RetrogeneDB ID: retro_alyr_27

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 2:13253792..13254275(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: scaffold_201707.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Al_scaffold_0001_1541
• Aliases: None
• Description: None

Sequence

>retro_alyr_27
ATGAACCCTTCCTCCACCGACCAACCAAGCCAAGGCCGTGTCAAGGCCAAGGATTGGTCGACTGATTTGTGTGAATGTTG
GATGGACATAAACTCATGCTGCTTGACTTGTTGGTGCCCATGTGTTGCCTTTGGACGCATCGCGGAAGTTGTAGACAGAG
GATCCACATCGTGTGGTGTGAGCGGAGCGATGTACATGATCATATTCATGTTGACCGGATATGGAGGGAGCAGTCTCTAC
TCTTGCTTTTACCGAACCAAACTAAGAGCACAATACAATCTCAAGGAGAGACCTTGTTGTGACTGTTGTGTCCACTTTTG
TTGCGAGCCATGCGCTCTTTGTCAAGAGTATAGGCAACTTCAACACAACCACGATTTCGACTTGTCCATCGGGTGGCATG
GGAATATGGAACGAAATGCACGACTTGCCGCATCTGCGCCTTCGGCTCCTGCACTTCAACCGCCCATGTCTAGATTGAAT
TAG

Alignment

ORF - retro_alyr_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.48 %
• Parental protein coverage: 90.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EWSTGFCDCFSDCKNCCITFWCPCITFGQIADIVDRGATTCGTAGALYALITAVTGCG--CIYSCFYRQK
          .WST..C.C..D...CC.T.WCPC..FG.IA..VDRG.T.CG..GA.Y..I...TG.G....YSCFYR.K
Retrocopy DWSTDLCECWMDINSCCLTCWCPCVAFGRIAEVVDRGSTSCGVSGAMYMIIFMLTGYGGSSLYSCFYRTK

Parental  MRAQYNIRGDDCGDCLKHFCCELCALTQQYRELKH-RGFDMNLGWAGNMERQQNQGGVVMGAPAFQGGMT
          .RAQYN.....C.DC..HFCCE.CAL.Q.YR.L.H...FD...GW.GNMER..........APA.Q..M.
Retrocopy LRAQYNLKERPCCDCCVHFCCEPCALCQEYRQLQHNHDFDLSIGWHGNMERNARLAASAPSAPALQPPMS

Parental  R
          R
Retrocopy R

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_27 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis lyrata	Al_scaffold_0001_1541	1 retrocopy	retro_alyr_27 ,
Arabidopsis thaliana	AT1G14870	1 retrocopy	retro_atha_17,