RetrogeneDB ID: retro_alyr_5

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 5:16379530..16380226(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: fgenesh2_kg.5__1662__AT3G52960.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: fgenesh2_kg.2__836__AT1G65980.1
• Aliases: None
• Description: None

Sequence

>retro_alyr_5
ATGGCGACTTCTCTCTCCGTTTCTAGATTCATCTCCTCCTCCTCCGCCATCGCTAAGCCGTTACTATCCCCCACCGTCTC
CTTCACCGCGCCGCTCTCCTTCACACGCTCTCTCGCTCCTGATCTCTCCCTCAAATTCCGCAACCGCCGCACCAATTCCT
TCTCCGCCACCACCAGATCCTTCGCCACAACACCCGTCACCGCCTCCATATCCGTCGGAGACAAACTCCCAGACTCCACC
CTCTCCTACCTCGATCCATCCACCGGAGACGTCAAAACAGTAACCGTCTCATCCCTAACCGCCGGAAAGAAAACAATCCT
ATTCGCCGTACCCGGAGCATTCACACCAACCTGCTCACAAAAACACGTCCCTGGATTCGTATCTAAAGCTGGAGAACTCA
GATCTAAAGGCATCGATGTAATCGCATGTATCTCCGTCAACGACGCGTTTGTCATGGAAGCGTGGAGGAAAGATCTGGGA
ATCAACGATGAGGTAATGTTGCTTTCCGATGGTAACGGTGAATTCACAGGGAAGCTTGGAGTTGAATTGGATTTGAGGGA
TAAGCCTGTAGGACTTGGAGTTAGGTCAAGAAGATATGCGATATTGGCTGATGATGGTGTTGTGAAAGTTCTGAATCTTG
AAGAAGGAGGTGCTTTTACTAATAGTAGTGCTGAGGATATGCTTAAAGCTCTCTGA

Alignment

ORF - retro_alyr_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.37 %
• Parental protein coverage: 99.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APITVGDVVPDGTISFFDEND-QLQTASVHSLAAGKKVILFGVPGAFTPTCSMKHVPGFIEKAEELKSKG
          A.I.VGD..PD.T.S..D.......T..V.SL.AGKK.ILF.VPGAFTPTCS.KHVPGF..KA.EL.SKG
Retrocopy ASISVGDKLPDSTLSYLDPSTGDVKTVTVSSLTAGKKTILFAVPGAFTPTCSQKHVPGFVSKAGELRSKG

Parental  VDDIICFSVNDPFVMKAWGKTYPENKHVKFVADGSGEYTHLLGLELDLKDK--GLGVRSRRFALLLDNLK
          .D.I.C.SVND.FVM.AW.K....N..V....DG.GE.T..LG.ELDL.DK..GLGVRSRR.A.L.D...
Retrocopy IDVIACISVNDAFVMEAWRKDLGINDEVMLLSDGNGEFTGKLGVELDLRDKPVGLGVRSRRYAILADDGV

Parental  VTVANVESGGEFTVSSADDILKAL
          V.V.N.E.GG.FT.SSA.D.LKAL
Retrocopy VKVLNLEEGGAFTNSSAEDMLKAL

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_5 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G65980	1 retrocopy	retro_atha_13,
Arabidopsis lyrata	fgenesh2_kg.2__836__AT1G65980.1	1 retrocopy	retro_alyr_5 ,
Glycine max	GLYMA07G09240	1 retrocopy	retro_gmax_12,
Hordeum vulgare	MLOC_12954	1 retrocopy	retro_hvul_9,
Populus trichocarpa	POPTR_0018s09030	1 retrocopy	retro_ptri_12,
Prunus persica	PRUPE_ppa012586mg	1 retrocopy	retro_pper_22,
Sorghum bicolor	Sb03g030950	1 retrocopy	retro_sbic_22,
Selaginella moellendorffii	SELMODRAFT_159225	1 retrocopy	retro_smoe_4,
Solanum lycopersicum	Solyc07g020860.2	1 retrocopy	retro_slyc_41,
Theobroma cacao	TCM_028816	1 retrocopy	retro_tcac_8,