RetrogeneDB ID: retro_alyr_15

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 6:6725884..6726931(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: fgenesh2_kg.6__1640__AT5G16510.2
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: fgenesh2_kg.3__159__AT3G02230.1
• Aliases: None
• Description: None

Sequence

>retro_alyr_15
ATGTCTTCGGCCGAGATAAACAAGAATGAAGTCGACATTGTCATTGGGGCTCTTAATGCTGACCTTACACAGTTTTTGAC
CAGCTGGAGGCCCTTTTTCTCTGGATTCCATCTGATTGTTGTCAAAGATCCTGAGCTCAAGGAGGAACTTAACATACCAG
AAGGCTTTGATGTAGATGTCTACTCAAAGACTGACATGGAAAAAGTTGTGGGCGCATCCAATTCCACCATGTTCTCTGGC
TATTCTTGCAGATATTTCGGTTATCTCATATCTAAAAAGAAGTACATTGTCTCAATTGATGATGATTGTGTCCCTGCTAA
AGATCCCAAGGGGTTCCTAGTGGATGCTGTTACTCAGCACGTGACCAACCTCGAGAACCCTGCCACGCCTCTCTTCTTCA
ACACCCTTTATGATCCTTATCGCGAGGGAGCGGATTTTGTCCGTGGATACCCTTTCAGCCTCAGAAGTGGTGTCCCTTGT
GCTGCATCTTGTGGACTTTGGCTTAATCTAGCTGATCTTGATGCTCCAACACAAGCTCTCAAGACAGAGCAAAGGAACAC
TTCATATGTTGATGCGGTTATGACTGTCCCGGCCAAGGCTATGCTACCCATAAGCGGAATCAACATCGCTTTTAACCGTG
AGTTGGTGGGTCCAGCTTTGGTGCCTGCTCTTAGATTGGCTGGAGAAGGGAAAGTGAGATGGGAAACACTTGAAGATGTT
TGGTGTGGGATGTGTCTGAAACATATCTCTGATCATTTGGGTTATGGTGTGAAAACCGGACTGCCTTATGTGTGGAGAAA
CGAGAGAGGAGATGCAGTGGAGAGTTTGAGGAAGAAATGGGAAGGAATGAAACTGATGGAGAAAAGTGTTCCATTTTTCG
AGTCATTGAAATTGCCCGAGACTGCACTTAAAGTTGAAGATTGTGTGATCGAGCTTGCTAAAGCGGTGAAAGAGCAGTTG
GGTTCAGATGATCCTGCCTTCACGCAAGCTGCTGATGCTATGGTTAAGTGGATCCAGCTCTGGAATTCTGTTAATTCTAG
CTCTTGA

Alignment

ORF - retro_alyr_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.74 %
• Parental protein coverage: 93.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KDELDIVIPTIRN--LDFLEMWRPFLQPYHLIIVQDGDPSKTIAVPEGFDYELYNRNDINRILGPKASCI
          K.E.DIVI.........FL..WRPF....HLI.V.D.........PEGFD...Y...D.....G...S..
Retrocopy KNEVDIVIGALNADLTQFLTSWRPFFSGFHLIVVKDPELKEELNIPEGFDVDVYSKTDMEKVVGASNSTM

Parental  SFKDSACRCFGYMVSKKKYIFTIDDDCFVAKDPSGKAVNALEQHIKNLLCPSTPFFFNTLYDPYREGADF
          .F....CR.FGY..SKKKYI..IDDDC..AKDP.G..V.A..QH..NL..P.TP.FFNTLYDPYREGADF
Retrocopy -FSGYSCRYFGYLISKKKYIVSIDDDCVPAKDPKGFLVDAVTQHVTNLENPATPLFFNTLYDPYREGADF

Parental  VRGYPFSLREGVSTAVSHGLWLNIPDYDAPTQLVKPKERNTRYVDAVMTIPKGTLFPMCGMNLAFDRELI
          VRGYPFSLR.GV..A.S.GLWLN..D.DAPTQ..K...RNT.YVDAVMT.P.....P..G.N.AF.REL.
Retrocopy VRGYPFSLRSGVPCAASCGLWLNLADLDAPTQALKTEQRNTSYVDAVMTVPAKAMLPISGINIAFNRELV

Parental  GPAMYFGLMGDGQPIGRY---DDMWAGWCIKVICDHLGLGVKTGLPYIYHSKASNPFVNLKKEYKGIFWQ
          GPA....L...G....R.....D.W.G.C.K.I.DHLG.GVKTGLPY............L.K...G....
Retrocopy GPALVPALRLAGEGKVRWETLEDVWCGMCLKHISDHLGYGVKTGLPYVWRNERGDAVESLRKKWEGMKLM

Parental  EDIIPFFQSAKLTKEAVTVQQCYMELSKLVKEKLSPIDPYFDKLADAMVTWIEAWDELN
          E...PFF.S.KL...A..V..C..EL.K.VKE.L...DP.F...ADAMV.WI..W...N
Retrocopy EKSVPFFESLKLPETALKVEDCVIELAKAVKEQLGSDDPAFTQAADAMVKWIQLWNSVN

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_15 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 thaliana	AT3G02230	1 retrocopy	retro_atha_19,
Arabidopsis lyrata	fgenesh2_kg.3__159__AT3G02230.1	1 retrocopy	retro_alyr_15 ,