RetrogeneDB ID: retro_alyr_32

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 1:27613647..27614373(-)
• Located in intron of: fgenesh2_kg.1__4276__AT1G52030.1

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: fgenesh2_kg.3__2360__AT3G21380.1
• Aliases: None
• Description: None

Sequence

>retro_alyr_32
AAAGTGGAAGCTCAAGGAGGAAATGGTGGGGATACATTCGACGATGGTGCTTTCAATCATGTAAGAAAGGTTTATGTTGG
TCAAGGTGATTCTGGTGTAGCTTATGTCAAATTCGAATACGAAAAAGATGGGAAAAGTGAGACACGAGAGCATGGAAAAA
TGACAGTGTTAGGAACAGAGGAGTTTGAAGTTGATCCTGATGATTACATCACATCAGTTCAAGTTTCTGTCGACAATGTC
TTTGGTTTTAAGAGTGAAATCGTCACTTCTCTTGTCTTCAAGACCTTTAAGGGTAAAACCTCACAGCCTTTTGGAATGGT
GACTGAGAAGAAATTTGAACTTAACGATAAGGGAGGAAAACTTGTTGGTTTCCATGGGAAAGCTAGTGATGTTCTTTATG
CTCTTGGCGCTTATTTCGCTCCATCGACAACTTCAACTACTCCATCGGTGCCAACTTCGACTACTCCATCTACTCCTTCT
ACTGCTAAGAAGCTACAAGCAATAGGTGGTAATGGAGGAGCTTCTTGGGATGATGGTGTTTTTGATGGTGTTAGAAAGAT
ACTTGTAGGTCAAGGAAACGATGGAGTAGCTTTTGTCACGTTTGAGTACAACAAAGGCTCTCAAGCTATCATCGGTGATG
GGCATGGGAAACAAACAGCACTTGGAACTGAAACGGTTTGATTCTCTTTTGACCTCTCTAATATGTTTGATGTTTCTCCC
AAATAT

Alignment

ORF - retro_alyr_32 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.89 %
• Parental protein coverage: 53.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KVDAQGGKGGTSWDDGAHDHVRRVYTGQGDSGVTYVKFEYEKDGKKESREHGKKTLLGAEVFEVDPDDYI
          KV.AQGG.GG...DDGA..HVR.VY.GQGDSGV.YVKFEYEKDGK.E.REHGK.T.LG.E.FEVDPDDYI
Retrocopy KVEAQGGNGGDTFDDGAFNHVRKVYVGQGDSGVAYVKFEYEKDGKSETREHGKMTVLGTEEFEVDPDDYI

Parental  TSVEVQSDKIFGQDTEVITSLIFKTSKGKISPPFGLEGSQKYELKDKNGGKLVGFHGRVGELLHALGAYF
          TSV.V..D..FG...E..TSL.FKT.KGK.S.PFG.....K.EL.DK.GGKLVGFHG.....L.ALGAYF
Retrocopy TSVQVSVDNVFGFKSEIVTSLVFKTFKGKTSQPFGMVTEKKFELNDK-GGKLVGFHGKASDVLYALGAYF

Parental  APSSGGSRTPSATQPAGSAQSAGSAGAKKLEAKGGNVGNPWDDGPHDGVRKVYIGQGDSGVSYVKFVYDK
          APS...S.TPS...P.....S..S..AKKL.A.GGN.G..WDDG..DGVRK...GQG..GV..V.F.Y.K
Retrocopy APST-TSTTPSV--PTSTTPSTPST-AKKLQAIGGNGGASWDDGVFDGVRKILVGQGNDGVAFVTFEYNK

Parental  DSKEVPGNDHGKRTLLAPEEFVLEYPNEHITSVEINY
          .S....G..HGK.T.L..E.............V...Y
Retrocopy GSQAIIGDGHGKQTALGTETV*FSFDLSNMFDVSPKY

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_32 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Arabidopsis lyrata	fgenesh2_kg.3__2360__AT3G21380.1	1 retrocopy	retro_alyr_32 ,