RetrogeneDB - Retrocopy retro_mdom

                        
>retro_mdom_1
ATGTTTGTTAACGGAGCTTCTGAGCACATTGCTGAATATATCCCAGAAAAAGTGAAGAAAGCAGAAAAGAAACTAGAAAA

TAATTCATATGACCTTACTGCTTGGAGCATTCTGATTAGAGAGGCACAGAGTCAATCTGTAGAAAAAGCACGGAAGACAC

TTGAACGTCTTGTTGCTCAATTCCCCAGTTCTGGCAGATTCTGGAAACTGTACATTGAAGCAGAGATTAAAACTAAAAAT

TTTGACAAGGCTGAAAAGTTATTTCAGAGATGCCTCATAAAAGTTTTACATATTGACTTGTGGAAGTGTTATCTGACTTA

TATCAGAGAAACCAAGGCAAGACTTCCCAGTTTCAAAGAAAAAATGGCACAAGCATATGACTTTACTTTGGATAAAATTG

GAATGGAGATTATGTCTCATCAAATTTGGATGGATTACATCAATTTCTTGAAAGGGGTAGAAGCTATTGGATCTTATGCA

GAAAATCAAAGAATAACAGCTGTCCGAAGAGTTTATCAACGTGGTTGTGTTAATCCAATGATCAATATTGAGCAACTTTG

GAAGGACTATAATAAATATGAAGAGGGCATCAACATACATATAGCTAAAAAAATGATTGATGATAGAAGCAGAGATTACA

TGAATGCAAGACGTGTGGCAAAGGAGTATGAAACAGTCGTGAAAGGTTTAGACCGCAATGCTCCTTCAGTACCTCCACAG

AATACTCCCCAAGAAGCTCAGCAAGTAGACATGTGGAAGAAATACATCCAGTGGGAAAAGAACAATCCTCTCCGAACAGA

AGATCACACGCTCATAACAAAAAGAGTGATATTTGCATATGAGCAGTGCCTGCTTGTGCTGGGTCATCACCCAGATATTT

GGCACGAAGCTGCGCAGTACCTGGAGCAATCCAGTAAGCTGTTGGCTGAGAAAGGGGACATGAACAATTCCAAATTATTT

AGCAATGAAGCCGCTAATATATATGAAAGAGCTATCAGCTCTTTACTGAAGAAAAATATGCTGCTTTATTTTGCATATGC

AGATTATGAAGAAAGTCGAATGAAATACGAGAAGGTACATAGCATATATAATAGATTTCTAGTTATTGAAGATATTGATC

CTACTCTGGTTTATATCCAATATATGAAATTTGCAAGGCGAGCAGAAGGCATCAAAGCTGGAAGGATGGTATTTAAAAGA

GCGAGAGGAGACACTAGAGCACGCTACCATATCTATGTTGCAGCAGCATTAACGGAGTACTACTGTAGTAAAGATAAAAT

AGTGGCCTTTAAGATTTTTGAGCTGGGGTTAAAAAAATATGGGAACATTCCAGAATATGTATTAGCCTATATTGACTACC

TCTCTCACCTTAATGAGGACAATAATACACGAGTTTTGTTTGAACGAGTATTAACATCTGGAGTCCTTCCACCTGACAAA

TCTGGAGAAATCTGGGCCAGATATCTAGCTTTTGAAAGTAGCTTTGGTGATCTAGTCAGTATCCTGAAAGTGGAGAAGAG

ACTGTTCACAGCGTTCAAGGAAGAATATGAATTCAAGGAAACAGCGTTACGGGTTGATAGATATAAGTTCCTGGATTTGT

ATCCCTGCCGTGCAAGTGAATTAAAGGCTTTTGGCTATAAAGATGTTTCTCGGACCAAGCTAGGAATCATCATTCCTGAC

CCCATGGTAACTCCTTCTGTAGTGTCTGTTCTTAAAAATGAAGAGGATAGAAAACCGAAATACCCCAGACCAGACGTCCG

GCAGATGATACCCTTTCAGCCAAGGCATTTTGCATCCCCAGGCTTACACCCTGTGTCTGGTGGAGTGTTTCCGGTGCCAC

CTGCTGCTGTACTTTTAATGAAACTCCTCCCTCCTCCAGTCTGTTTCCAGGGTCCTTTTGTGCAAGTAGATGAATTGATG

GAAATTTTCCGAAGATGTGAGATCCCGAGCACTCTTGATGAAGCTGTGAAAATCATCACTGGAAGAGTACCATACCGGGC

CAGGGACCGAAACAGTTTTCTGGAAAGCAGTAGCACAGTGAAAAGAGTAGCCAAACGACCCAATGAAGATATGAATGAGG

AAGGAGGAAAACACAAAGCAAGGCCACCTGTCCACGACATTTACAGAGCCCGACAACAGAAGAGAATCCGATGA

ORF - retro_mdom_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	84.87 %
Parental protein coverage:	99.58 %
Number of stop codons detected:	0
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalDGAAEQAAEYVPEKVKKAEKKLEENPYDLDAWSILIREAQNQPIDKARKTYERLVAQFPSSGRFWKLYIE
.GA.E..AEY.PEKVKKAEKKLE.N.YDL.AWSILIREAQ.Q...KARKT.ERLVAQFPSSGRFWKLYIE
RetrocopyNGASEHIAEYIPEKVKKAEKKLENNSYDLTAWSILIREAQSQSVEKARKTLERLVAQFPSSGRFWKLYIE
ParentalAEIKAKNYDKVEKLFQRCLMKVLHIDLWKCYLSYVRETKGKLPSYKEKMAQAYDFALDKIGMEIMSYQIW
AEIK.KN.DK.EKLFQRCL.KVLHIDLWKCYL.Y.RETK..LPS.KEKMAQAYDF.LDKIGMEIMS.QIW
RetrocopyAEIKTKNFDKAEKLFQRCLIKVLHIDLWKCYLTYIRETKARLPSFKEKMAQAYDFTLDKIGMEIMSHQIW
ParentalVDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVNPMINIEQLWRDYNKYEEGINIHLAKKMIEDRSRDY
.DYINFLKGVEA.GSYAENQRITAVRRVYQRGCVNPMINIEQLW.DYNKYEEGINIH.AKKMI.DRSRDY
RetrocopyMDYINFLKGVEAIGSYAENQRITAVRRVYQRGCVNPMINIEQLWKDYNKYEEGINIHIAKKMIDDRSRDY
ParentalMNARRVAKEYETVMKGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQC
MNARRVAKEYETV.KGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEK.NPLRTED.TLITKRV.FAYEQC
RetrocopyMNARRVAKEYETVVKGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEKNNPLRTEDHTLITKRVIFAYEQC
ParentalLLVLGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESR
LLVLGHHPDIW.EAAQYLEQSSKLLAEKGDMNN.KLFS.EAANIYERAIS.LLKKNMLLYFAYADYEESR
RetrocopyLLVLGHHPDIWHEAAQYLEQSSKLLAEKGDMNNSKLFSNEAANIYERAISSLLKKNMLLYFAYADYEESR
ParentalMKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDTRTRHHVYVTAALMEYYCS
MKYEKVHSIYNR.L.IEDIDPTLVYIQYMKFARRAEGIK.GRM.FK.AR.DTR.R.H.YV.AAL.EYYCS
RetrocopyMKYEKVHSIYNRFLVIEDIDPTLVYIQYMKFARRAEGIKAGRMVFKRARGDTRARYHIYVAAALTEYYCS
ParentalKDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFES
KDK.VAFKIFELGLKKYG.IPEYVLAYIDYLSHLNEDNNTRVLFERVLTSG.LPP.KSGEIWAR.LAFES
RetrocopyKDKIVAFKIFELGLKKYGNIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGVLPPDKSGEIWARYLAFES
ParentalNIGDLASILKVEKRRFTAFKEEYEGKETALLVDRYKFMDLYPCSASELKALGYKDVSRAKLATIIPDPVV
..GDL.SILKVEKR.FTAFKEEYE.KETAL.VDRYKF.DLYPC.ASELKA.GYKDVSR.KL..IIPDP.V
RetrocopySFGDLVSILKVEKRLFTAFKEEYEFKETALRVDRYKFLDLYPCRASELKAFGYKDVSRTKLGIIIPDPMV
ParentalAPSIVPVLKDEVDRKPEYPKPDTQQMIPFQPRHLAPPGLHPVPGGVFPVPPAAVVLMKLLPPPVCFQGPF
.PS.V.VLK.E.DRKP.YP.PD..QMIPFQPRH.A.PGLHPV.GGVFPVPPAAV.LMKLLPPPVCFQGPF
RetrocopyTPSVVSVLKNEEDRKPKYPRPDVRQMIPFQPRHFASPGLHPVSGGVFPVPPAAVLLMKLLPPPVCFQGPF
ParentalVQVDELMEIFRRCKIPSTVDEAVRIITGGVPDLAVEGNGPVESSAVLTKAVKRPNEDSDEDEEKGAVVPP
VQVDELMEIFRRC.IPST.DEAV.IITG.VP..A...N...ESS.......KRPNED..E...K....PP
RetrocopyVQVDELMEIFRRCEIPSTLDEAVKIITGRVPYRARDRNSFLESSSTVKRVAKRPNEDMNEEGGKHKARPP
ParentalIHDIYRARQQKRIR
.HDIYRARQQKRIR
RetrocopyVHDIYRARQQKRIR

                            

                            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_1 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1 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
Macropus eugenii	ENSMEUG00000005640	1 retrocopy	retro_meug_1862,
Myotis lucifugus	ENSMLUG00000003073	1 retrocopy	retro_mluc_240,
Monodelphis domestica	ENSMODG00000009745	1 retrocopy	retro_mdom_1 ,

	RetrogeneDB ID:	retro_mdom_1
Retrocopy location	Organism:	*Opossum (Monodelphis domestica)*
	Coordinates:	X:46041739..46043893(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSMODG00000025205
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	None
	Ensembl ID:	ENSMODG00000009745
	Aliases:	None
	Description:	None

Parental	DGAAEQAAEYVPEKVKKAEKKLEENPYDLDAWSILIREAQNQPIDKARKTYERLVAQFPSSGRFWKLYIE
	.GA.E..AEY.PEKVKKAEKKLE.N.YDL.AWSILIREAQ.Q...KARKT.ERLVAQFPSSGRFWKLYIE
Retrocopy	NGASEHIAEYIPEKVKKAEKKLENNSYDLTAWSILIREAQSQSVEKARKTLERLVAQFPSSGRFWKLYIE

Parental	AEIKAKNYDKVEKLFQRCLMKVLHIDLWKCYLSYVRETKGKLPSYKEKMAQAYDFALDKIGMEIMSYQIW
	AEIK.KN.DK.EKLFQRCL.KVLHIDLWKCYL.Y.RETK..LPS.KEKMAQAYDF.LDKIGMEIMS.QIW
Retrocopy	AEIKTKNFDKAEKLFQRCLIKVLHIDLWKCYLTYIRETKARLPSFKEKMAQAYDFTLDKIGMEIMSHQIW

Parental	VDYINFLKGVEAVGSYAENQRITAVRRVYQRGCVNPMINIEQLWRDYNKYEEGINIHLAKKMIEDRSRDY
	.DYINFLKGVEA.GSYAENQRITAVRRVYQRGCVNPMINIEQLW.DYNKYEEGINIH.AKKMI.DRSRDY
Retrocopy	MDYINFLKGVEAIGSYAENQRITAVRRVYQRGCVNPMINIEQLWKDYNKYEEGINIHIAKKMIDDRSRDY

Parental	MNARRVAKEYETVMKGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEKSNPLRTEDQTLITKRVMFAYEQC
	MNARRVAKEYETV.KGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEK.NPLRTED.TLITKRV.FAYEQC
Retrocopy	MNARRVAKEYETVVKGLDRNAPSVPPQNTPQEAQQVDMWKKYIQWEKNNPLRTEDHTLITKRVIFAYEQC

Parental	LLVLGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAISTLLKKNMLLYFAYADYEESR
	LLVLGHHPDIW.EAAQYLEQSSKLLAEKGDMNN.KLFS.EAANIYERAIS.LLKKNMLLYFAYADYEESR
Retrocopy	LLVLGHHPDIWHEAAQYLEQSSKLLAEKGDMNNSKLFSNEAANIYERAISSLLKKNMLLYFAYADYEESR

Parental	MKYEKVHSIYNRLLAIEDIDPTLVYIQYMKFARRAEGIKSGRMIFKKAREDTRTRHHVYVTAALMEYYCS
	MKYEKVHSIYNR.L.IEDIDPTLVYIQYMKFARRAEGIK.GRM.FK.AR.DTR.R.H.YV.AAL.EYYCS
Retrocopy	MKYEKVHSIYNRFLVIEDIDPTLVYIQYMKFARRAEGIKAGRMVFKRARGDTRARYHIYVAAALTEYYCS

Parental	KDKSVAFKIFELGLKKYGDIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSGEIWARFLAFES
	KDK.VAFKIFELGLKKYG.IPEYVLAYIDYLSHLNEDNNTRVLFERVLTSG.LPP.KSGEIWAR.LAFES
Retrocopy	KDKIVAFKIFELGLKKYGNIPEYVLAYIDYLSHLNEDNNTRVLFERVLTSGVLPPDKSGEIWARYLAFES

Parental	NIGDLASILKVEKRRFTAFKEEYEGKETALLVDRYKFMDLYPCSASELKALGYKDVSRAKLATIIPDPVV
	..GDL.SILKVEKR.FTAFKEEYE.KETAL.VDRYKF.DLYPC.ASELKA.GYKDVSR.KL..IIPDP.V
Retrocopy	SFGDLVSILKVEKRLFTAFKEEYEFKETALRVDRYKFLDLYPCRASELKAFGYKDVSRTKLGIIIPDPMV

Parental	APSIVPVLKDEVDRKPEYPKPDTQQMIPFQPRHLAPPGLHPVPGGVFPVPPAAVVLMKLLPPPVCFQGPF
	.PS.V.VLK.E.DRKP.YP.PD..QMIPFQPRH.A.PGLHPV.GGVFPVPPAAV.LMKLLPPPVCFQGPF
Retrocopy	TPSVVSVLKNEEDRKPKYPRPDVRQMIPFQPRHFASPGLHPVSGGVFPVPPAAVLLMKLLPPPVCFQGPF

Parental	VQVDELMEIFRRCKIPSTVDEAVRIITGGVPDLAVEGNGPVESSAVLTKAVKRPNEDSDEDEEKGAVVPP
	VQVDELMEIFRRC.IPST.DEAV.IITG.VP..A...N...ESS.......KRPNED..E...K....PP
Retrocopy	VQVDELMEIFRRCEIPSTLDEAVKIITGRVPYRARDRNSFLESSSTVKRVAKRPNEDMNEEGGKHKARPP

Parental	IHDIYRARQQKRIR
	.HDIYRARQQKRIR
Retrocopy	VHDIYRARQQKRIR

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

RetrogeneDB ID:

retro_mdom_1