RetrogeneDB ID: retro_alyr_11

Retrocopy location

• Organism: Lyre-leaved rock-cress (Arabidopsis lyrata)
• Coordinates: 3:11844809..11845256(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: fgenesh2_kg.3__2660__AT3G24500.1
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: scaffold_503053.1
• Aliases: None
• Description: None

Sequence

>retro_alyr_11
ATGCCGAGCAGATACCCAGGAGCAGTAACACAAGACTGGGAACCAGTAATTCTCCACAAATCAAAACAAAAGAGTCAAGA
CCTACGCGATCCAAAAGCGGTTAACGCAGCGCTTAGAAACGGCGTCGCGGTTCAAACGGTTAAGAAATTCGACGCCGGTT
CTAACAAAAAGGGGAAATCTACGGCGGTTCCGGTGATTAACACGAAGAAACTTGAGGAAGAAACAGAGCCTGCGGCGATG
GATCGTGTGAAAGCAGAGGTGAGGTTGATGATACAGAAGGCGAGGTTGGAGAAGAAGATGTCGCAAGCAGATTTGGCGAA
ACAGATAAATGAAAGGACTCAGGTGGTTCAGGAATATGAGAATGGTAAAGCTGTTCCTAATCAGGCTGTGCTTGCGAAGA
TGGAGAAGGTTCTAGGTGTTAAACTTAGGGGTAAAATTGGTAAATGA

Alignment

ORF - retro_alyr_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.24 %
• Parental protein coverage: 96.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GPITQDWEPVVIRKKAPNSAAKRDEKTVNAARRSGADIETVRKFNAGSNKAASSGT--SLNTKKLDDDTE
          G..TQDWEPV...K....S...RD.K.VNAA.R.G....TV.KF.AGSNK...S......NTKKL...TE
Retrocopy GAVTQDWEPVILHKSKQKSQDLRDPKAVNAALRNGVAVQTVKKFDAGSNKKGKSTAVPVINTKKLEEETE

Parental  NLSHDRVPTELKKAIMQARGEKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILSKLERALGAKLRGK
          ....DRV..E....I..AR.EKK..Q..LA..INE..QV.QEYE.GKA.PNQ..L.K.E..LG.KLRGK
Retrocopy PAAMDRVKAEVRLMIQKARLEKKMSQADLAKQINERTQVVQEYENGKAVPNQAVLAKMEKVLGVKLRGK

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_11 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 20 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI2G06560	1 retrocopy	retro_bdis_21,
Medicago truncatula	MTR_2g084220	1 retrocopy	retro_mtru_80,
Oryza brachyantha	OB08G20790	1 retrocopy	retro_obra_22,
Oryza barthii	OBART08G12410	1 retrocopy	retro_obar_10,
Oryza glumaepatula	OGLUM08G13370	1 retrocopy	retro_oglu_20,
Oryza meridionalis	OMERI08G10430	1 retrocopy	retro_omer_26,
Oryza nivara	ONIVA08G13070	1 retrocopy	retro_oniv_14,
Oryza punctata	OPUNC08G11340	1 retrocopy	retro_opun_15,
Oryza glaberrima	ORGLA08G0109300	1 retrocopy	retro_ogla_35,
Oryza rufipogon	ORUFI08G14100	1 retrocopy	retro_oruf_7,
Oryza sativa japonica	OS08G0366100	1 retrocopy	retro_osat_47,
Populus trichocarpa	POPTR_0001s40090	1 retrocopy	retro_ptri_9,
Physcomitrella patens	PP1S96_94V6	1 retrocopy	retro_ppat_19,
Prunus persica	PRUPE_ppa013074mg	1 retrocopy	retro_pper_2,
Sorghum bicolor	Sb07g014940	1 retrocopy	retro_sbic_34,
Arabidopsis lyrata	scaffold_503053.1	1 retrocopy	retro_alyr_11 ,
Solanum lycopersicum	Solyc10g007350.2	1 retrocopy	retro_slyc_40,
Theobroma cacao	TCM_001730	1 retrocopy	retro_tcac_24,
Triticum aestivum	Traes_3AS_719D37CCA	1 retrocopy	retro_taes_74,
Vitis vinifera	VIT_12s0028g02020	1 retrocopy	retro_vvin_6,