RetrogeneDB ID:

retro_alyr_9

Retrocopy
location
Organism:Lyre-leaved rock-cress (Arabidopsis lyrata)
Coordinates:3:11969176..11971390(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:scaffold_303017.1
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:Al_scaffold_0001_2882
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_alyr_9
ATGATTAATTCATCCTGTAGCAGCTCCTCCACAAACAAAACCCTATCGTCCCCGGCAAGGAACCTAACTCTGCAAAGTCG
GATCGAAGCGGCTTTAGAAAAGAAAGCAGAAATCACTACGGTGCTTGAGCAATGGCGACAACAACAAGAACAAGGGAAGC
AATTAAACCCTTCGTTGGTGAGAGGTGTCGTCGAGAACCTACGCGATTCCCAGCGATGTCGCGAAGCCCTAGAGGTATCA
AATTGGATGATTGTACAAAAGATCTGCAATCTCATCCCTGAAGATTTCACTACTCGATTTCATCTGATTGAGAACGTATT
TGGATTGGAAGAAGCAGGGAATTTCGTCGAGAGCATCCCGGAGAATTTAAGAAACGAATCTATCTACAATTCTCTTCTAA
GCAGCTACGTAAGACGAAATGATTTGGATAAAGCCGAATCTACTTTCAAGAAGATGAGGGAGCTAGGGTTGCTATTGAGA
GCTTCACCGTATAACTCGATGACTTCACTCTACAGGCGTATCCCTCACGGTAACCGGTGTAAGGTCGATGAGATTCTGCG
AGAGATGAAGGAGAGCAACATTAAGCTTGATAGAGACACCGTGAACAATGCTTTGCGAGTATACGCTGATGTAACTCACA
TAGCGACAATGGAGAAGTTTCTTGCTGAATGGGAAGGGAATACACCGCTTGACTGGCTCACAAGACTTGACATGGCTAAG
GCTTATCTCAGAAGTGGTTTTAAGGGAAAGGCTAAAGAGATGCTTCGTAGAACAGAGGAATTGAGGGATCCAAAGTCCTA
TGAGGAACTCATGAGGCTATATGGTGAAGCAGGAGGGAGAAAGGACGTTTACCGTGTATGGGACTTGTACAAGAAGTTAA
GTAAGAAAGACAACGAAGGATTCCGAGCTTTGATTGGTTCACTATTGAAGCTTGATGATATAAACGGAGCAGAGGAGTTC
TACTACAAAGAGTGGGAGTGCTCGGGACTTCCGTTCGATGTCCGAATCCCGACTATGTTGGTGTCTAGTTACCGCGAAAA
GGGAATGGTGGAGAAGGCAGATAAACTAATAAAGGAGATTATGAAGAATGAAGAATCTGTTAAACCAATCACTCCGTTGT
TGGAGTCATTGGAAAGAAAAGGGAATGTAGTGAAGCCTTCGGAGTTAAGAGATCTCATCAAGAATCTCTGTGACTCAAAT
CAATTCTATAAAGCACTTGAGGCATCAAAATGGATGAGTACAAAAACATCTTTCAATCTTTTCCCTCAAGATTATGCAGC
TAGGCTTCATATGATTGAAAACGTGTTAGGTTTTGAGGAAGCAGAGAAGTTTTTCGAAAGAAGCATTCCGGAGAACATGA
AGGATGACTATGTCTACGGTACACTCTTAAGCTGTTACGCGAAATCTCACAAAACTTTGGATAAAGCCGAGGCCATTTTC
GAGAAGATGGGAGACCTCGGTTTCCTCTCGAAACCTTCTCCATTCAACTCGATGATATCTCTTTACAGTCAGCTAGGAAA
ACGAGAGAAGGTGGAAAATCTTATATCGAAGATGAAATGTATGAACATAGAGCCGGATAGTCTCACGATGAACAACGTTT
TGAGAATGTACGCAGATGAAACCGACATAAAGACAATGGACAAGTATAAAAGAGAGTGGATTAATGCTGAGAAAAACACC
AAGCTTGAGATGAGGACCATGGTTGCAATGGCGAATGCTTACGAGAGAGCCGGTCTACTACTAAAGGCGATTGAGATAAC
AAGGAGTAAAAATGAAGTTCACCGTCTATGGAATGAGTACAAGGAGAAGGAAAAGAGAAATTATAAAATAGATGACGCCA
ATCTATGTAAGTGTAGAAGTGCGGTTGGTGATGAAGAATATCAAAGTGTGATTAGCTCTTTGTTGAAGCTAGACGATTTA
AAAGGAGCAGAGGAGATATATGGAGAGTGGGAACCAGAAGGACCCGAGTTCAATACTCGAATACCGTGTTTGATAATCTC
TCGTTACTGCAAGGAAGGCGATGAAGTGAAGGTAAGGGAAGTAGTGTACTCGAGTATAAAGAAGCGGAAGCTAATGCAGT
TTGAGAGTTTCAAGGAAGATGTGTACGTCTTTGGTGCCATATGTATAGTGTGTGTGGGTTTTGTGGGCGTGCTATTAATG
ATTATAACGAACCCCTTGCTCTTTTTTTTTCTCCTAATTCATTTGTCTCGTTAA

ORF - retro_alyr_9 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 54.8 %
Parental protein coverage: 73.46 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalTLNHRITDALHRNAQIIPVLEQWRQ---QGNQVNPSHVRVIIKKLRDSDQSLQALQVSEWMSKEKICNLI
TL..RI..AL...A.I..VLEQWRQ...QG.Q.NPS.VR.....LRDS.....AL.VS.WM...KICNLI
RetrocopyTLQSRIEAALEKKAEITTVLEQWRQQQEQGKQLNPSLVRGVVENLRDSQRCREALEVSNWMIVQKICNLI
ParentalPEDFAARLHLIENVVGLEEAEKFFESIPKNARDDSVYTTLLNWYARSDKTLCKAEATFQKMRELGLLSRP
PEDF..R.HLIENV.GLEEA..F.ESIP.N.R..S.Y..LL..Y.R....L.KAE.TF.KMRELGLL.R.
RetrocopyPEDFTTRFHLIENVFGLEEAGNFVESIPENLRNESIYNSLLSSYVRRN-DLDKAESTFKKMRELGLLLRA
ParentalSPYNAMMSLY--IALNDREKVEELLREMKDNDVEADSITVNNVLKLYSAVCDVTAMEKFLNKWEGINGIK
SPYN.M.SLY..I....R.KV.E.LREMK......D..TVNN.L..Y..V.....MEKFL..WEG.....
RetrocopySPYNSMTSLYRRIPHGNRCKVDEILREMKESNIKLDRDTVNNALRVYADVTHIATMEKFLAEWEG--NTP
ParentalLEWLTTLDMAKAYLRARSNGKAIKMLRLTEELADRKSLKSAYDHLMKLYGEAGNREEVLRIWNLYKMNIG
L.WLT.LDMAKAYLR....GKA..MLR.TEEL.D.KS....Y..LM.LYGEAG.R..V.R.W.LYK....
RetrocopyLDWLTRLDMAKAYLRSGFKGKAKEMLRRTEELRDPKS----YEELMRLYGEAGGRKDVYRVWDLYK-KLS
ParentalQRDNKGYRTVIRSLLKVDDIFGAEEI-YKVWESLSLEFDIRIPTMLASGYRERGMTEKAEKLINSKTIKD
..DN.G.R..I.SLLK.DDI.GAEE..YK.WE...L.FD.RIPTML.S.YRE.GM.EKA.KLI.....K.
RetrocopyKKDNEGFRALIGSLLKLDDINGAEEFYYKEWECSGLPFDVRIPTMLVSSYREKGMVEKADKLI-KEIMKN
ParentalRKMNKPVTPLLE---QWGDQMKPSDLKCLIKNLRDSNQFSKALQVSEWMGEKRVCDLYSEDYAARLYLTE
....KP.TPLLE.....G...KPS.L..LIKNL.DSNQF.KAL..S.WM..K....L...DYAARL...E
RetrocopyEESVKPITPLLESLERKGNVVKPSELRDLIKNLCDSNQFYKALEASKWMSTKTSFNLFPQDYAARLHMIE
ParentalNVLGLEKAEKYFE-NIPENMKDYSVYVALLSSYAKSDKNLENMVEEILREMEENNVDPDSITVNYVLKVY
NVLG.E.AEK.FE..IPENMKD..VY..LLS.YAKS.K.L....E.I...M............N.....Y
RetrocopyNVLGFEEAEKFFERSIPENMKDDYVYGTLLSCYAKSHKTLDK-AEAIFEKMGDLGFLSKPSPFNSMISLY
ParentalAAASKVEAME
....K.E..E
RetrocopySQLGKREKVE

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_9 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Arabidopsis lyrata Al_scaffold_0001_2882 1 retrocopy
retro_alyr_9 ,


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