RetrogeneDB ID: retro_brap_54

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A10:14978636..14979044(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra003745
• Aliases: None
• Description: None

Sequence

>retro_brap_54
ATGGCTCGTACCAAGCAGACCGCGAGAAAATCCACCGGAGGAAAGGCTCCGAGGAAGCAGCTGGCAACCAAAGCGGCGAG
GAAATCGGCTCCGGCGACCGGAGGAGTGAAGAAGCCGCACAGATTCCGTCCCGGAACGGTGGCGTTGAGGGAGATCAGGA
AGTACCAGAAGAGCACCGAGCTTCTGATCCGCAAGCTTCCTTTCCAGCGTCTGGTCCGTGAGATAGCTCAGGATTTCAAG
ACGGATCTGAGGTTCCAGAGCAGCGCTGTCGCGGCTCTTCAGGAAGCTGCGGAGGCTTACCTCGTTGGTTTGTTCGAAGA
CACGAATCTCTGTGCGATTCACGCGAAGAGGGTTACGATTATGCCTAAGGACATCCAGCTTGCAAGAAGAATCAGGGGTG
AGAGGGCT

Alignment

ORF - retro_brap_54 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.06 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARTKQTARKSTGGKAPRKQLATKAARKSAPTTGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQR
          MARTKQTARKSTGGKAPRKQLATKAARKSAP.TGGVKKPHR.RPGTVALREIRKYQKSTELLIRKLPFQR
Retrocopy MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRFRPGTVALREIRKYQKSTELLIRKLPFQR

Parental  LVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
          LVREIAQDFKTDLRFQS.AV.ALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
Retrocopy LVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

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_54 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 2 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica rapa	Bra003745	4 retrocopies	retro_brap_3, retro_brap_36, retro_brap_54 , retro_brap_55,
Solanum lycopersicum	Solyc05g051500.2	1 retrocopy	retro_slyc_13,