RetrogeneDB ID:

retro_alyr_1

Retrocopy
location
Organism:Lyre-leaved rock-cress (Arabidopsis lyrata)
Coordinates:8:12479503..12480007(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:scaffold_801255.1
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:scaffold_403747.1
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_alyr_1
ATGGCTAGTGGAAGTGAGCGTGTGGTGGTCGTAGGAGTAGATGATTCAGCCCATAGCTACCATGCACTCGAGACGGCTCT
TGATCTCTTTTTCATACCTTTCAAGGCCAACCCACAATTCAAACTTGTCGTTGTTCACGGACGACCAACAGCGACCTCCT
TCCTCGGTGTTGCTGGTCCTGGAACGGTGGATATTATACCAATGGTGGAACAAGATTTAAACAAGACCGCAGAATTGGTT
AAGAAGAAGTGCTCCGAAGTGTGCTCGGCTAAGTCCGTTGAGATCTCGTCTTTGGAGGTGATTGAAGGAGATCCAAGGAA
TATTATGTTGGAAGCCGTGGAGAGACATCATGCATGTGTTATTGTCCTTGGTAGCCATGGTTATGGAGCTGTCAAGAGGG
TGTTTTTGGGGAGTGTGAGTGATTATTTAGCTCATCACGCACATTGCTCCGTTATGATCGTCAAGAAACCTAAGGCTAAA
CCTACTTCTACGGAAACACACTAA

ORF - retro_alyr_1 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.76 %
Parental protein coverage: 99.38 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMATGDEKSVMVVGVDDSEQSTYALEWTLDRFFAPYAPNYPFKLFIVHAKPNAVSAVGLAGPGTAEVVPYV
MA.G.E..V.VVGVDDS..S..ALE..LD.FF.P...N..FKL..VH..P.A.S..G.AGPGT....P.V
RetrocopyMASGSER-VVVVGVDDSAHSYHALETALDLFFIPFKANPQFKLVVVHGRPTATSFLGVAGPGTVDIIPMV
ParentalDADLKHTAAKVVEKAKAICQSKSVHGAVIEVFEGDARNILCEVVDKHHASILVVGSHGYGAIKRAVLGST
..DL..TA..V..K....C..KSV.....EV.EGD.RNI..E.V..HHA...V.GSHGYGA.KR..LGS.
RetrocopyEQDLNKTAELVKKKCSEVCSAKSVEISSLEVIEGDPRNIMLEAVERHHACVIVLGSHGYGAVKRVFLGSV
ParentalSDYCAHHAHCSVMIVKKPKIK
SDY.AHHAHCSVMIVKKPK.K
RetrocopySDYLAHHAHCSVMIVKKPKAK

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






Arabidopsis lyrata was not studied using RNA-Seq expression data.
Arabidopsis lyrata was not studied using ChIP-Seq data.
Arabidopsis lyrata was not studied using EST data.
Arabidopsis lyrata was not studied using FANTOM5 data.
retro_alyr_1 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 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Brassica oleracea Bo3g0397401 retrocopy
Brassica rapa Bra0004581 retrocopy
Arabidopsis lyrata scaffold_403747.1 1 retrocopy
retro_alyr_1 ,



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