RetrogeneDB - Retrocopy retro_mdom

                        
>retro_mdom_224
TGTGGTTCGATGGCGGACCTGGACTCCCGTGGCGTGCGCCTGCTCACTCTAAGTGGCCATGTGGGCTTCGACAGCCTCCC

AGAGCAGCTGGTGTGCAGGCAGTTGTGCCAAGGCTTCACCTTCAACATCATGTGCGTGGGTGAGACAGGCATTGGCAAGT

CTACGCTTATGAACACACTCTTCAACACGGACTTCGACTCCCAGGAGTGCAGCCACTTTGAGAGGTGCGTGCGGCTCCGG

CAGTGCTGCTACAACCTGTGCGAGTGTGACGTGCACCTGCGGCTGACCATCGTGGAAGCCCAGGGCTTTGGGGACCAAAT

GGACAAGGATGTGGAGCCCATCGTGAACTACGTGGATGCACAGTTCGAGAGCTACCTGCAGGAGGAGCTCAAGGTGCAGC

GCTGCCTCTACGATTACCTGGACACACGTGTGCACGTGTGCCTCTACTTCATCACACCCACCGGGCACTCTCTCAAGTCC

CTGGACCTGGTGACTCTGAAGCGGCTGGACAGCAAGGTGAACATCATCCCCATCATCGCCAAGGCCGACACCCTGACCAA

ATGCGAGCTGCTCAAGTTCAAGAACAAGATCAAGAACGATCTGGGTAGAAACGGTGTCCGCATCTATCAGTTCCCCACAG

ATGACGAAGCCGTGGCCCAGATCAATGTCGCCATGAACGCCCACTTGCCTTTCGCGGTGGTGGGCAGCATGGACGAGGTT

TGTGTGAACAACAAGCTGGTGCGAGCCCGGGAATACCCATGGGGCGTCGTGCAGGTGGATGATGATGATCACAGCGACTT

TGGGAAGCTCCGTGAGATGCTGATCCGCGTAAACATGGAAGACCTCCGTGAGCAGACCCACCGCTGTCACTACGAGCTCT

ACCGCTGCTGTAGGCTGAAGGAGATGGGCTACCAGTCCTCTCTGCGGGAGTACAAACCCTCT

ORF - retro_mdom_224 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	65.91 %
Parental protein coverage:	71.79 %
Number of stop codons detected:	0
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalNNEDLRNLSLSGHVGFDSLPDQLVNKSTSQGFCFNILCVGETGIGKSTLMDTLFNTKFESDPATHNEPGV
.....R.L.LSGHVGFDSLP.QLV.....QGF.FNI.CVGETGIGKSTLM.TLFNT.F.S....H.E..V
RetrocopyDSRGVRLLTLSGHVGFDSLPEQLVCRQLCQGFTFNIMCVGETGIGKSTLMNTLFNTDFDSQECSHFERCV
ParentalRLKARSYELQESNVRLKLTIVDTVGFGDQINKDDSYKPIVEYIDAQFEAYLQEELKIKRSLFNYHDTRIH
RL....Y.L.E..V.L.LTIV...GFGDQ..KD....PIV.Y.DAQFE.YLQEELK..R.L..Y.DTR.H
RetrocopyRLRQCCYNLCECDVHLRLTIVEAQGFGDQMDKD--VEPIVNYVDAQFESYLQEELKVQRCLYDYLDTRVH
ParentalACLYFIAPTGHSLKSLDLVTMKKLDSKVNIIPIIAKADTIAKNELHRFKSKIMSELVSNGVQIYQFPTDE
.CLYFI.PTGHSLKSLDLVT.K.LDSKVNIIPIIAKADT..K.EL..FK.KI...L..NGV.IYQFPTD.
RetrocopyVCLYFITPTGHSLKSLDLVTLKRLDSKVNIIPIIAKADTLTKCELLKFKNKIKNDLGRNGVRIYQFPTDD
ParentalETVAEINATMSVHLPFAVVGSTEEVKIGNKMAKARQYPWGVVQVENENHCDFVKLREMLIRVNMEDLREQ
E.VA.IN..M..HLPFAVVGS..EV...NK...AR.YPWGVVQV....H.DF.KLREMLIRVNMEDLREQ
RetrocopyEAVAQINVAMNAHLPFAVVGSMDEVCVNNKLVRAREYPWGVVQVDDDDHSDFGKLREMLIRVNMEDLREQ
ParentalTHTRHYELYRRCKLEEMGFKDTDPDSKP
TH..HYELYR.C.L.EMG........KP
RetrocopyTHRCHYELYRCCRLKEMGYQSSLREYKP

                            

                            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 .12 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	55 .98 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_224 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_224 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003906	1 retrocopy	retro_chof_1543,
Callithrix jacchus	ENSCJAG00000014744	1 retrocopy	retro_cjac_2336,
Monodelphis domestica	ENSMODG00000003104	1 retrocopy	retro_mdom_93,
Monodelphis domestica	ENSMODG00000011825	1 retrocopy	retro_mdom_224 ,
Monodelphis domestica	ENSMODG00000016041	1 retrocopy	retro_mdom_888,
Monodelphis domestica	ENSMODG00000021167	1 retrocopy	retro_mdom_1672,
Oryctolagus cuniculus	ENSOCUG00000001289	1 retrocopy	retro_ocun_1758,
Otolemur garnettii	ENSOGAG00000005210	1 retrocopy	retro_ogar_2831,
Pan troglodytes	ENSPTRG00000016192	1 retrocopy	retro_ptro_2753,

	RetrogeneDB ID:	retro_mdom_224
Retrocopy location	Organism:	*Opossum (Monodelphis domestica)*
	Coordinates:	1:13438904..13439846(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSMODG00000010954
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	SEPT11
	Ensembl ID:	ENSMODG00000011825
	Aliases:	None
	Description:	septin 11 [Source:HGNC Symbol;Acc:25589]

Parental	NNEDLRNLSLSGHVGFDSLPDQLVNKSTSQGFCFNILCVGETGIGKSTLMDTLFNTKFESDPATHNEPGV
	.....R.L.LSGHVGFDSLP.QLV.....QGF.FNI.CVGETGIGKSTLM.TLFNT.F.S....H.E..V
Retrocopy	DSRGVRLLTLSGHVGFDSLPEQLVCRQLCQGFTFNIMCVGETGIGKSTLMNTLFNTDFDSQECSHFERCV

Parental	RLKARSYELQESNVRLKLTIVDTVGFGDQINKDDSYKPIVEYIDAQFEAYLQEELKIKRSLFNYHDTRIH
	RL....Y.L.E..V.L.LTIV...GFGDQ..KD....PIV.Y.DAQFE.YLQEELK..R.L..Y.DTR.H
Retrocopy	RLRQCCYNLCECDVHLRLTIVEAQGFGDQMDKD--VEPIVNYVDAQFESYLQEELKVQRCLYDYLDTRVH

Parental	ACLYFIAPTGHSLKSLDLVTMKKLDSKVNIIPIIAKADTIAKNELHRFKSKIMSELVSNGVQIYQFPTDE
	.CLYFI.PTGHSLKSLDLVT.K.LDSKVNIIPIIAKADT..K.EL..FK.KI...L..NGV.IYQFPTD.
Retrocopy	VCLYFITPTGHSLKSLDLVTLKRLDSKVNIIPIIAKADTLTKCELLKFKNKIKNDLGRNGVRIYQFPTDD

Parental	ETVAEINATMSVHLPFAVVGSTEEVKIGNKMAKARQYPWGVVQVENENHCDFVKLREMLIRVNMEDLREQ
	E.VA.IN..M..HLPFAVVGS..EV...NK...AR.YPWGVVQV....H.DF.KLREMLIRVNMEDLREQ
Retrocopy	EAVAQINVAMNAHLPFAVVGSMDEVCVNNKLVRAREYPWGVVQVDDDDHSDFGKLREMLIRVNMEDLREQ

Parental	THTRHYELYRRCKLEEMGFKDTDPDSKP
	TH..HYELYR.C.L.EMG........KP
Retrocopy	THRCHYELYRCCRLKEMGYQSSLREYKP

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

RetrogeneDB ID:

retro_mdom_224