RetrogeneDB ID: retro_alyr_8

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 8:20815157..20815640(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: scaffold_802989.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: fgenesh2_kg.1__358__AT1G04270.1
• Aliases: None
• Description: None

Sequence

>retro_alyr_8
ATGGCGATCAACGAATCAGAGTTTGCCACGGCCGTGGCGGTGGCGACAAAGAAGAGAACATTCAAGAAATTCTCATTCAG
AGGATTCAACGTCGATGCTCTTCTCAAAATGTCAAACGTTGATCTCGCTAAGCTCTTCAACGCTCGTGTTCGCAGAAGAT
TCTATAGAGGATTAAAGAAGAAACCTCTGATTCTGATCAAGAAGCTACGGAGGGCGAAAAAAGAAGCAAGTGATGAGAAC
AAGAAGAAGCCTCAAGTAGTGAAAACACATCTAAGGAACATGATCATTGTCCCCGAGATGATTGGAAGTGTTGTCGGAGT
TCACAATGGAAAGAAGTTTAATGAAATCGTGATTAAGCCTGAGATGATTGGTCATTATCTTGCGGAGTTTTCGTTAACTT
GCAAGAAGGTTAATCACTATAGACCACGTATTTGTGGTTGTGGTTGTTTCCGTCGGTCCACCAGGTTTATTCCTCTCAGG
TGA

Alignment

ORF - retro_alyr_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.33 %
• Parental protein coverage: 94.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAAGVPKKRTFKKFAFRGVDLDALLDMSTDDLVKLFSSRIRRRFSRGLTRKPMALIKKLRKAKREAPQG-
          A.A...KKRTFKKF.FRG...DALL.MS..DL.KLF..R.RRRF.RGL..KP..LIKKLR.AK.EA....
Retrocopy AVAVATKKRTFKKFSFRGFNVDALLKMSNVDLAKLFNARVRRRFYRGLKKKPLILIKKLRRAKKEASDEN

Parental  -EKPEPVRTHLRNMVIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKHGRP---GVGAT
          ..KP..V.THLRNM.IVPEMIGS..GV.NGK.FN...IKPEMIGHYLAEFS...K.V.H.RP...G.G..
Retrocopy KKKPQVVKTHLRNMIIVPEMIGSVVGVHNGKKFNEIVIKPEMIGHYLAEFSLTCKKVNHYRPRICGCGCF

Parental  HSS-RFIPLK
          ..S.RFIPL.
Retrocopy RRSTRFIPLR

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_8 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G04270	1 retrocopy	retro_atha_20,
Brassica oleracea	Bo5g004420	1 retrocopy	retro_bole_33,
Brassica rapa	Bra032519	1 retrocopy	retro_brap_20,
Arabidopsis lyrata	fgenesh2_kg.1__358__AT1G04270.1	1 retrocopy	retro_alyr_8 ,
Medicago truncatula	MTR_1g070450	1 retrocopy	retro_mtru_46,
Solanum tuberosum	PGSC0003DMG400007336	1 retrocopy	retro_stub_80,
Solanum lycopersicum	Solyc02g082000.2	1 retrocopy	retro_slyc_75,
Triticum aestivum	Traes_2AL_52D3F9AF41	1 retrocopy	retro_taes_67,