RetrogeneDB ID: retro_alyr_14

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 4:11692521..11693073(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: fgenesh2_kg.4__719__AT2G28420.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: fgenesh1_pm.C_scaffold_2001978
• Aliases: None
• Description: None

Sequence

>retro_alyr_14
ATGGAGGAGAAGAAGAAGAAAGGCGATGATGAATCGAACTCGAAAGCACCGTTAATGGCGTTGAACCATGTGTCAAGGCT
TTGCAAAGACGTCAAAAAGTCTCTGGAGTTTTACACAAAGGTATTAGGATTCGTGGAGATAGAGCGTCCAGCGTCGTTTG
ACTTCAACGGCGCGTGGCTTTTTAACTACGGTGTTGGGATCCATTTGGTGCAAGCCAAGGACCAAGACAAGTTACCTTCC
GACACGAACCATTTGGACCCAATGGATAACCACATCTCTTTCCAGTGTGAAGATATGGAAGCTTTGGAAAAGAGGATCAA
GGAGGTGAAGGTTAAGTACATCAAGAGGACGGTGGGTGATGAGAAAGATGCAGCCATCGACCAGCTCTTCTTCAATGACC
CTGACGGCTTTATGGTCGAGATCTGTAACTGCGAGAATCTCGAGCTTGTTCCGCGCCATTCAGCCGATGCCATACACCTC
CCAGAAGACCGACACGCACCTCCTGTTACCCTCCCTGACTCCGACGATAGGATGCCCCAACCCAATTCTTAA

Alignment

ORF - retro_alyr_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.15 %
• Parental protein coverage: 86.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EDTTGNPLHIKSLNHISLLCRSVEESISFYHNVLGFLPIRRPGSFDFDGAWLFGHGIGIHLLQSPEPEKL
          .D..........LNH.S.LC..V..S..FY..VLGF..I.RP.SFDF.GAWLF..G.GIHL.Q.....KL
Retrocopy DDESNSKAPLMALNHVSRLCKDVKKSLEFYTKVLGFVEIERPASFDFNGAWLFNYGVGIHLVQAKDQDKL

Parental  LKKT-EINPKDNHISFQCESMEAVEKKLKELEIKYV-RAVVEEGGIQVDQLFFHDPDAFMIEICNCDSLP
          ...T....P.DNHISFQCE.MEA.EK..KE...KY..R.V..E.....DQLFF.DPD.FM.EICNC..L.
Retrocopy PSDTNHLDPMDNHISFQCEDMEALEKRIKEVKVKYIKRTVGDEKDAAIDQLFFNDPDGFMVEICNCENLE

Parental  VVP
          .VP
Retrocopy LVP

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_14 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 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,