RetrogeneDB ID: retro_alyr_7

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 4:4389388..4390009(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: scaffold_400690.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: scaffold_803473.1
• Aliases: None
• Description: None

Sequence

>retro_alyr_7
ATGGCCAAGAAGGCGATGGAGAAAGGATTTAAGCTGATTCTTGGTTCTCAGTCGATGGCAAGAAAGCAGATTCTGGCTGA
AATGGGCTATGATTTCACTATTGTGACTGCAGACATTGATGAGAAAGCTATTAGGAAAGAGAAGCCTGAAGATTTGGTTG
TGGCTATTGCTGAAGCCAAAGCAAATGAGATTATATTGAAATTGGGAGGTGAAAGTCAGTTTGCACAAGATTGTCAACCA
ACTCTATTGATTACTTCAGACACTGTTGTTGTGTACAAAGGTGTCATCAGAGAAAAACCAACCAGTAAAGAAGAAGCTCG
CGAGTTTATCAAAGGCTATTCCGGGTCACATGGGGGCGTTGTGGGATCTGTTCTTGTGAGAAACTTGAAAACTGGAGTTA
GAAGAGGAGGATGGGACAAAGCAGAGGTTTATTTCCATGAGATACCAGAACATGTCATCGACGATCTTATTGATGATTCA
ATAACTTTCAAGGTTGCTGGAGGTTTAATGCTTGAGCATCCCCTCATTTCACCTTTTATCGATTCCGTGGTGGGAGGCGT
TGATACAGTCATGGGACTTCCTAAAGAACTTACTGAAAAATTCATTAACGATGTTTTGTAG

Alignment

ORF - retro_alyr_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.29 %
• Parental protein coverage: 96.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTTKAMQRGFKLILGSQSMARKRILADMGYDYTIVTADIDEKAIRTEKPEDLVVALAEAKANEIISKLGG
          M..KAM..GFKLILGSQSMARK.ILA.MGYD.TIVTADIDEKAIR.EKPEDLVVA.AEAKANEII.KLGG
Retrocopy MAKKAMEKGFKLILGSQSMARKQILAEMGYDFTIVTADIDEKAIRKEKPEDLVVAIAEAKANEIILKLGG

Parental  ESQFAQDPQPTLLITADTVVVYKGVIREKPTTKEEAREFIKGYSGSHGGVVGSVLVRNLKTGVRRGGWDK
          ESQFAQD.QPTLLIT.DTVVVYKGVIREKPT.KEEAREFIKGYSGSHGGVVGSVLVRNLKTGVRRGGWDK
Retrocopy ESQFAQDCQPTLLITSDTVVVYKGVIREKPTSKEEAREFIKGYSGSHGGVVGSVLVRNLKTGVRRGGWDK

Parental  AEVYFHEIPEQIIDDLIDDAITYKVAGGLTLEHPLISPFIDAVVGGVDTVMGLPKELTEKCINDVL
          AEVYFHEIPE..IDDLIDD.IT.KVAGGL.LEHPLISPFID.VVGGVDTVMGLPKELTEK.INDVL
Retrocopy AEVYFHEIPEHVIDDLIDDSITFKVAGGLMLEHPLISPFIDSVVGGVDTVMGLPKELTEKFINDVL

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_7 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	scaffold_803473.1	1 retrocopy	retro_alyr_7 ,