RetrogeneDB ID: retro_alyr_2

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 5:16044775..16045330(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: fgenesh2_kg.5__1594__AT3G52350.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: fgenesh1_pg.C_scaffold_6000712
• Aliases: None
• Description: None

Sequence

>retro_alyr_2
ATGCAAGGAACAAAATCTCTGGCTTGTACACAGAGAGAAACGTCCGTTGTTCAGCTCCGAAAGAGGCAAGGTTGGAAGGA
AAGTACTGGTCTGGGAATCATCAAACAGGGACTAGGAGCAGAGACAAATATACAAAGGAGGAAGAAAACAGACAAGTCTC
AGGCTACAACTTCTCCAAATAGTGAAAAAGTGTCCAGTGTTATTGGTGATTCTTCTGAATCAAGCAATTCATTGGCTGCT
ATCAATTCTTCTAACATTGGATTTCAGCTCCTAAAGAAGCATGGCTGGAAGGAAGGTACTGGTCTTGGAATCGCTGAACA
AGGTATATTGGAGCCTCTACAAGCAGAGCCAAAACATAACAAACAAGGACTAGGATCTGAAAAACCAGCTAAGAGAAAAG
CGGCACAGACTCAGGATACATCTTCTGAAGAAGTATCAAAGAAGAGCAAGAAACTTTCTAAGAAATTGCGGAAGATGATT
GAGCACGAAAAACGCTTAGCTGAAAACGAATTAGAACGAGCCTTCCGCAGGGAGTTCTGGCCTGATAATATATAA

Alignment

ORF - retro_alyr_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.59 %
• Parental protein coverage: 95.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TSSWAAIDSANRFPVSNVMGESSGSSSSLAAINSSNIGFQLLKKHGWKEGTGLGITEQGILVPVQAEPKH
          T....A..S.N...VS.V.G.SS.SS.SLAAINSSNIGFQLLKKHGWKEGTGLGI.EQGIL.P.QAEPKH
Retrocopy TDKSQATTSPNSEKVSSVIGDSSESSNSLAAINSSNIGFQLLKKHGWKEGTGLGIAEQGILEPLQAEPKH

Parental  NKRGLGAKQPAKRKPAQPQ-AKDEEVSKQSKKLSKKMRKMMEHEKHLQEKEFERAFCREFWPDNV
          NK.GLG...PAKRK.AQ.Q....EEVSK.SKKLSKK.RKM.EHEK.L.E.E.ERAF.REFWPDN.
Retrocopy NKQGLGSEKPAKRKAAQTQDTSSEEVSKKSKKLSKKLRKMIEHEKRLAENELERAFRREFWPDNI

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_2 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo9g174360	1 retrocopy	retro_bole_19,
Brassica rapa	Bra009348	1 retrocopy	retro_brap_28,
Arabidopsis lyrata	fgenesh1_pg.C_scaffold_6000712	1 retrocopy	retro_alyr_2 ,