RetrogeneDB ID:

retro_xtro_59

Retrocopy
location
Organism:Xenopus (Xenopus tropicalis)
Coordinates:GL181791.1:12310..13111(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:agmat
Ensembl ID:ENSXETG00000025999
Aliases:None
Description:agmatine ureohydrolase (agmatinase) [Source:Jamboree;Acc:XB-GENE-997016]


Retrocopy-Parental alignment summary:






>retro_xtro_59
GACCTGGGCACATCCAACCGCACCGGAGCACGTTTCGGCCCACGGGCCATCCGGGCCGAATCCGTGCTGCTGCGCCCCTA
CAACATGGCCACCCGTGCCGCGCCGTTCGACTCGCTGCAAGTCGCAGACCTGGGCGATGTGGCCATCAATCCGTACAACC
TGGCCGACTCGATTGCGCGGATCGAAGGGGCGTACGACCAGATCGTGTCCAGCGGCTGCCGCCCCATCACACTCGGTGGA
GATCACACGGTGACGCTGCCGGTGCTTCGTGCGATGAAGCGTCGCTATGGTTCGCTGGCCTTGATTCATGTGGACGCGCA
CGCCGACGTGAACGACACCATGTTCGGTGAAAAGATCGCCCACGGTACACCGTTCCGGCGGGCGGTCGAGGAAGGCCTGT
TGCTCACCAGCCGGGTGACCCAGATCGGACTGCGTGGCACCGGTTATTCAGCAGAGGATTTCGACTGGTGCCGCGATCAG
GGCTTTACCGTCGTGCAGGTCGAACAGGTGTGGAGACGGTCGCTCGAACCGCTGATGGATGCGGTGAGAACCCGCGTGGG
TGAAGCGCCGGTGTACCTGAGTTTCGACATCGACGGCATCGACCCGGCGTTCGCACCGGGCACCGGCACGCCCGAAATTG
CAGGACTGACGGTGCCGCAGGCGCTGGAGATCATCCGGGGCTGCCGGGGCCTGAACCTGGTGGGTGCCGATCTGGTCGAG
GTGTCACCACCCTACGACGCTGCTGGTACCACCGCGCTACTGGGCGCCAACCTTGCCTACGAGATGCTCTGTGTGATGCC
G

ORF - retro_xtro_59 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.42 %
Parental protein coverage: 78.3 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalDTGTSNRPGARFGPRHIRGESCMVRRYNISTRAAPFESLMVADIGDVNVNLYDLKDSCRRIRETYQKIMA
D.GTSNR.GARFGPR.IR.ES...R.YN..TRAAPF.SL.VAD.GDV..N.Y.L.DS..RI...Y..I..
RetrocopyDLGTSNRTGARFGPRAIRAESVLLRPYNMATRAAPFDSLQVADLGDVAINPYNLADSIARIEGAYDQIVS
ParentalAGCIPLTLGGDHTITYPILQAVAEKHGPVGLVHVDAHTDTGDTALGEKIYHGTPFRRCVDEGLLDCKRVV
.GC.P.TLGGDHT.T.P.L.A.....G...L.HVDAH.D..DT..GEKI.HGTPFRR.V.EGLL...RV.
RetrocopySGCRPITLGGDHTVTLPVLRAMKRRYGSLALIHVDAHADVNDTMFGEKIAHGTPFRRAVEEGLLLTSRVT
ParentalQIGIRGSSYSADPYGFCREQGFRVVLAEDCWFRSLVPLMAEVRSQMGAGPVYISFDIDGLDPSFAPGTGT
QIG.RG..YSA.....CR.QGF.VV..E..W.RSL.PLM..VR...G..PVY.SFDIDG.DP.FAPGTGT
RetrocopyQIGLRGTGYSAEDFDWCRDQGFTVVQVEQVWRRSLEPLMDAVRTRVGEAPVYLSFDIDGIDPAFAPGTGT
ParentalPEIAGLTTSQGLEIIRGCRGLNVVGCDLVEVAPVYDQSGNTALTGANLLFEMLCVLP
PEIAGLT..Q.LEIIRGCRGLN.VG.DLVEV.P.YD..G.TAL.GANL..EMLCV.P
RetrocopyPEIAGLTVPQALEIIRGCRGLNLVGADLVEVSPPYDAAGTTALLGANLAYEMLCVMP

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 2 .56 RPM
SRP007412_heart 0 .00 RPM 1 .71 RPM
SRP007412_kidney 0 .00 RPM 1 .71 RPM
SRP007412_liver 0 .00 RPM 25 .97 RPM
SRP007412_skeletal_muscle 0 .00 RPM 12 .70 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_59 retrocopy.

TSS - click to see more details

Xenopus tropicalis was not studied using FANTOM5 data.

Lab - click to see more details

retro_xtro_59 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 2 retrocopies.

Species Parental gene accession Retrocopies number
Xenopus tropicalis ENSXETG00000025999 2 retrocopies
retro_xtro_47, retro_xtro_59 ,


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