RetrogeneDB ID: retro_alyr_19

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 6:9810516..9811362(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: scaffold_602371.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: fgenesh2_kg.3__818__AT3G07800.1
• Aliases: None
• Description: None

Sequence

>retro_alyr_19
ATGTTTGGTGTTTCGATGAGAACATTAATCTCACCATCTCTTGCTCCTTTCTCTCTTCATCTCCCTAAACCTTCTCTCTT
CTCCACCGCTCTTCGCTTCTCCTCCCTCACCACTTCCACCATCTCAATCAACAACAGATCCCCCACAAATGCACCTCCCT
CCGCCATTTCCACCAGAAAACTACAAACGAAAGCGACGGCGCCGCTCTCTTTCACAACTCCCGGCGAAATACACGTAGTC
GTCGGACCAATGTTCTCCGGTAAAACCACAACACTTCTCCGCCGTATCCTCGCCGAAAAAGAAACCGGTAAACAAATCGC
AATCATCAAATCAAACAAAGACACAAGATACTGCACTGAATCAATAGTTACTCACGACGGTGAGAAATTCCCTTGCTGGT
CACTTCCCGATCTCTCGTCCTTCAAAGAGAGGTTCGGATTCGACGAATACGAGAATCGATTAGATGTGATTGGAATCGAC
GAAGCTCAATTCTTCGGAGATCTATACGAGTTTTGCCGTCAAGCTGCTGATAGAGAGGGTAAAACTGTAATTGTTGCTGG
ATTGGATGGTGATTTTAAGCGGAGGAGGTTTGGTTCGGTGCTTGATTTGATTCCAATTGCGGATACGGTTACGAAGCTGA
CGTCACGGTGTGAGGTTTGTGGGAAGAGAGCTTTGTTTACGATGAGGAAGACGGAGGAGAAAGAGACGGAGTTGATCGGC
GGAGCTGAAGTTTATATGCCTGTGTGTCGGAGTCATTACGTTTGCGGTCAAAGCGTTTTGGAAACCGCTCGTGCCGTTTT
GGATTCTTCAAGCAATAAGCATGATGTTGTAGCAAGTTTGCTTTAA

Alignment

ORF - retro_alyr_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70. %
• Parental protein coverage: 75.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GAIHVIMGPMFSGKSTSLLRRIKSEISDGRSVAMLKSSKDTRYAKDSVVTHDGIGFPCWALPDLMSFPEK
          G.IHV..GPMFSGK.T.LLRRI..E...G...A..KS.KDTRY...S.VTHDG..FPCW.LPDL.SF.E.
Retrocopy GEIHVVVGPMFSGKTTTLLRRILAEKETGKQIAIIKSNKDTRYCTESIVTHDGEKFPCWSLPDLSSFKER

Parental  FGQDAY-NKLDVIGIDEAQFFGDLYEFCCKVADDDGKTVIVAGLDGDYLRRSFGAVLDIIPIADSVTKLT
          FG.D.Y.N.LDVIGIDEAQFFGDLYEFC...AD..GKTVIVAGLDGD..RR.FG.VLD.IPIAD.VTKLT
Retrocopy FGFDEYENRLDVIGIDEAQFFGDLYEFCRQAADREGKTVIVAGLDGDFKRRRFGSVLDLIPIADTVTKLT

Parental  ARCEVCGHKAFFTLRKNCDTRTELIGGADVYMPVCRKHYI
          .RCEVCG..A.FT.RK.....TELIGGA.VYMPVCR.HY.
Retrocopy SRCEVCGKRALFTMRKTEEKETELIGGAEVYMPVCRSHYV

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_19 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT3G07800	1 retrocopy	retro_atha_9,
Brassica oleracea	Bo3g061430	1 retrocopy	retro_bole_16,
Brassica rapa	Bra001266	1 retrocopy	retro_brap_33,
Arabidopsis lyrata	fgenesh2_kg.3__818__AT3G07800.1	1 retrocopy	retro_alyr_19 ,