RetrogeneDB ID: retro_alyr_12

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 5:13248722..13249940(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: scaffold_501683.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: fgenesh2_kg.3__1630__AT3G15020.2
• Aliases: None
• Description: None

Sequence

>retro_alyr_12
ATGGCAGCAGCAACATCAGCAGCATCTCTGTTTTCAACTGTTTCTTCTTACTCCTCTAAACCCAGTTCCTTACCACATTC
AAGACTCCAAGCTGTGAAATTTAACTCAGTCCCTAGCTTCACCGGTCTCAGATCAACAACGTCTCTCATCTCTGGATCTG
ATGCCTCTTCCTTAACCAAGACTCTCCGCGGTTCCGTAACGAAAGCTCAAACATCTGACAAGAAGCCTTACGGATTCAAA
ATCAATGCTTCGTACAAAGTAGCTGTTCTTGGTGCTGCTGGTGGTATAGGTCAGCCTTTATCACTTCTCATCAAGATGTC
TCCGTTAGTTTCGACGCTTCATCTTTACGATATTGCGAATGTTAAAGGAGTTGCTGCTGATCTGAGTCATTGTAATACTC
CTTCTCAAGTTCGTGATTTCACCGGTCCTTCTGAGTTGGCTGATTGTTTGAAAGATGTGAATGTTGTTGTTATTCCTGCT
GGTGTACCGAGGAAACCGGGTATGACTCGTGATGATCTTTTCAACATCAATGCCAACATTGTGAAGACGCTTGTTGAAGC
TGTTGCTGATAACTGTCCTAATGCTTTTATTCATATTATTAGTAACCCGGTTAACTCTACGGTACCGATTGCTGCTGAAG
TGTTGAAAAAGAAAGGTGTTTATGATCCTAAGAAGTTGTTTGGTGTCACTACGTTGGATGTTGTGAGGGCTAACACTTTT
GTTTCTCAGAAAAAGAACCTTAAGCTTATTGATGTGGATGTTCCGGTTATTGGTGGACATGCTGGAATCACCATTTTGCC
TCTTCTGTCAAAAACAAAACCATCTGTGAACTTTACCGATGAAGAGATCCAAGAGCTCACAGTTAGGATTCAGAACGCTG
GAACTGAGGTTGTGGATGCTAAGGCAGGTGCTGGTTCAGCTACTTTGTCAATGGCATATGCTGCAGCAAGATTTGTCGAG
TCATCTCTCCGTGCTCTTGATGGAGACGGAGATGTCTATGAGTGCTCGTTTGTGGAGTCAACTCTGACTGATCTTCCTTT
CTTTGCATCGCGGATCAAGCTTGGGAAGAACGGTCTTGAAGCTGTGATTGAGTCAGACCTTCAGGGTTTAACTGAGTATG
AGCAGAAAGCACTAGAAGCTCTTAAACCAGAACTGAAAGCTAGCATCGAGAAGGGTGTCGCATTTGCAAACAAACCAGCT
GCTGCAGCAGCTAACTAG

Alignment

ORF - retro_alyr_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.54 %
• Parental protein coverage: 92.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KVVILGAAGGIGQPLSLLMKLNPLVSSLSLYDIANTPGVAADVGHINTRSQVSGYMGDDNLGKALEGADL
          KV..LGAAGGIGQPLSLL.K..PLVS.L.LYDIAN..GVAAD..H.NT.SQV....G...L...L.....
Retrocopy KVAVLGAAGGIGQPLSLLIKMSPLVSTLHLYDIANVKGVAADLSHCNTPSQVRDFTGPSELADCLKDVNV

Parental  VIIPAGVPRKPGMTRDDLFNINAGIVKNLSIAIAKYCPQALVNMISNPVNSTVPIAAEIFKKAGTYDEKK
          V.IPAGVPRKPGMTRDDLFNINA.IVK.L..A.A..CP.A....ISNPVNSTVPIAAE..KK.G.YD.KK
Retrocopy VVIPAGVPRKPGMTRDDLFNINANIVKTLVEAVADNCPNAFIHIISNPVNSTVPIAAEVLKKKGVYDPKK

Parental  LFGVTTLDVVRAKTFYAGKSNLNVAEVNVPVVGGHAGITILPLFSQASPQANLSDDLIKALTKRTQDGGT
          LFGVTTLDVVRA.TF...K.NL....V.VPV.GGHAGITILPL.S...P..N..D..I..LT.R.Q..GT
Retrocopy LFGVTTLDVVRANTFVSQKKNLKLIDVDVPVIGGHAGITILPLLSKTKPSVNFTDEEIQELTVRIQNAGT

Parental  EVVEAKAGKGSATLSMAYAGALFADGCLKGLNGVPDVVECSFVQSTITELPFFASKVRLGKNGVEEVL--
          EVV.AKAG.GSATLSMAYA.A.F....L..L.G..DV.ECSFV.ST.T.LPFFAS...LGKNG.E.V...
Retrocopy EVVDAKAGAGSATLSMAYAAARFVESSLRALDGDGDVYECSFVESTLTDLPFFASRIKLGKNGLEAVIES

Parental  DLGPLSDFEKEGLEALKAELKSSIEKGIKFANQ
          DL..L...E...LEALK.ELK.SIEKG..FAN.
Retrocopy DLQGLTEYEQKALEALKPELKASIEKGVAFANK

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_12 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	fgenesh2_kg.3__1630__AT3G15020.2	1 retrocopy	retro_alyr_12 ,
Sorghum bicolor	Sb09g029240	1 retrocopy	retro_sbic_5,