RetrogeneDB ID: retro_atha_15

Retrocopy location

• Organism: Mouse-ear cress (Arabidopsis thaliana)
• Coordinates: 2:12157945..12158500(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AT2G28420
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AT1G80160
• Aliases: None
• Description: None

Sequence

>retro_atha_15
ATGGAGGAGAAGAAGAAGAAAGGCGATGATGAATTGAACTCGAAACCGCCGTTAATGGCGTTGAACCATGTGTCAAGGCT
TTGTAAAGACGTCAAAAAGTCTCTCGAGTTCTACACAAAGGTATTAGGGTTCGTGGAGATAGAGCGTCCAGCTTCTTTCG
ACTTCGACGGTGCGTGGCTTTTCAACTACGGCGTTGGGATCCACTTGGTGCAGGCCAAGGACCAAGATAAGTTACCTTCT
GACACGGACCATTTGGACCCAATGGATAACCACATCTCTTTCCAGTGTGAAGATATGGAAGCTTTGGAGAAGAGGCTCAA
GGAGGTGAAGGTAAAGTACATCAAGAGGACGGTGGGTGATGAGAAAGATGCAGCTATCGACCAGCTCTTCTTCAATGACC
CTGACGGCTTTATGGTTGAAATCTGTAACTGCGAGAATCTCGAACTTGTCCCGTGCCATTCAGCCGACGCCATACGCCTC
CCAGAAGACCGACATGCACCTCCTGTTGCCCTCCCTGACTCCTCCAACCGTAGGATGCCCCAGCCCAATTCTTAA

Alignment

ORF - retro_atha_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.23 %
• Parental protein coverage: 83.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DETGNPLHIKSLNHISLLCRSVEESISFYQNVLGFLPIRRPDSFDFDGAWLFGHGIGIHLLQSPEPEKLL
          DE.........LNH.S.LC..V..S..FY..VLGF..I.RP.SFDFDGAWLF..G.GIHL.Q.....KL.
Retrocopy DELNSKPPLMALNHVSRLCKDVKKSLEFYTKVLGFVEIERPASFDFDGAWLFNYGVGIHLVQAKDQDKLP

Parental  KKTE-INPKDNHISFQCESMEAVEKKLKEMEIEYV-RAVVEEGGIQVDQLFFHDPDAFMIEICNCDSLPV
          ..T....P.DNHISFQCE.MEA.EK.LKE....Y..R.V..E.....DQLFF.DPD.FM.EICNC..L..
Retrocopy SDTDHLDPMDNHISFQCEDMEALEKRLKEVKVKYIKRTVGDEKDAAIDQLFFNDPDGFMVEICNCENLEL

Parental  IP
          .P
Retrocopy VP

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_15 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G80160	1 retrocopy	retro_atha_15 ,
Brassica oleracea	Bo2g096220	1 retrocopy	retro_bole_1,
Brassica rapa	Bra008491	1 retrocopy	retro_brap_10,
Arabidopsis lyrata	fgenesh1_pm.C_scaffold_2001978	1 retrocopy	retro_alyr_14,
Medicago truncatula	MTR_2g103490	1 retrocopy	retro_mtru_44,
Setaria italica	Si023259m.g	1 retrocopy	retro_sita_39,