RetrogeneDB ID:

retro_alyr_26

Retrocopy
location
Organism:Lyre-leaved rock-cress (Arabidopsis lyrata)
Coordinates:8:16843234..16845058(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:fgenesh2_kg.8__1395__AT5G54960.1
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:fgenesh2_kg.7__814__AT4G33070.1
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_alyr_26
ATGGACACTAAGATCGGATCCATCGACGTTTGTAACCCGACCCATGACGATATCGGCGGTCCTCCAAACGGCGGTGTCTC
TACCGTCCAAAACTCAAGTCCACTTCACTCCATCACCGTCAGCCCCTGCGAGGCGACTCTTGGCCGTTACTTAGCAAGAC
GGTTAGTCGAAATCGGAGTCACCGATGTTTTTTCCGTTCCTGGTGATTTCAACCTAACGCTTCTCGATCACCTCATCGCC
GAACCAAGCCTCAAGCTGATCGGTTGCTGTAACGAGCTTAACGCCGGATACGCTGCTGACGGTTACGCCAGATCTCGCGG
TGTTGGTGCGTGCGTCGTTACGTTCACCGTCGGTGGATTGAGTGTCTTGAACGCGATAGCCGGTGCTTATAGTGAGAATC
TGCCTTTGATTTGCATCGTCGGTGGTCCAAACTCCAACGATTACGGCACCAATAGGATTCTTCATCATACGATTGGTTTA
CCTGATTTCACTCAAGAGCTTAGGTGTTTTCAAGCTGTTACTTGTTATCAAGCTGTGATTAATAACTTGGAAGAAGCTCA
TGAACTCATCGATACTGCGATTTCAACTGCTTTGAAAGAAAGCAAACCTGTTTATATCAGTATCAGCTGTAATTTGCCGG
CGATTCCTCTTCCGACTTTTAGTCGTCATCCTGTTCCGTTCATGCTTACGCCGAAGGTGAGTAATCAGATGGGTATAGAT
GCGGCGGTAGAGGCAGCTGCTGAATTCTTGAACAAAGCTGTGAAGCCAGTTCTTGTTGGTGGGCCTAAAATGCGGGTTGC
GAAAGCCGCGGATGCTTTTGTTGAGCTTGCTGATGCTTCTGGTTATGGTCTTGCTGTGATGCCTTCTGCTAAAGGACAAG
TACCTGAGCATCACAAGCATTTTATAGGGACGTATTGGGGAGCTGTGAGTACAGCTTTCTGTGCTGAAATTGTTGAATCT
GCGGATGCTTATTTGTTTGCAGGTCCAATTTTCAACGATTACAGTTCTGTTGGGTACTCTCTGCTTCTCAAGAAAGAGAA
AGCGATCATTGTGCAGCCTGATCGGGTTACTATTGGTAACGGACCTGCGTTTGGGTGTGTTCTTATGAAGGATTTTCTTA
GCGGGTTGGCTAAACGAATTAAGCACAACAACACTTCTTATGAGAATTACCACAGGATCTTTGTCCCAGAAGGAAAGCCT
TTGAGAGATAACCCAAATGAGCCTTTGAGGGTTAATGTGCTGTTCCAACACATTCAAAATATGCTCTCTTCTGAAACTGC
TGTGCTTGCTGAGACAGGAGATTCCTGGTTCAATTGTCAGAAGCTGAAGCTCCCTGAAGGATGCGGTTACGAATTCCAAA
TGCAGTACGGATCAATTGGTTGGTCAGTGGGTGCTACTCTGGGCTATGCTCAAGCCATGCCAAACAGGCGTGTCATTGCT
TGTATTGGAGATGGTAGTTTCCAGGTAACTGCTCAGGATGTATCTACGATGATACGGTGTGGGCAAAAGACCATAATCTT
CCTCATCAACAACGGAGGCTACACAATTGAGGTGGAGATTCACGATGGTCCTTACAATGTCATAAAGAACTGGAACTACA
CAGCCTTTGTCGATGCCATCCACAATGGAGAAGGAAAATGCTGGACTGCCAAGGTGAGATGCGAGGAGGAGCTTGTGAAA
GCGATCAACACGGCAACCAATGAGGAAAAAGATAGCTTTTGTTTCATTGAAGTGATAGTGCACAAAGACGATACAAGCAA
GGAGCTTTTGGAGTGGGGTTCTAGAGTCTCTGCTGCCAATAGTCGTCCCCCAAATCCTCAGTAG

ORF - retro_alyr_26 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.53 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMDTKIGSIDYCKPTNGDVGSPPNGAVSTIHNSVPSSAITVNSCDSTIGRYIARRLVQAGVTDIFSVPGDF
MDTKIGSID.C.PT..D.G.PPNG.VST..NS.P...ITV..C..T.GRY.ARRLV..GVTD.FSVPGDF
RetrocopyMDTKIGSIDVCNPTHDDIGGPPNGGVSTVQNSSPLHSITVSPCEATLGRYLARRLVEIGVTDVFSVPGDF
ParentalNLTLLDHLMAEPELNLIGCCNELNAGYAADGYARSRGVGACVVTFTVGGLSVLNAIAGAYSENLPLICIV
NLTLLDHL.AEP.L.LIGCCNELNAGYAADGYARSRGVGACVVTFTVGGLSVLNAIAGAYSENLPLICIV
RetrocopyNLTLLDHLIAEPSLKLIGCCNELNAGYAADGYARSRGVGACVVTFTVGGLSVLNAIAGAYSENLPLICIV
ParentalGGPNSNDYGTNRILHHTIGLPDFSQELRCFQTVTCYQAVVNNLEDAHEQIDTAISTALKESKPVYISISC
GGPNSNDYGTNRILHHTIGLPDF.QELRCFQ.VTCYQAV.NNLE.AHE.IDTAISTALKESKPVYISISC
RetrocopyGGPNSNDYGTNRILHHTIGLPDFTQELRCFQAVTCYQAVINNLEEAHELIDTAISTALKESKPVYISISC
ParentalNLAAIPHHTFSRAPVPFSLAPRLSNKMGLEAAVEATLEFLNKAVKPVMVGGPKLRVAKACDVFVELADAS
NL.AIP..TFSR.PVPF.L.P..SN.MG..AAVEA..EFLNKAVKPV.VGGPK.RVAKA.D.FVELADAS
RetrocopyNLPAIPLPTFSRHPVPFMLTPKVSNQMGIDAAVEAAAEFLNKAVKPVLVGGPKMRVAKAADAFVELADAS
ParentalGYAMAAMPSAKGLVPEHHPHFIGTYWGAVSTPFCSEIVESADAYIFAGPIFNDYSSVGYSLLLKKEKAIV
GY..A.MPSAKG.VPEHH.HFIGTYWGAVST.FC.EIVESADAY.FAGPIFNDYSSVGYSLLLKKEKAI.
RetrocopyGYGLAVMPSAKGQVPEHHKHFIGTYWGAVSTAFCAEIVESADAYLFAGPIFNDYSSVGYSLLLKKEKAII
ParentalVHPDRVTVANGPTFGCVQMSDFFRELAKRVKRNETAYENYHRIFVPEGKPLKCESKEPLRVNTMFQHIQK
V.PDRVT..NGP.FGCV.M.DF...LAKR.K.N.T.YENYHRIFVPEGKPL.....EPLRVN..FQHIQ.
RetrocopyVQPDRVTIGNGPAFGCVLMKDFLSGLAKRIKHNNTSYENYHRIFVPEGKPLRDNPNEPLRVNVLFQHIQN
ParentalMLSSETAVIAETGDSWFNCQKLKLPRGCGYEFQMQYGSIGWSVGATLGYAQASPEKRVLAFIGDGSFQVT
MLSSETAV.AETGDSWFNCQKLKLP.GCGYEFQMQYGSIGWSVGATLGYAQA.P..RV.A.IGDGSFQVT
RetrocopyMLSSETAVLAETGDSWFNCQKLKLPEGCGYEFQMQYGSIGWSVGATLGYAQAMPNRRVIACIGDGSFQVT
ParentalAQDISTMLRNRQKTIIFLINNGGYTIEVEIHDGPYNVIKNWNYTGLVDAIHNGEGNCWTTKVRYEEELVE
AQD.STM.R..QKTIIFLINNGGYTIEVEIHDGPYNVIKNWNYT..VDAIHNGEG.CWT.KVR.EEELV.
RetrocopyAQDVSTMIRCGQKTIIFLINNGGYTIEVEIHDGPYNVIKNWNYTAFVDAIHNGEGKCWTAKVRCEEELVK
ParentalAIKTATMEKKDCLCFIEVILHKDDTSKELLEWGSRVSAANSRPPNPQ
AI.TAT.E.KD..CFIEVI.HKDDTSKELLEWGSRVSAANSRPPNPQ
RetrocopyAINTATNEEKDSFCFIEVIVHKDDTSKELLEWGSRVSAANSRPPNPQ

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






RNA-Seq - click to see more details

Arabidopsis lyrata was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Arabidopsis lyrata was not studied using ChIP-Seq data.

EST - click to see more details

Arabidopsis lyrata was not studied using EST data.

TSS - click to see more details

Arabidopsis lyrata was not studied using FANTOM5 data.

Lab - click to see more details

retro_alyr_26 was not experimentally validated.

Retrocopy orthology:
Arabidopsis lyrata 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 4 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Arabidopsis thaliana AT4G330701 retrocopy
retro_atha_21,
Brassica oleracea Bo2g0013201 retrocopy
retro_bole_3,
Brassica rapa Bra0288961 retrocopy
retro_brap_2,
Arabidopsis lyrata fgenesh2_kg.7__814__AT4G33070.1 1 retrocopy
retro_alyr_26 ,




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