RetrogeneDB ID: retro_alyr_28

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 3:11712653..11714021(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: fgenesh2_kg.3__2649__AT3G24330.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: scaffold_200850.1
• Aliases: None
• Description: None

Sequence

>retro_alyr_28
ATGGCGAGTCACCAGCTTCCACCAGAAAAGGTAGTGAAGATGCTACAAGACAATGGTTTCACTAAGCTGAAACTGTTTGA
AGCCGACCAAAACATCTTAGACGCTCTAATTGGCTCACAGATCGAAGTCATGATCGGAATACCAAACCGGTTTCTTAAAG
AATTGGCTCAAGATACATCTGTAGCAGCTTCGTGGGTTGAAGAAAACGTTACTGCTTATTCTTACAATGGTGGAGTCAAC
ATCAAGTACATAGCTGTTGGAAACGAGCCTTTTCTTCAGACATATAATGGAACTTACGTTGAGTTCACTTTACCAGCTCT
TATCAACATCCAACGAGCCTTAGAGGAAGCTGATTTGAAAGGTGTGACAGTCACTGTTCCTTTCAACGCAGACATCTATT
TTTCTCCTGAAGCGAACCCGGTTCCATCAGCTGGAGACTTTAGGCCTGAGCTAAGGGATGCAACGATTGAGATAATCAAT
TTCTTGTATTCACATGATTCGCCTTTCACGGTTAACATATACCCTTTTCTTAGTCTCTATGGAAATGCTTACTTTCCTTT
GGACTTTGCCTTCTTTGATGGGACTAACAAATCTTTGAGAGATGGAAATTTGGTCTACACTAATGTGTTTGATGCGAATC
TCGACACTTTGATTTGTGCTATGGAGAAATATAGCTTCTTGGGGATGAAGATCATCGTGGGAGAAGTCGGATGGCCTACA
GATGGAGACAAGAACGCTAATTTAAAGAGTGCAAAGAGATTCAATCAGGGAATGGTAAAGCATGCTATGTCTGGAAATGG
AACGCCTGCGAGGAAAGGAGTGATCATGGATGTTTACCTTTTCAGCCTTGTCGATGAGGACGCCAAGAGTATAGCACCGG
GGACTTTTGAGAGACATTGGGGGATCTTTGGGTTTGATGGGAGACCGAAATACGAGCTTGACTTGTCGGGTAAAGGCAAT
GACAAGCCTTTGGTTCCTGTGGAAGATGTTAACTATCTGCCAAAAACTTGGTGTGTTCTTGACCCTAATGCATATAACCT
CGATGACTTGCCTGATAATATCGACTATGCTTGTAGCTTATCTGATTGCACAGCACTTGGGTATGGATCCTCTTGTAACC
ATCTTACTGCTATAGGCAATGCTTCATATGCCTTTAACATGTATTATCAGATGCACGATCAGAAAACCTGGGACTGCGAT
TTCTTGGGGTTGGGTTTGATCACAGATGAAGATCCATCTGATGAACTTTGTGAGTTCCCTGTGATGATTGATACAGGAAA
TTCCCCGAGGTTGCAACCTGGATCTTCAAGAGTGTTCACCAGAGTCGCAGCCGCGGTTTTAGTTATGTTGGTCCTTCCCA
TCTTGTAG

Alignment

ORF - retro_alyr_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.19 %
• Parental protein coverage: 88.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATHKLPPKTVVQMLKDNNINKVKLFDADETTMGALAGSGLEVMVAIPNDQLKVMTSYDR-AKDWVRKNV
          MA.H.LPP..VV.ML.DN...K.KLF.AD.....AL.GS..EVM..IPN..LK........A..WV..NV
Retrocopy MASHQLPPEKVVKMLQDNGFTKLKLFEADQNILDALIGSQIEVMIGIPNRFLKELAQDTSVAASWVEENV

Parental  TRYNFDGGVNITFVAVGNEPFLKSYNGSFINLTFPALTNIQNALNEAGLGNSVKATVPLNADVYDSPASN
          T.Y...GGVNI...AVGNEPFL..YNG.....T.PAL.NIQ.AL.EA.L...V..TVP.NAD.Y.SP..N
Retrocopy TAYSYNGGVNIKYIAVGNEPFLQTYNGTYVEFTLPALINIQRALEEADL-KGVTVTVPFNADIYFSPEAN

Parental  PVPSAGRFRPDIIGQMTQIVDFLGKNNAPITINIYPFLSLYGNDDFPLNYAFFDGA-QPINDNGIDYTNV
          PVPSAG.FRP........I..FL.....P.T.NIYPFLSLYGN..FPL..AFFDG......D....YTNV
Retrocopy PVPSAGDFRPELRDATIEIINFLYSHDSPFTVNIYPFLSLYGNAYFPLDFAFFDGTNKSLRDGNLVYTNV

Parental  FDANFDTLVSSLKAVGHGDMPIIVGEVGWPTEGDKHANSGNAYRFYNGLLPRLGTNKGTPLRPTYI-EVY
          FDAN.DTL...........M.IIVGEVGWPT.GDK.AN...A.RF..G.........GTP.R...I..VY
Retrocopy FDANLDTLICAMEKYSFLGMKIIVGEVGWPTDGDKNANLKSAKRFNQGMVKHAMSGNGTPARKGVIMDVY

Parental  LFGLLDEDAKSIAPGPFERHWGIFKFDGQPKFPIDLSGQGQNKLLIGAQNVPYLPNKWCTFNPEAKDLTK
          LF.L.DEDAKSIAPG.FERHWGIF.FDG.PK...DLSG.G..K.L.....V.YLP..WC...P.A..L..
Retrocopy LFSLVDEDAKSIAPGTFERHWGIFGFDGRPKYELDLSGKGNDKPLVPVEDVNYLPKTWCVLDPNAYNLDD

Parental  LAANIDFACTFSDCTALGYGSSCNTLDANGNASYAFNMYFQVKNQDESACFFQGLATITTQNISQGQCNF
          L..NID.AC..SDCTALGYGSSCN.L.A.GNASYAFNMY.Q...Q....C.F.GL..IT....S...C.F
Retrocopy LPDNIDYACSLSDCTALGYGSSCNHLTAIGNASYAFNMYYQMHDQKTWDCDFLGLGLITDEDPSDELCEF

Parental  PIQI
          P..I
Retrocopy PVMI

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_28 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
Brassica rapa	Bra036718	1 retrocopy	retro_brap_4,
Arabidopsis lyrata	scaffold_200850.1	1 retrocopy	retro_alyr_28 ,