RetrogeneDB ID: retro_alyr_36

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 5:368412..368827(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: fgenesh1_pg.C_scaffold_5000340
• Aliases: None
• Description: None

Sequence

>retro_alyr_36
CTAAGACATGGTCATCATTTATCCCAGTGTTAGAAAAACTGGTTTTACTACCTGAATCAAATAAAAGTGTACAACAACAG
TTCGAGACAATTGGCAACCAATCGTTGTATGCCTATTTCATTGAGGCTACTTCTTTTCGACCGGAGCGTCGATTGAAAAT
TGGGATGATTCCTCGTACAAGGTGGATAAGCTAATAAATTTGGTGACTGCGACGAAGAGGTGTGAGTGTCGTGTGATGCG
TTGTGCCATGGGGGAGGAGGCAATATTTTTATCAGCCCGGGAATATGATCACCACACAGCTTCTAGGGCTTTTTCAAGAA
CCGTCGGACCCTTTGTCGTCTTTGTTGGTGCTTTTGGATTCAAGACTTCTATGTCTTACTTGTGGAACTCATACAAAGAG
GGTGTCACAGTACTT

Alignment

ORF - retro_alyr_36 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.19 %
• Parental protein coverage: 79.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LRYIHSIVDIYGNFLLYILADVYGHNANVGATDNQ-LYAYFIEASAFRIERRLK-NWNPSSKKVEKLIKL
          LR..H.......N...Y........N.......N..LYAYFIEA..FR.ERRLK.NW..SS.KV.KLI.L
Retrocopy LRHGHHLSQC*KNWFYYLNQIKVYNNSSRQLATNR<LYAYFIEATSFRPERRLK<NWDDSSYKVDKLINL

Parental  VSATKRAECRVMRWAMGEESVFLKARDYDQQSASRAFSRTIGLLLVFLGFWELKRTASYAWDSYKEDFAV
          V.ATKR.ECRVMR.AMGEE..FL.AR.YD...ASRAFSRT.G...VF.G....K...SY.W.SYKE...V
Retrocopy VTATKRCECRVMRCAMGEEAIFLSAREYDHHTASRAFSRTVGPFVVFVGAFGFKTSMSYLWNSYKEGVTV

Parental  V
          .
Retrocopy L

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_36 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	fgenesh1_pg.C_scaffold_5000340	1 retrocopy	retro_alyr_36 ,