRIHTG
Retrocopy	NNSSLSVHQRIHTGEKPYECKQYGKTFSQSSHLAVHQRIHTGEKPYECKQYGKTFSQSSHLAVHQRIHTG

Parental	EKPYECKQCGKAFSCSSTLAVHQRIHTGEKPYECKQCGKAFSCSSTLAEH
	EKPYECKQCGKAF..SS.LAVHQR.HT.EK.Y.CKQCGKAF..SS.L..H
Retrocopy	EKPYECKQCGKAFRQSSHLAVHQRVHTREKTYQCKQCGKAFRQSSNLSSH

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

RetrogeneDB ID:

retro_mdom_7