RetrogeneDB ID: retro_brap_10

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A07:11039756..11040311(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra011950
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra008491
• Aliases: None
• Description: None

Sequence

>retro_brap_10
ATGGAGCAAAAGAACAAAAGCGACGAATCAAGGCCGCCATTGATGGCGTTAAACCATGTATCAAGACTTTGCAGAGACGT
CAAAAAGTCTCTCGAGTTCTACACGAAAGTGTTAGGGTTCGTGGAGACAGAGCGACCCGCGTCGCTAGACTTCGACGGTG
CGTGGCTATTCAACTACGGTGTTGGGATCCATTTGGTGCAGGCTAAAGACGAAGAGAAGCTACCTTCCAACACGGACCAT
TTGGACCCGATGGATAACCACATCTCGTTCCAGTGCGAAGACATGGAAGCTTTGGAGAAGAGGCTCAAGGAAGTGGATGT
GAAGTACATCAAGAGGACGGTCGGTGAGCAGGAAGACGCAGCTATCGACCAGCTCTTCTTTAATGACCCCGATGGTTTCA
TGGTCGAGATTTGTAACTGCGAGAATCTGGAGCTTAAACCGCGTGATTCAGCTGATGCTATACGTCTCCCGGGTGATCGA
CACGCGCCTCCTGTTTCTCTCCCTGGCTCGTCCGACCATGCAGATGATACTAGGCTCCCTCAGACCAATTCTTAA

Alignment

ORF - retro_brap_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.46 %
• Parental protein coverage: 79.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKSLNHISLLCRSVEESMSFYQHVLGFLPIRRPGSFDFDGAWLFGHGVGIHLLQSTEPEKLLKKTE-INP
          L..LNH.S.LCR.V..S..FY..VLGF....RP.S.DFDGAWLF..GVGIHL.Q....EKL...T....P
Retrocopy LMALNHVSRLCRDVKKSLEFYTKVLGFVETERPASLDFDGAWLFNYGVGIHLVQAKDEEKLPSNTDHLDP

Parental  KDNHISFQCESMGAVEKKLKEMGIEYV-RAVVEEGGIQVDQLFFHDPDGFMIEICNCDSLPVVP
          .DNHISFQCE.M.A.EK.LKE....Y..R.V.E......DQLFF.DPDGFM.EICNC..L...P
Retrocopy MDNHISFQCEDMEALEKRLKEVDVKYIKRTVGEQEDAAIDQLFFNDPDGFMVEICNCENLELKP

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Brassica rapa was not studied using RNA-Seq expression data.

ChIP-Seq

Brassica rapa was not studied using ChIP-Seq data.

EST

Brassica rapa was not studied using EST data.

TSS

Brassica rapa was not studied using FANTOM5 data.

Lab

retro_brap_10 was not experimentally validated.

Homology

Retrocopy orthology:

Brassica rapa 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G80160	1 retrocopy	retro_atha_15,
Brassica oleracea	Bo2g096220	1 retrocopy	retro_bole_1,
Brassica rapa	Bra008491	1 retrocopy	retro_brap_10 ,
Arabidopsis lyrata	fgenesh1_pm.C_scaffold_2001978	1 retrocopy	retro_alyr_14,
Medicago truncatula	MTR_2g103490	1 retrocopy	retro_mtru_44,
Setaria italica	Si023259m.g	1 retrocopy	retro_sita_39,