RetrogeneDB ID: retro_alyr_23

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 1:7266791..7267829(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: scaffold_101935.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: scaffold_600253.1
• Aliases: None
• Description: None

Sequence

>retro_alyr_23
ATGGCTTCTTCTTCTAACTACGATGGAATCCTTCTCGGAATGGGTAACCCACTCCTCGATATCTCTGCCGTCGTCGACGA
CGAATTTCTCACCAAATACGACATCAAGTTGAACAATGCGATTCTCGCTGAGGACAAACATTTGCCCATGTATGATGAGA
TGAGTAGCAAGTTCAATGTTGAATACATTGCCGGAGGTGCTACTCAGAACTCAATCAAAGTGGCTCAGTGGATGCTTCAA
ATTCCTGGGGCAACCAGTTACATGGGATCCATTGGAAAGGACAAATATGGAGAGGCCATGAAGAAGGATGCTACAGCAGC
TGGTGTCAATGTTCACTATTATGAAGATGAGTCGGCACCTACTGGAACTTGCGGTGTCTGTGTTGTTGGTGGAGAAAGGT
CTCTTATTGCGAATCTTTCAGCTGCAAACTGCTACAAGGTTGATCACCTTAAGAAGCCTGAAAACTGGGCATTGGTTGAG
AAGGCCAAGTTCTATTACATTGCTGGATTCTTCCTCACAGTATCGCCTGAATCCATTCAGTTGGTATCTGAGCATGCTGC
TGCAAACAACAAGGTGTTCACAATGAACCTTTCTGCTCCATTCATTTGTGAATTCTTCAAAGATGTGCAGGAGAAGTTCT
TGCCATACATGGACTTCGTTTTCGGCAATGAAACAGAAGCAAGAACCTTCTCCAGGGTTCACGGCTGGGAGACTGAAGAT
GTCGAACAAATAGCCATCAAGATTTCACAGCTTCCCAAGGCCACGGGAACATACAAGAGGACCACTGTGATAACACAGGG
CGCAGATCCAGTGGTTGTTGCTGAAGATGGAAAGGTGAAGAAATATCCAGTCATCCCTCTCCCAAAAGAGAAGCTGGTTG
ACACCAACGGTGCAGGTGATGCATTTGTGGGAGGATTCATGTCACAGTTGGTGAAAGAGAAATCGATTGAGGAATGCGTG
AAAGCTGGATGCTATGCGTCGAACGTGGTGATCCAAAGATCTGGCTGCACTTACCCTGAGAAGCCCGACTTTAACTAA

Alignment

ORF - retro_alyr_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MASSSNYDGILLGMGNPLLDISAVVDDEFLTKYDIKLNNAILAEDKHLPMYDEMSSKFNVEYIAGGATQN
          MASSSNYDGILLGMGNPLLDISAVVDDEFLTKYDIKLNNAILAEDKHLPMYDEMSSKFNVEYIAGGATQN
Retrocopy MASSSNYDGILLGMGNPLLDISAVVDDEFLTKYDIKLNNAILAEDKHLPMYDEMSSKFNVEYIAGGATQN

Parental  SIKVAQWMLQIPGATSYMGSIGKDKYGEAMKKDATAAGVNVHYYEDESAPTGTCGVCVVGGERSLIANLS
          SIKVAQWMLQIPGATSYMGSIGKDKYGEAMKKDATAAGVNVHYYEDESAPTGTCGVCVVGGERSLIANLS
Retrocopy SIKVAQWMLQIPGATSYMGSIGKDKYGEAMKKDATAAGVNVHYYEDESAPTGTCGVCVVGGERSLIANLS

Parental  AANCYKVDHLKKPENWALVEKAKFYYIAGFFLTVSPESIQLVSEHAAANNKVFTMNLSAPFICEFFKDVQ
          AANCYKVDHLKKPENWALVEKAKFYYIAGFFLTVSPESIQLVSEHAAANNKVFTMNLSAPFICEFFKDVQ
Retrocopy AANCYKVDHLKKPENWALVEKAKFYYIAGFFLTVSPESIQLVSEHAAANNKVFTMNLSAPFICEFFKDVQ

Parental  EKFLPYMDFVFGNETEARTFSRVHGWETEDVEQIAIKISQLPKATGTYKRTTVITQGADPVVVAEDGKVK
          EKFLPYMDFVFGNETEARTFSRVHGWETEDVEQIAIKISQLPKATGTYKRTTVITQGADPVVVAEDGKVK
Retrocopy EKFLPYMDFVFGNETEARTFSRVHGWETEDVEQIAIKISQLPKATGTYKRTTVITQGADPVVVAEDGKVK

Parental  KYPVIPLPKEKLVDTNGAGDAFVGGFMSQLVKEKSIEECVKAGCYASNVVIQRSGCTYPEKPDFN
          KYPVIPLPKEKLVDTNGAGDAFVGGFMSQLVKEKSIEECVKAGCYASNVVIQRSGCTYPEKPDFN
Retrocopy KYPVIPLPKEKLVDTNGAGDAFVGGFMSQLVKEKSIEECVKAGCYASNVVIQRSGCTYPEKPDFN

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_23 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_600253.1	1 retrocopy	retro_alyr_23 ,