RetrogeneDB ID:

retro_xtro_2

Retrocopy
location
Organism:Xenopus (Xenopus tropicalis)
Coordinates:GL173441.1:386499..387861(-)
Located in intron of:ENSXETG00000005043
Retrocopy
information
Ensembl ID:ENSXETG00000032820
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:fbxw7
Ensembl ID:ENSXETG00000009388
Aliases:None
Description:F-box and WD repeat domain containing 7 [Source:Jamboree;Acc:XB-GENE-1000486]


Retrocopy-Parental alignment summary:






>retro_xtro_2
ACTGGGGCCTCCCACCAGCCTACAGGAGGAGCCCAAATTGCTGCTAAACTGGTCGGCCGGAAGGAGAAGCAGAAGAAAAT
GGAAGCCGGGGAGCCCCAGGACTTTATCTCTTCATTCCCTGATGAGTTGGCATTGCGCATCCTCTCGTACCTTGATGCCA
AGGATATCCTGCAGGTGGCGCAGACTTGCCAGCGCTGGAGAGAGTTGGCTGAGGATGAAGGCCTGTGGCAGGGAAAGTGC
AAAGTGGATCGGATCGACGTGGCGAGAAGCAGAGATCCGGGTTCGCCGGCCGACCCATGGAAAAGCGCCTACATCCGTCA
GCACCAGATCAACACCAACTGGCGCCGGGGGAGATTCCGATCCATAAACTTACGCCTGCGGCACGACGACGAGGTCATTA
CCTGCTTGGAGTTTGATGGGAGCCGAATACTCAGCAGCGACAGTTGGAAGACAATCAAGGTCTGGTCGGCGGTTACGGGC
GAATGTCTGAGGACGCTCGTCGGTCACGCGGATATTATATTTACAATGCAAATGAGCTCGGAGATTATAATTAGCGGATC
CCTGGATCAGACCTTGAAAGTGTGGGACGCAGAGACCGGGGATTGTATTCACACGTTACGCGGCCATAGCGCCGGCGTGG
AGTGCGTGCATCTCTGCGGGAAAAGGGCCGTCAGTGGCTCCCAAGACAGAACCATCAGAGTCTGGGACATCGAGACCGGC
CGCTGCCTTCACCTCCTCACCGGGCACCGAGACTTCATCAAATGTGTTCGGTATCACGGGCAAAGGGTGGTGAGCTTTGC
GTACGATTCCACCGTGAAAATATGGGACCCCGAGAGTGAGAGCTGCGTGCGCACCCTGCAAGGCCGCGCCGACAAGACCT
CCAGTTTAGAGTCCGACGGGGTCCACGTGGTCACCGTGTCCGACAGAACCACCATAAGAGTCTGGGATGAGGCGACGGGG
CGATGTATCCAAACACTGACCGGATACCCGTTCGCCATTAGTGCGGTGGCGCTGGCGGGCAATATCCTCGTGTCCGGAAA
CGCTGATTGCACCGCTAACGTGTGGGACATAAAAACGGGGCGGTGCTTGCACACTCTGCGCGGCCCTGCCCACATGAGAA
GCCGATTGGAAAGCGTTCAGCTGAGGAGGGACTGCGTCATAGCCAGCGCCGAAGACGGAACCGTCACCCTGTGGGACTGG
AAAAGTGGGGCCTTCTTGCAGAACCTGGCGCTGTCGCACACCAAGGGGCCCTGTTCCATCCAGTTCCAAGTCTCCAACAC
AAAACTCGTCTGCGCCGTCTCGAAAAGATCCAGAGTCGCGTTCGAGCCAACAAAGGTGGTGGTTCTGGACTTTGGTGCCG
AC

ORF - retro_xtro_2 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 56.87 %
Parental protein coverage: 51.49 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalPGFTHSPWKSAYIRQHRIDTNWRRGELKSPKVLKGHDDHVITCLQFCGNRIVSGSDDNTLKVWSAVTGKC
PG....PWKSAYIRQH.I.TNWRRG...S......HDD.VITCL.F.G.RI.S.....T.KVWSAVTG.C
RetrocopyPGSPADPWKSAYIRQHQINTNWRRGRFRSINLRLRHDDEVITCLEFDGSRILSSDSWKTIKVWSAVTGEC
ParentalLRTLVGHTGGVWSSQMRDNIIISGSTDRTLKVWNAETGECIHTLYGHTSTVRCMHLHEKRVVSGSRDATL
LRTLVGH.......QM...IIISGS.D.TLKVW.AETG.CIHTL.GH...V.C.HL..KR.VSGS.D.T.
RetrocopyLRTLVGHADIIFTMQMSSEIIISGSLDQTLKVWDAETGDCIHTLRGHSAGVECVHLCGKRAVSGSQDRTI
ParentalRVWDIETGQCLHVLMGHVAAVRCVQYDGRRVVSGAYDFMVKVWDPETETCLHTLQGHTNRVYSLQFDGIH
RVWDIETG.CLH.L.GH.....CV.Y.G.RVVS.AYD..VK.WDPE.E.C..TLQG......SL..DG.H
RetrocopyRVWDIETGRCLHLLTGHRDFIKCVRYHGQRVVSFAYDSTVKIWDPESESCVRTLQGRADKTSSLESDGVH
ParentalVVSGSLDTSIRVWDVETGNCIHTLTGHQSLTSGMELKDNILVSGNADSTVKIWDIKTGQCLQTLQGPNKH
VV..S..T.IRVWD..TG.CI.TLTG.....S...L..NILVSGNAD.T...WDIKTG.CL.TL.GP...
RetrocopyVVTVSDRTTIRVWDEATGRCIQTLTGYPFAISAVALAGNILVSGNADCTANVWDIKTGRCLHTLRGPAHM
ParentalQSAVTCLQFNKNFVITSSDDGTVKLWDLKTGEFIRNLVTLESGGSGGVVWRIRASNTKLVCAVG--SRNG
.S.....Q.....VI.S..DGTV.LWD.K.G.F..NL......G..........SNTKLVCAV...SR..
RetrocopyRSRLESVQLRRDCVIASAEDGTVTLWDWKSGAFLQNLALSHTKGPCSIQFQV--SNTKLVCAVSKRSRVA
ParentalTEETKLLVLDFDVD
.E.TK..VLDF..D
RetrocopyFEPTKVVVLDFGAD

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 .14 RPM 68 .47 RPM
SRP007412_heart 0 .06 RPM 9 .81 RPM
SRP007412_kidney 0 .06 RPM 9 .81 RPM
SRP007412_liver 0 .76 RPM 3 .45 RPM
SRP007412_skeletal_muscle 0 .12 RPM 7 .09 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_2 retrocopy.

TSS - click to see more details

Xenopus tropicalis was not studied using FANTOM5 data.

Lab - click to see more details

retro_xtro_2 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Xenopus tropicalis ENSXETG00000009388 1 retrocopy
retro_xtro_2 ,


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