RetrogeneDB ID: retro_alyr_16

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 2:11797105..11797891(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: scaffold_201451.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: fgenesh2_kg.6__3062__AT4G10850.1
• Aliases: None
• Description: None

Sequence

>retro_alyr_16
ATGGTACATGCACAGTTGAATCTTATTCGGAAGATTGTAGGAATATTAGGAAACTTCATCTCTCTATGTTTGTTTCTGTC
ACCAACGCCAACGTTTGTACACATAGTGAAAAAAAAATCAGTGGAAAAATACTCACCAATGCCATATTTAGCCACTCTCC
TAAACTGTATGGTTCGGGCTCTTTATGGACTTCCTATGGTTCATCCTGATAGCACCTTGCTCGTTACAATCAGCGGTATA
GGAATCGTGATCGAAATCGTTTTCCTTACCATCTTTTTCGTTTTTTGTGATCGTCAACAACATCGGTTGGTAATATCCGC
TGTTTTAACCGTTCAAGCTGCGTTTGTGGCTACTCTTGCGGTTTTGGTATTAACCCTCGAACACACTACCGAACAACGGA
CAATAAGCGTTGGGATTGTTTCTTGCGTTTTCAACGCTATGATGTATGCTTCTCCATTGTCCGTCATGAAAATGGTAATA
AAAACAAAAAGTTTAGAGTTCATGCCGTTTTTGTTATCCGTAGTTAGTTTTATAAATGCAGGTGTTTGGACAATTTATGG
CTTTGTGCCTTTTGATCCATTTTTGGCTATACCAAATGGGATTGGGTGTGTGTTTGGACTAGTACAATTAATATTGTATG
GTACCTACTATGAATCCACCAAAGGGATAATGGCGGAAAGGAAGGAGCGACTCGGCTACGTTGGTGAAGTTGGGTTATCT
ATTGCGATCGGTCAAACGGAACCTGAGAACATCGCATATTTCAACAAAAGAGTTAACGGTGTTTGA

Alignment

ORF - retro_alyr_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.56 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVVAHLNLLRKIVGIIGNFIALCLFLSPTPTFVRIVKKKSVEEYSPIPYLATLINCLVWVLYGLPTVHPD
          MV.A.LNL.RKIVGI.GNFI.LCLFLSPTPTFV.IVKKKSVE.YSP.PYLATL.NC.V..LYGLP.VHPD
Retrocopy MVHAQLNLIRKIVGILGNFISLCLFLSPTPTFVHIVKKKSVEKYSPMPYLATLLNCMVRALYGLPMVHPD

Parental  STLVVTINGTGILIEIVFLTIFFVYCGRQKQRLVISAVIAGETAFIAILAVLVFTLQHTTEKRTMSVGIV
          STL.VTI.G.GI.IEIVFLTIFFV.C.RQ..RLVISAV.....AF.A.LAVLV.TL.HTTE.RT.SVGIV
Retrocopy STLLVTISGIGIVIEIVFLTIFFVFCDRQQHRLVISAVLTVQAAFVATLAVLVLTLEHTTEQRTISVGIV

Parental  CCVFNVMMYASPLSVMKMVIKTKSVEFMPFWLSVAGFLNAGVWTIYALMPFDPFMAIPNGIGCLFGLAQL
          .CVFN.MMYASPLSVMKMVIKTKS.EFMPF.LSV..F.NAGVWTIY...PFDPF.AIPNGIGC.FGL.QL
Retrocopy SCVFNAMMYASPLSVMKMVIKTKSLEFMPFLLSVVSFINAGVWTIYGFVPFDPFLAIPNGIGCVFGLVQL

Parental  ILYGAYYKSTKKILAEREKQSGYIG---LSSAIAHTESEKTANTNQELNNV
          ILYG.YY.STK.I.AER....GY.G...LS.AI..TE.E..A..N...N.V
Retrocopy ILYGTYYESTKGIMAERKERLGYVGEVGLSIAIGQTEPENIAYFNKRVNGV

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_16 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT4G10850	1 retrocopy	retro_atha_2,
Arabidopsis lyrata	fgenesh2_kg.6__3062__AT4G10850.1	1 retrocopy	retro_alyr_16 ,