RetrogeneDB ID: retro_atha_11

Retrocopy location

• Organism: Mouse-ear cress (Arabidopsis thaliana)
• Coordinates: 2:1033906..1034953(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AT2G03410
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AT5G47540
• Aliases: None
• Description: None

Sequence

>retro_atha_11
ATGAAAGGTCTCTTCAAGAACAAATCACGTCTTCCTGGTGAAATCGTACGTCAGACTCGAGATCTCATCGCTTTAGCGGA
ATCCGAAGAAGAAGAAACCGATGCGAGAAACTCGAAAAGGTTAGGGATTTGTGCGGAGTTGTGTCGAAACATTAGAGATT
TGAAATCGATTCTTTATGGTAATGGTGAAGCTGAGCCTGTTCCTGAAGCTTGTCTTTTGTTAACTCAAGAGTTTTTCCGA
GCAGACACGCTTCGTCCTTTGATCAAATCTATACCAAAACTTGACCTAGAAGCAAGAAAAGACGCGACACAGATTGTCGC
GAATCTTCAGAAGCAACAAGTCGAATTTCGACTCGTTGCTTCTGAATATCTTGAATCGAACTTAGATGTTATCGATTCGT
TAGTCGAAGGTATCGATCACGACCATGAGCTGGCGTTGCATTACACGGGAATGCTTAAAGAATGTGTGCGGCATCAGGTT
GTTGCAAAGTACATACTCGAATCGAAGAATTTGGAGAAGTTTTTCGATTATGTTCAGCTTCCGTATTTCGATGTAGCTAC
CGATGCTAGCAAGATCTTCAGAGAGCTTTTGACGAGGCATAAATCGACTGTAGCGGAGTATCTTGCGAAGAACTACGAAT
GGTTTTTCGCAGAGTATAACACCAAGTTGTTGGAGAAAGGAAGCTATTTTACGAAGAGACAAGCGTCGAAATTGCTTGGA
GATGTGTTGATGGATCGTTCGAATTCAGGTGTGATGGTAAAGTATGTGAGCAGTTTGGATAATTTGAGAATCATGATGAA
TCTTTTAAGAGAACCAACCAAGAACATTCAGTTAGAAGCATTTCATATCTTTAAACTCTTTGTGGCAAACGAGAACAAAC
CTGAGGATATCGTGGCGATTCTCGTGGCGAATCGGACCAAGATTCTTCGTTTGTTTGCTGATTTGAAACCTGAGAAAGAA
GATGTAGGTTTTGAAACTGATAAAGCATTGGTTATGAATGAGATTGCTACACTTTCTCTTCTCGATATCAAAACCGCAGA
TCGATAA

Alignment

ORF - retro_atha_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.6 %
• Parental protein coverage: 99.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKGLFKSKPRTPADLVRQTRDLLLFSDRSTSLPDLRDSKRDEKMAELSRNIRDMKSILYGNSEAEPVAEA
          MKGLFK.K.R.P...VRQTRDL...........D.R.SKR....AEL.RNIRD.KSILYGN.EAEPV.EA
Retrocopy MKGLFKNKSRLPGEIVRQTRDLIALAESEEEETDARNSKRLGICAELCRNIRDLKSILYGNGEAEPVPEA

Parental  CAQLTQEFFKEDTLRLLITCLPKLNLETRKDATQVVANLQRQQVNSRLIASDYLEANIDLMDVLIEGFEN
          C..LTQEFF..DTLR.LI...PKL.LE.RKDATQ.VANLQ.QQV..RL.AS.YLE.N.D..D.L.EG...
Retrocopy CLLLTQEFFRADTLRPLIKSIPKLDLEARKDATQIVANLQKQQVEFRLVASEYLESNLDVIDSLVEGIDH

Parental  T-DMALHYGAMFRECIRHQIVAKYVLESDHVKKFFDYIQLPNFDIAADAAATFKELLTRHKSTVAEFLTK
          ....ALHY..M..EC.RHQ.VAKY.LES....KFFDY.QLP.FD.A.DA...F.ELLTRHKSTVAE.L.K
Retrocopy DHELALHYTGMLKECVRHQVVAKYILESKNLEKFFDYVQLPYFDVATDASKIFRELLTRHKSTVAEYLAK

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.ADLKP.KED..FE.DK..V..EIA.L...D.
Retrocopy FHIFKLFVANENKPEDIVAILVANRTKILRLFADLKPEKEDVGFETDKALVMNEIATLSLLDI

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Arabidopsis thaliana was not studied using ChIP-Seq data.

EST

Arabidopsis thaliana was not studied using EST data.

TSS

Arabidopsis thaliana was not studied using FANTOM5 data.

Lab

retro_atha_11 was not experimentally validated.

Homology

Retrocopy orthology:

Arabidopsis thaliana 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,