RetrogeneDB ID: retro_alyr_39

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 8:17571156..17571405(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Al_scaffold_0007_2598
• Aliases: None
• Description: None

Sequence

>retro_alyr_39
ACTCCTCCGCGAGAATTCACCTGAAAAATCTCATGTCTCGATAGGCCTTCGACCAACCCACACCGTAGCCACCTTCTGGA
ACTCATATTTCTTAAACGCAACACAAGAGATGGATCCGCCGTGACCACCGGTGACCAGAGCAAACCTAGCCTCATTGGAA
ACATCAATAGGGAAACCATTCGAGCCACGGGTGAGACTTTTCACCTTCTTGTTTCCATAAATCTGATGGTTTGTTTACTA
ATTCCTCTT

Alignment

ORF - retro_alyr_39 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.12 %
• Parental protein coverage: 77.27 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TPPREFTWKISCLDRPSTNPHRSHLLELIFLKRNTRDRSAVITGDRSKPSLIGNINRKTIQATGFRFHLV
          TPPREFT.KISCLDRPSTNPHRSHLLELIFLKRNTRD.SAV.TGD.SKPSLIGNINR.TI.ATG..FHL.
Retrocopy TPPREFT*KISCLDRPSTNPHRSHLLELIFLKRNTRDGSAVTTGDQSKPSLIGNINRETIRATGETFHLL

Parental  TWIKVLDSICAILKM
          ..I......C.....
Retrocopy VSINLM--VCLLIPL

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_39 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	Al_scaffold_0007_2598	1 retrocopy	retro_alyr_39 ,