RetrogeneDB - Retrocopy retro_mdom

                        
>retro_mdom_1019
GGGGAAGGTAAAGCTGGCCCTCCAGGAGGCAGTTCAGGAGCAGTATTTCCATAAGGTGGTAGGGGACAGGGCTGTTTTCC

AGGGGCTGTTCCAGGTGGGTACAGATTTCCTGGACCAGGTGGACCAGGAGGGTCACCTTCCACCTTTCCCAGCTGGACAA

ACTCCACCACGTTCACTGCTAGGTCCTCCACCTCCTGATCAGGTTCTTCCTCCTCCATTAGCTGGGCCTCCTAATCAAGG

TGATCACCCTCCACCACCAGTTCTTTTTCCAGGACAGCCTCCATTGGGTCCACTTCCTCCTGGTCCTCCACCTCCATAGC

AGGGATGGCCTCTGCCTCCAGGCCCTTTTCTACCTCACTCACCTGCCCCTCTCCGGCCACTCCTTACACTTGTTCCTCCT

CCACATCTTCCTGGACCACCTCCAGGTGCCCCACTACCAGCTCCACACATGAACCCAGTTTTCTTTCCCCCACCAACCAA

CAGTGGCATGTCAACATCAGACATTCTGGGTCCATCACCCACAGACCCATATGACTGACCTCCCCCCTATTATAGAGGTG

ACTATGGGGCCCCTGGAAGAGAAATGGATGCTACAAGAATGCCATTAAGTGAAGCAGAGTTTGAAGAAATTATGACTAGA

AACAGGGCAATTTCAAGGAGCACCATTTCAAGAGCTATGTCTGACACCAGTGCTGATGATTATGGGAGTGCTATTGAGAC

CTTGCTAACTGCTATTTCCTTAATTAAACAATGCAAAGTATCCATTGATGATCATTGCAAAGTGCTTATTAGTTCTTTGC

AGGATTGCCTTCATGGAATTGAGTCCAAATCTTATGGTTCTGGATAAAGACGTGAACACTCAAGAGAGAGGGACTAGAGT

AGATCCAGAGAAAAGAGTAGACATCACAAATTTCATAGTAGAGATCGTCATGATGATTATTATATAGAGAGAAGCAGAGA

ATGAGGAAGGCATCGGGATCGTGACCAAGACCCAGATTGTGATAGAGAATGTGACAGAAAGTGAGACTATTGCCAC

ORF - retro_mdom_1019 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	66.57 %
Parental protein coverage:	63.52 %
Number of stop codons detected:	7
Number of frameshifts detected:	1

Retrocopy - Parental Gene Alignment:

                                ParentalGRGRGRFPGAVPGGDRFPGPAGPGGPPPPFPAGQTPPRPPLGPPGPPGPPG-PPPPGQVLPPPLAGPPNR
G.G....PG...G.....G..G.G..P...P.G...P....GP.GP.G.P..P.P.GQ..P..L.GPP..
RetrocopyGEGKAGPPGGSSGAVFP*GGRGQGCFPGAVPGGYRFP----GPGGPGGSPS>PFPAGQTPPRSLLGPPPP
ParentalGDRPPPPVLFPGQPFGQPPLGPLPPGPPPPVPGYGPPPGPPPPQQGPPPPPGPFPPRPPGPLGPPLTLAP
....PPP...P......PP...L.PG.PP..P....PPGPPPP.QG.P.PPGPF.P..P.PL.P.LTL.P
RetrocopyDQVLPPPLAGPPNQGDHPPPPVLFPGQPPLGP---LPPGPPPP*QGWPLPPGPFLPHSPAPLRPLLTLVP
ParentalPPHLPGPPPGAPPPAPHVNPAFFPPPTNSGMPTSDSRGPPPTDPYGRPPPYDRGDYGPPGREMDAARTPL
PPHLPGPPPGAP.PAPH.NP.FFPPPTNSGM.TSD..GP.PTDPY..PPPY.RGDYG.PGREMDA.R.PL
RetrocopyPPHLPGPPPGAPLPAPHMNPVFFPPPTNSGMSTSDILGPSPTDPYD*PPPYYRGDYGAPGREMDATRMPL
ParentalSEAEFEEIMNRNRAISSSAISRAVSDASAGDYGSAIETLVTAISLIKQSKVSADDRCKVLISSLQDCLHG
SEAEFEEIM.RNRAIS.S.ISRA.SD.SA.DYGSAIETL.TAISLIKQ.KVS.DD.CKVLISSLQDCLHG
RetrocopySEAEFEEIMTRNRAISRSTISRAMSDTSADDYGSAIETLLTAISLIKQCKVSIDDHCKVLISSLQDCLHG
ParentalIESKSYGSGSRRERSRERDHSRSREKSRRHKSRSRDRHDDYYRERSRERERHRDRDRDR--DRERDRERE
IESKSYGSG.RRE.SRERD.SRSREKSR.HK..SRDRHDDYY.ERSRE..RHRDRD.D...DRE.DR...
RetrocopyIESKSYGSG*RREHSRERD*SRSREKSRHHKFHSRDRHDDYYIERSRE*GRHRDRDQDPDCDRECDRK*D
ParentalYRH
Y.H
RetrocopyYCH

                            

                            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_1019 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_1019 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Microcebus murinus	ENSMICG00000007385	1 retrocopy	retro_mmur_1005,
Myotis lucifugus	ENSMLUG00000004172	3 retrocopies	retro_mluc_2155, retro_mluc_2238, retro_mluc_2588,
Monodelphis domestica	ENSMODG00000007123	1 retrocopy	retro_mdom_1019 ,

	RetrogeneDB ID:	retro_mdom_1019
Retrocopy location	Organism:	*Opossum (Monodelphis domestica)*
	Coordinates:	3:234377489..234378525(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	CPSF6
	Ensembl ID:	ENSMODG00000007123
	Aliases:	None
	Description:	cleavage and polyadenylation specificity factor subunit 6 [Source:RefSeq peptide;Acc:NP_001165832]

Parental	GRGRGRFPGAVPGGDRFPGPAGPGGPPPPFPAGQTPPRPPLGPPGPPGPPG-PPPPGQVLPPPLAGPPNR
	G.G....PG...G.....G..G.G..P...P.G...P....GP.GP.G.P..P.P.GQ..P..L.GPP..
Retrocopy	GEGKAGPPGGSSGAVFP*GGRGQGCFPGAVPGGYRFP----GPGGPGGSPS>PFPAGQTPPRSLLGPPPP

Parental	GDRPPPPVLFPGQPFGQPPLGPLPPGPPPPVPGYGPPPGPPPPQQGPPPPPGPFPPRPPGPLGPPLTLAP
	....PPP...P......PP...L.PG.PP..P....PPGPPPP.QG.P.PPGPF.P..P.PL.P.LTL.P
Retrocopy	DQVLPPPLAGPPNQGDHPPPPVLFPGQPPLGP---LPPGPPPP*QGWPLPPGPFLPHSPAPLRPLLTLVP

Parental	PPHLPGPPPGAPPPAPHVNPAFFPPPTNSGMPTSDSRGPPPTDPYGRPPPYDRGDYGPPGREMDAARTPL
	PPHLPGPPPGAP.PAPH.NP.FFPPPTNSGM.TSD..GP.PTDPY..PPPY.RGDYG.PGREMDA.R.PL
Retrocopy	PPHLPGPPPGAPLPAPHMNPVFFPPPTNSGMSTSDILGPSPTDPYD*PPPYYRGDYGAPGREMDATRMPL

Parental	SEAEFEEIMNRNRAISSSAISRAVSDASAGDYGSAIETLVTAISLIKQSKVSADDRCKVLISSLQDCLHG
	SEAEFEEIM.RNRAIS.S.ISRA.SD.SA.DYGSAIETL.TAISLIKQ.KVS.DD.CKVLISSLQDCLHG
Retrocopy	SEAEFEEIMTRNRAISRSTISRAMSDTSADDYGSAIETLLTAISLIKQCKVSIDDHCKVLISSLQDCLHG

Parental	IESKSYGSGSRRERSRERDHSRSREKSRRHKSRSRDRHDDYYRERSRERERHRDRDRDR--DRERDRERE
	IESKSYGSG.RRE.SRERD.SRSREKSR.HK..SRDRHDDYY.ERSRE..RHRDRD.D...DRE.DR...
Retrocopy	IESKSYGSGRREHSRERDSRSREKSRHHKFHSRDRHDDYYIERSREGRHRDRDQDPDCDRECDRKD

Parental	YRH
	Y.H
Retrocopy	YCH

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

RetrogeneDB ID:

retro_mdom_1019