RetrogeneDB - Retrocopy retro_xtro

						
>retro_xtro_7
ATGAATGCTTTGATAGTAAAGAGAAGATTGCCAGTGCTGCTTTTTCTTTTTTACATTTCCCTGAGTTCCATCTCATCAAA

TACCATATTGGAGAATGATTTTCACTCCAGTTTTGTCCAGAGGAGACTGAAAGGCCATGAACGCAGGGAGATTCAAAAAG

AGATCTTGACTATTTTAGGTTTGCAACACAGACCAAGGCCATATTTACCAGAAAAGAAGAAGTCTGCACCATTATTCATG

ATGGACTTGTACAATGCAGTAAATATTGAAGATTTGAATGCTGAAGATGTCTCCTACTTTAACAAGCCAGTCTCCTTAAA

TGAACATTCTTCACTGGCCACTGACCAAGAAAATGACTTTCTTGCACACGCCGACACAGTCATGAGTTTTGCTAATTTAG

TTGAAAATGACAACGAACTGTATAAAAATCGCCAAAAATTCAAGTTTGATTTAACTGATATCCCTCTTGGAGATGAACTG

ACAGCTGCTGAATTTCGCATTTATAAAGATTATGTAGAAAATAATGAGACATACCAAGTCACTGTCTACCAGGTGCTCCA

GAAACAATACGACAAAGAGCCTTATCTTTTCCAGGTAGACTCAAGAACTATCTGGGGCACAGAAAAGGGGTGGCTGACAT

TTGATATCACTGCGACCAGTAATCACTGGGTGATCAACCCACATTACAACCTTGGATTGCAGTTATCAATAGAGAGTATG

GATATGCAAAGTGTTAATCCCAGGCATGTTGGCCTTTTTGGAAGGAATGGACCTCAAGATAAACAGCCATTTATGGTAGC

TTTCTTTAAAACCTCAGAAATCCATCTCCGTAGTATCCGATCTACCAGCAATAAGCACTGGAACCAGGAAAGAGCCAAGA

CCTACAAGGAACAAGATAATTTCCCTCCAGCAAATATTTCCGATGGCATCATGCCCACTGCCAAACGTAGATTTTTTAAA

CAAGCTTGCAAGAAACATGAACTCTTTGTAAGCTTCCGTGATCTTGGTTGGCAAGACTGGATCATTGCACCAGAAGGATA

TGCTGCCTACTACTGTGATGGAGAATGCGCTTTCCCACTTAACTCTTTCATGAATGCCACAAACCATGCAATTGTACAGA

CTCTGGTACACTTCGTTAACCCAGAGACTGTCCCTAAGCCATGCTGTGCTCCAACTCAACTGAATGGTATTTCTGTTTTA

TATTTTGATGACAGTTCCAATGTTATATTAAAGAAATATAAAAATATGGTGGTTCAAGCATGTGGATGCCATTGA

ORF - retro_xtro_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	54.14 %
Parental protein coverage:	73.65 %
Number of stop codons detected:	0
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalMNVLQKNKTGSVLLWTYFLWRIILADFT-LDNEVHSSFIQRRLRGQERREMQREILSILGLPHRPRPHLY
		MN.L.......VLL.............T.L.N..HSSF.QRRL.G.ERRE.Q.EIL.ILGL.HRPRP.L.
RetrocopyMNALIVKRRLPVLLFLFYISLSSISSNTILENDFHSSFVQRRLKGHERREIQKEILTILGLQHRPRPYLP
ParentalGKQNSAPMFMLDLYNAMTVDEEEAEGFSYPYKPIFTTQGPPLASQQDSNFLNDADMVMSFVNLVEHDKEF
		.K..SAP.FM.DLYNA.......AE..SY..KP........LA..Q...FL..AD.VMSF.NLVE.D.E.
RetrocopyEKKKSAPLFMMDLYNAVNIEDLNAEDVSYFNKPVSLNEHSSLATDQENDFLAHADTVMSFANLVENDNEL
ParentalFHQRRHHREFRFDIAKIPEGEAVTAAEFRIYKDYIRERFENETFQISVYQVLQEHQGRDSDLYELDSRTI
		...R.....F.FD...IP.G...TAAEFRIYKDY......NET.Q..VYQVLQ........L...DSRTI
RetrocopyYKNRQ---KFKFDLTDIPLGDELTAAEFRIYKDYVEN---NETYQVTVYQVLQKQYDKEPYLFQVDSRTI
ParentalWAAEEGWLVFDITTTSNHWVVNPQHNLGLQLSVESIDGQSINPKMAGLIGTNGPHNKQPFMVAFFKATEI
		W..E.GWL.FDIT.TSNHWV.NP..NLGLQLS.ES.D.QS.NP...GL.G.NGP..KQPFMVAFFK..EI
RetrocopyWGTEKGWLTFDITATSNHWVINPHYNLGLQLSIESMDMQSVNPRHVGLFGRNGPQDKQPFMVAFFKTSEI
ParentalHLRSIRSAGGKHRNQNRSKAPKSQEALRVSNIAE
		HLRSIRS...KH.NQ.R.K..K.Q......NI..
RetrocopyHLRSIRSTSNKHWNQERAKTYKEQDNFPPANISD

							

							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	31 .22 RPM
SRP007412_heart	0 .00 RPM	2 .53 RPM
SRP007412_kidney	0 .00 RPM	2 .53 RPM
SRP007412_liver	0 .00 RPM	5 .82 RPM
SRP007412_skeletal_muscle	0 .00 RPM	1 .05 RPM

ChIP-Seq - click to see more details

Xenopus tropicalis was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_xtro_7 retrocopy.

TSS - click to see more details

Xenopus tropicalis was not studied using FANTOM5 data.

Lab - click to see more details

retro_xtro_7 was not experimentally validated.

Retrocopy orthology:

Xenopus tropicalis 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000025711	1 retrocopy	retro_ocun_394,
Xenopus tropicalis	ENSXETG00000011272	1 retrocopy	retro_xtro_7 ,

	RetrogeneDB ID:	retro_xtro_7
Retrocopy location	Organism:	*Xenopus (Xenopus tropicalis)*
	Coordinates:	GL172944.1:269539..270814(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSXETG00000016386
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	bmp7.1
	Ensembl ID:	ENSXETG00000011272
	Aliases:	None
	Description:	bone morphogenetic protein 7, gene 1 [Source:Jamboree;Acc:XB-GENE-486014]

Parental	MNVLQKNKTGSVLLWTYFLWRIILADFT-LDNEVHSSFIQRRLRGQERREMQREILSILGLPHRPRPHLY
	MN.L.......VLL.............T.L.N..HSSF.QRRL.G.ERRE.Q.EIL.ILGL.HRPRP.L.
Retrocopy	MNALIVKRRLPVLLFLFYISLSSISSNTILENDFHSSFVQRRLKGHERREIQKEILTILGLQHRPRPYLP

Parental	GKQNSAPMFMLDLYNAMTVDEEEAEGFSYPYKPIFTTQGPPLASQQDSNFLNDADMVMSFVNLVEHDKEF
	.K..SAP.FM.DLYNA.......AE..SY..KP........LA..Q...FL..AD.VMSF.NLVE.D.E.
Retrocopy	EKKKSAPLFMMDLYNAVNIEDLNAEDVSYFNKPVSLNEHSSLATDQENDFLAHADTVMSFANLVENDNEL

Parental	FHQRRHHREFRFDIAKIPEGEAVTAAEFRIYKDYIRERFENETFQISVYQVLQEHQGRDSDLYELDSRTI
	...R.....F.FD...IP.G...TAAEFRIYKDY......NET.Q..VYQVLQ........L...DSRTI
Retrocopy	YKNRQ---KFKFDLTDIPLGDELTAAEFRIYKDYVEN---NETYQVTVYQVLQKQYDKEPYLFQVDSRTI

Parental	WAAEEGWLVFDITTTSNHWVVNPQHNLGLQLSVESIDGQSINPKMAGLIGTNGPHNKQPFMVAFFKATEI
	W..E.GWL.FDIT.TSNHWV.NP..NLGLQLS.ES.D.QS.NP...GL.G.NGP..KQPFMVAFFK..EI
Retrocopy	WGTEKGWLTFDITATSNHWVINPHYNLGLQLSIESMDMQSVNPRHVGLFGRNGPQDKQPFMVAFFKTSEI

Parental	HLRSIRSAGGKHRNQNRSKAPKSQEALRVSNIAE
	HLRSIRS...KH.NQ.R.K..K.Q......NI..
Retrocopy	HLRSIRSTSNKHWNQERAKTYKEQDNFPPANISD

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

RetrogeneDB ID:

retro_xtro_7