RetrogeneDB ID: retro_alyr_30

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 1:8101168..8101768(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: fgenesh2_kg.1__2096__AT1G19180.2
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: fgenesh2_kg.2__1763__AT1G74950.1
• Aliases: None
• Description: None

Sequence

>retro_alyr_30
ATGAGTTTATTCCCTTGTGAAGCTTCAAACATGGATTATATGGCAGCACCAGTTCAAGATGTTAAACCGACGAATTTGTT
TCCACGGCAACTAAGTTTTTCTTCCTCATCTTCCTCTGTTCCAAAGGAAGATGTTCTGAAAATGACACAGACTACCAGAT
CTGTGAAACCAGAGTCTCAAACTGCACCATTGACTATATTCTACGCCGGGCAAGTGATTGTATTCAATGACTTTTCTGCT
GAGAAAGCCAAAGAAGTGATGAACTTGGCTAGCAAAGGCACAGCTAATAGCTTCACCGGTTTCACATCTAATGTCATCTT
AGCCAAGAATCAAAGCGAGATCAGAAGCAACATCGCTACCATCACAAACCAAGTTCCTCATCCAAGAAAAACCCCAACAC
AAGAGCCAATCCAATCCTCCCCAACACCACTGACAGAACTTCCTATTGCTAGAAGAGCTTCACTTCACCGGTTCTTGGAG
AAGAGAAAGGACAGAGTTACGTCAAAGGCACCATACCAATTATGCGATCCAGCCAAAGCGTCTTCAAAGCCTCAAACCGC
AGACAACATGTCCTGGCTCGGTTTGGCAGCTGAAATATGA

Alignment

ORF - retro_alyr_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60. %
• Parental protein coverage: 74.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNLFPCEASGMDSSAA--QDIKPKNVFPRQSSFSSSSCSSGAKEDVHMIKETKSVKPESQSAPLTIFYAG
          M.LFPCEAS.MD..AA..QD.KP.N.FPRQ.SFSSSS.S........M...T.SVKPESQ.APLTIFYAG
Retrocopy MSLFPCEASNMDYMAAPVQDVKPTNLFPRQLSFSSSSSSVPKEDVLKMTQTTRSVKPESQTAPLTIFYAG

Parental  RVMVFDDFSAEKAKQVIDLANKGSSKGFTAEVNNSQSAYSQHLAKTQKEIASSPNPVYSPAKTAAQESIQ
          .V.VF.DFSAEKAK.V..LA.KG....FT....N...A..Q........IA...N.V..P.KT..QE.IQ
Retrocopy QVIVFNDFSAEKAKEVMNLASKGTANSFTGFTSNVILAKNQ--SEIRSNIATITNQVPHPRKTPTQEPIQ

Parental  PNPASLACELPIARRASLHRFLEKRKDRITSKAPYQIDGSAEASSKPNPA
          ..P..L..ELPIARRASLHRFLEKRKDR.TSKAPYQ....A.ASSKP..A
Retrocopy SSPTPLT-ELPIARRASLHRFLEKRKDRVTSKAPYQLCDPAKASSKPQTA

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_30 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	fgenesh2_kg.2__1763__AT1G74950.1	1 retrocopy	retro_alyr_30 ,