RetrogeneDB ID: retro_brap_9

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A02:2365308..2365923(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra028725
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_brap_9
ATGAGCGATGACGAATTGCAAGGGAGTACTGATCCAGTGGACCTTAGCAACCATCCTTCAGGGCTAGTCCCCACTCTTCA
AAACATCGTCTCGACGGTTAACTTGGACTGCAAGATAGACCTAAAAGAGATAGCTTTGAAAGCACGTAACGCCGAATACA
ACCCTAAACGTTTTGCTGCCGTGATCATGAGGATAAGGGAACCAAAAACCACGGCGTTGATCTTCGCCTCGGGGAGAATG
GTCTGTACTGGAGCCAAGACCGAGTGCTTCTCCAAGCTGGCTGCTAGAAAGTACGCTCGCATAGTTCAGAAACTTGGGTT
CGACGCAAGGTTCAAAGACTTCAAGATCCAGAACATTGTAGCTTCTTGTGATGTGAAGTTCCCTATAAGGCTTGAGATTC
TTGCCGTCTCTGTTCACCGCGACTTCTTGAGCTACGAGCCGGAGATGTTTCCAGGACTCATTTATAGGATGAGAGAACCA
AAGATTGTGCTACTGATCTTTGTGTCTGGGAAGATTGTTATCACTGGAGCCAAGAAGAGAGAGGACACTTTCAGAGCCTT
TGAGAATATATACCCGGTGCTCACACAGTTTAAGAAGATATGCATTCATAGGTAG

Alignment

ORF - retro_brap_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.0 %
• Parental protein coverage: 99.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTDQGLEGS-NPVDLAEHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKT
          M.D..L.GS..PVDL..HPSG.VPTLQNIVSTVNLDCK.DLK.IAL.ARNAEYNPKRFAAVIMRIREPKT
Retrocopy MSDDELQGSTDPVDLSNHPSGLVPTLQNIVSTVNLDCKIDLKEIALKARNAEYNPKRFAAVIMRIREPKT

Parental  TALIFASGKMVCTGAKSEYFSKMAARKYARIVQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYS-HA
          TALIFASG.MVCTGAK.E.FSK.AARKYARIVQKLGF.A.FKDFKIQNIV.SCDVKFPIRLE.LA.S.H.
Retrocopy TALIFASGRMVCTGAKTECFSKLAARKYARIVQKLGFDARFKDFKIQNIVASCDVKFPIRLEILAVSVHR

Parental  AFSSYEPELFPGLIYRMKVPKIVLLIFVSGKIVITGAKMREETYKAFENIYPVLTEFRKI
          .F.SYEPE.FPGLIYRM..PKIVLLIFVSGKIVITGAK.RE.T..AFENIYPVLT.F.KI
Retrocopy DFLSYEPEMFPGLIYRMREPKIVLLIFVSGKIVITGAKKREDTFRAFENIYPVLTQFKKI

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_9 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,