RetrogeneDB ID: retro_brap_53

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A09:35807654..35808139(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra030855
• Aliases: None
• Description: None

Sequence

>retro_brap_53
ATGAGTGATCAAGATTTTGAAGGGAGTAGTGAACCAGTGGACCTTATCAATCATCCTTCAGGGATCGTTCCCACTCTTCA
AAACATCGTCTCTACAGTTAACTTGGACTGCAAGCTTGACCTAAAAGCGATAGCTTTGCAAGCACGTAACGCCGAATATA
ACCCTAAACGTTTTGCTGCTGTGATCATGAGGATAAGGGAACCGAAGACCACAGCGTTGATATTTGCCTCGGGAAGAATG
GTCTGTACCGGAGCCAAGACCGAAGACTCCTCCAAGCTGGCGGCTAGGAAGTACGCTAGGATATATAATTCAGAAACTTG
GATTCCAAGCAAAGTTCAAAGATTTCAAGATTCAGAACATCGTAGCTTCTTGTGATGTGAAGTTTTCCTATATGGCTTGA
AGGTCTTGCCTACTATCACCACGCTTTCGCAAGCTACGAGCCGGAGATGTTTCCGGGTCTTATTTACAGGATCAGAGGGA
TGAAA

Alignment

ORF - retro_brap_53 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.14 %
• Parental protein coverage: 79.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAEQGMEGS-QPVDLMKHPSGIIPTLQNIVSTVNLDCKLDLKSIALQARNAEYNPKRFAAVIMRIREPKT
          M..Q..EGS..PVDL..HPSGI.PTLQNIVSTVNLDCKLDLK.IALQARNAEYNPKRFAAVIMRIREPKT
Retrocopy MSDQDFEGSSEPVDLINHPSGIVPTLQNIVSTVNLDCKLDLKAIALQARNAEYNPKRFAAVIMRIREPKT

Parental  TALIFASGKMVCTGAKSEHFSKLAARKYARIV-QKLGFPAK-FKDFKIQNIVGSCDVK-FPIRLEGLAYS
          TALIFASG.MVCTGAK.E..SKLAARKYARI.......P.K.FKDFKIQNIV.SCDVK.FPI.LEGLAY.
Retrocopy TALIFASGRMVCTGAKTEDSSKLAARKYARIYNSETWIPSK>FKDFKIQNIVASCDVK>FPIWLEGLAYY

Parental  HSAFSSYEPELFPGLIYRMKQPK
          H.AF.SYEPE.FPGLIYR....K
Retrocopy HHAFASYEPEMFPGLIYRIRGMK

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_53 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,