RetrogeneDB ID: retro_alyr_29

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 1:28280182..28281001(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: scaffold_105127.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: fgenesh2_kg.1__4381__AT1G53080.1
• Aliases: None
• Description: None

Sequence

>retro_alyr_29
ATGAAGATCCAAATACTCTGTTTCACCACTCTGTTCTTAGCTATCTTCACCCCTCAAGTCACCACTGCTTACAAATTCAA
ATTCGATTACTTTGGTAATGGTACTGATCTAATATCATTCCATGGTGACGCTGAGTATGGTCCTGACACTGATGGCATGA
GCCGGTCCGGAGCCATCGCATTGACTCGAGACAACATCCCTTTCTCTCATGGTCGAGCTATTTTAACCACTCCAATCACT
TTCAAGCCTAATGCTTCAGCTCTTTACCCTTTTAAAACCTCTTTCACTTTCTCCATTACTCCTAAAACAAACCCTAATCA
AGGTCATGGCCTTGCCTTCATCGTCGTCCCAAGTAACCGAAACGACGCCGGTTCCGGTTTAGGCTATCTCAGTCTTCTGA
ACCGAACCAACAACGGTAATCCTAATAACCACCTTTTTGCCGTTGAATTTGATGTCTTTCAAGACAAATCTCTTGGCGAC
GTGAACGATAACCATGTCGGAATCGATATTAATTCGGTTGATTCGGTGGTTTCTGTGAAATCCGGTTATTGGGTTATGAC
AAGAAACGGTTGGTTGTTTAAGGAATTGAAGTTGAGTAGTGGAGATAGATACAAGGCTTGGATTGAGTACAACAATAATT
ATAAAGTCATCTCTGTTACGATTGGTTTGGCGCATTTGAAGAAACCGAACCGGCCATTGATTGAAGCAAAATTCGATCTT
TCCAAGGTTATTCACGAGCAAATGTATACCGGTTTTGCCGGTTCGATGGGTCGTGGTGTCGAGCGTCACGAGATTTGGGA
CTGGACTTTCCAGAACTAA

Alignment

ORF - retro_alyr_29 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.36 %
• Parental protein coverage: 99.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQIQKLCFFALFISLFSTKTISAVKFNFNHF-DGTDLI-FLGYAELGPATDGMSRSGALSMTRDKNPFSH
          M.IQ.LCF..LF...F......A.KF.F..F..GTDLI.F.G.AE.GP.TDGMSRSGA...TRD..PFSH
Retrocopy MKIQILCFTTLFLAIFTPQVTTAYKFKFDYFGNGTDLISFHGDAEYGPDTDGMSRSGAIALTRDNIPFSH

Parental  GRGLYTDLIPFKSSNNISSSVYSFKTSFTFSITPRRSNPNPGHGLAFIVVPTIHYDQDSTRGFLGLVNRT
          GR...T..I.FK......S..Y.FKTSFTFSITP...NPN.GHGLAFIVVP....D..S..G.L.L.NRT
Retrocopy GRAILTTPITFKPN---ASALYPFKTSFTFSITPK-TNPNQGHGLAFIVVPSNRNDAGSGLGYLSLLNRT

Parental  TNGNPNNHLFAVEFDVFQDKRFGDINDNHVGININSVTSKVSEKAGYWVQTRTGGNNQWLFKEVKLSSGD
          .NGNPNNHLFAVEFDVFQDK..GD.NDNHVGI.INSV.S.VS.K.GYWV.TR.G....WLFKE.KLSSGD
Retrocopy NNGNPNNHLFAVEFDVFQDKSLGDVNDNHVGIDINSVDSVVSVKSGYWVMTRNG----WLFKELKLSSGD

Parental  NYKAWIEYKNS-KVI-VWLAPAHLKKPKRPLIETQVDLSEVVLETMYTGFAGSMGRGIERHDIWSWSFEN
          .YKAWIEY.N..KVI.V....AHLKKP.RPLIE...DLS.V..E.MYTGFAGSMGRG.ERH.IW.W.F.N
Retrocopy RYKAWIEYNNNYKVISVTIGLAHLKKPNRPLIEAKFDLSKVIHEQMYTGFAGSMGRGVERHEIWDWTFQN

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_29 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.1__4381__AT1G53080.1	1 retrocopy	retro_alyr_29 ,