RetrogeneDB ID: retro_brap_12

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A03:1120792..1121419(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra005902
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra027434
• Aliases: None
• Description: None

Sequence

>retro_brap_12
ATGAGTGATCAAGATTTCGAAGCGAGTAGTAATCCAGTGGACCGTACCAATCATCCTTCAGGGATAGTTCCCACTCTTCA
AAACATCGTCTCTACAGTTAACTTGGATTGCAAGCTTGACCTAAAATCGATAGCTTTGCAAGCACGGAACGCTGAGTATA
ACCCTAAACGTTTGGCTGCTGTGATCATGAGGATACGGGAACCAAAGACCACAGCGTTGATCTTCGCCTCGGGAAGAATG
GTGTGTACCGGAGCCAAGACCGAAGACTCCTCTAAGCTGGCGGCTAGGAAGTACGCTCGGATAATTCAGAAACTTGGATT
CCAAGCAAAGTTCAAAGACTTCAAGATTCAGAGCATCGTAGCTTCTTGTGATGTGAAGTTTCCTATAAGGCTTGAAGGTC
TTGCCTGCTATCGCCACGCTTTCGCAAGCTACGAGCCAGAGATATTTCCAGGACTTATTTACAGGATCAGAGGAAAGATA
GGGATGAAAGGAGCACAGATTGTGCTACTAATCTTTGTGTCTGGGAAGATGGTTATCACTGGATCCAAGAAGAGAGAGGA
CACATACAAAGCCTTTGAGAATATATACCCGGTCCTCACTCAATTCCAGAAGAAGTTCACCCGCTAG

Alignment

ORF - retro_brap_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.8 %
• Parental protein coverage: 78. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTDQGLEGS-NPVDLAEHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKT
          M.DQ..E.S.NPVD...HPSGIVPTLQNIVSTVNLDCKLDLK.IALQARNAEYNPKR.AAVIMRIREPKT
Retrocopy MSDQDFEASSNPVDRTNHPSGIVPTLQNIVSTVNLDCKLDLKSIALQARNAEYNPKRLAAVIMRIREPKT

Parental  TALIFASGKMVCTGAKSEYFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHAA
          TALIFASG.MVCTGAK.E..SK.AARKYARI.QKLGF.AKFKDFKIQ.IV.SCDVKFPIRLEGLA....A
Retrocopy TALIFASGRMVCTGAKTEDSSKLAARKYARIIQKLGFQAKFKDFKIQSIVASCDVKFPIRLEGLACYRHA

Parental  FSSYEPELFPGLIYRMK
          F.SYEPE.FPGLIYR..
Retrocopy FASYEPEIFPGLIYRIR

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_12 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica rapa	Bra027434	2 retrocopies	retro_brap_12 , retro_brap_9,
Brassica rapa	Bra030855	1 retrocopy	retro_brap_53,
Theobroma cacao	TCM_026453	1 retrocopy	retro_tcac_19,