RetrogeneDB ID: retro_alyr_20

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 5:1846261..1847305(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: scaffold_500325.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: scaffold_800035.1
• Aliases: None
• Description: None

Sequence

>retro_alyr_20
ATGAAAGGTCTCTTCAAGAACAAATCACGTCTTCCTGGTGAAATCGTTCGTCAGACTCGAGATCTCATTGCTTTAGCCGA
ATCCGAAGAAGAAATCGATTCGAGAAACTCGAAAAGGTTAGGGATTTGTGCGGAATTGTGTCGAAACATTAGTGATTTGA
AATCGATTCTTTATGGTAATAGTGAAGCTGAGCCTGTTCCTGAAGCTTGTCTTATGTTAACTCAAGAGTTTTTCCGAGAA
GATACGCTTCGTCCTTTGATCAAATCTATTCCAAAACTTGATCTAGAAGCAAGAAAAGACGCGACGCAGATTGTTGCGAA
TTTGCAGAAACAACAAGTCGAATCTCGACTCGTTGCTTCTGAATATCTTGAATCGAATTTAGATGTTATTGATTCGTTAG
TCGAAGGTATCGATCATGATCACGAGTTGGCGTTGCATTATACAGGAATGCTTAAAGAATGTGTGCGGCATCAGGTTGTT
GCCAAGTACATACTCGAATCGAAGAATTTGGACAAGTTTTTCGATTATGTTCAGCTTCCGTATTTTGATGTAGCTACCGA
TGCTAGCAAGATCTTTAGGGAGCTTTTGACGAGGCATAAATCGACTGTAGCTGAGTATCTTACCAAGAACTACGAGTGGT
TTTTCGCAGAGTATAACACGAAGTTGTTGGAGAAAGGAAGCTACTTTACGAAGAGACAAGCGTCGAAATTGCTTGGAGAT
GTGTTGATGGATCGTTCGAATTCAGGTGTGATGGTTAAGTATGTGAGCAGTTTGGATAATTTGAGAATCATGATGAATCT
TTTAAGAGAACCAACCAAGAACATTCAGTTAGAAGCTTTTCATATCTTCAAGCTCTTTGTGGCGAACGAGAACAAACCAG
AGGACATTGTGGCGATTCTCGTGGCGAATCGGAACAAGATTCTTCGTTTGTTTGCTGATTTGAAAGCTGAAAAAGAAGAT
GTAGGTTTTGAAACTGACAAATCATTGGTTATGAATGAGATTGCTACACTTTCTCTTCTCGATATCAAAACCGCAGATCG
ATAA

Alignment

ORF - retro_alyr_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.06 %
• Parental protein coverage: 99.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKGLFKSKPRTPADLVRQTRDLLLYADRSTSLPDLRESKREEKMAELSRNIRDMKSILYGNSEAEPVAEA
          MKGLFK.K.R.P...VRQTRDL...A.......D.R.SKR....AEL.RNI.D.KSILYGNSEAEPV.EA
Retrocopy MKGLFKNKSRLPGEIVRQTRDLIALAESEEEI-DSRNSKRLGICAELCRNISDLKSILYGNSEAEPVPEA

Parental  CAQLTQEFFKEDTLRLLITCLPKLNLEARKDATQVVANLQRQQVNSRLIASDYLEANIDLMDVLIEGFEN
          C..LTQEFF.EDTLR.LI...PKL.LEARKDATQ.VANLQ.QQV.SRL.AS.YLE.N.D..D.L.EG...
Retrocopy CLMLTQEFFREDTLRPLIKSIPKLDLEARKDATQIVANLQKQQVESRLVASEYLESNLDVIDSLVEGIDH

Parental  T-DMALHYGAMFRECIRHQIVAKYVLESDHVKKFFDYIQLPNFDIAADAAATFKELLTRHKSTVAEFLTK
          ....ALHY..M..EC.RHQ.VAKY.LES....KFFDY.QLP.FD.A.DA...F.ELLTRHKSTVAE.LTK
Retrocopy DHELALHYTGMLKECVRHQVVAKYILESKNLDKFFDYVQLPYFDVATDASKIFRELLTRHKSTVAEYLTK

Parental  NEDWFFADYNSKLLESSNYITRRQAIKLLGDILLDRSNSAVMTKYVSSRDNLRILMNLLRESSKSIQIEA
          N..WFFA.YN.KLLE...Y.T.RQA.KLLGD.L.DRSNS.VM.KYVSS.DNLRI.MNLLRE..K.IQ.EA
Retrocopy NYEWFFAEYNTKLLEKGSYFTKRQASKLLGDVLMDRSNSGVMVKYVSSLDNLRIMMNLLREPTKNIQLEA

Parental  FHVFKLFAANQNKPADIVNILVANRSKLLRLLADLKPDKEDERFEADKSQVLREIAALEPRDL
          FH.FKLF.AN.NKP.DIV.ILVANR.K.LRL.ADLK..KED..FE.DKS.V..EIA.L...D.
Retrocopy FHIFKLFVANENKPEDIVAILVANRNKILRLFADLKAEKEDVGFETDKSLVMNEIATLSLLDI

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Arabidopsis lyrata was not studied using ChIP-Seq data.

EST

Arabidopsis lyrata was not studied using EST data.

TSS

Arabidopsis lyrata was not studied using FANTOM5 data.

Lab

retro_alyr_20 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT5G47540	1 retrocopy	retro_atha_11,
Brassica rapa	Bra022139	1 retrocopy	retro_brap_1,
Populus trichocarpa	POPTR_0006s01590	1 retrocopy	retro_ptri_1,
Arabidopsis lyrata	scaffold_800035.1	1 retrocopy	retro_alyr_20 ,