RetrogeneDB ID: retro_brap_56

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A10:14702783..14703065(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra029327
• Aliases: None
• Description: None

Sequence

>retro_brap_56
ATGTCTGAGACAATTCCAATAATTTCTTTTCTCTGCGATTTGCCGGTGATTGTTCCAAGGAGCGTTAAGCAGTCGGTGTG
GATTCTGAGATCGGCGATCTCTAGCTCCACAGCCTTCGATAGAGCCGCTCGAACCGCCATGGCTTCCGCCACTAGTGGTG
ATCCAACAAACTCCTCTACACGGGTTTCTTCCCATACGATCGGGGGGGATGAGCCTGAGAACGTCCAGGCTAGTCATGCT
CTCTTTCTCTCTTTCTCCCAAGCCGCGTCTGTGTGGCAGATG

Alignment

ORF - retro_brap_56 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.33 %
• Parental protein coverage: 57.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSETIPIISFLCDLPVIVPRSVKQSVWILRSAISSSTAFDRAARTAMASAASGDPTRNHSCIMVNHRHYI
          MSETIPIISFLCDLPVIVPRSVKQSVWILRSAISSSTAFDRAARTAMASA.SGDPT...........H.I
Retrocopy MSETIPIISFLCDLPVIVPRSVKQSVWILRSAISSSTAFDRAARTAMASATSGDPTNSSTRV---SSHTI

Parental  MSQEPKNQQLLNTLHKITKSRGAALQQL
          ...EP.N.Q....L.....S..A...Q.
Retrocopy XXXEPENVQASHALF-LSFSQAASVWQM

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_56 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica rapa	Bra029327	2 retrocopies	retro_brap_40, retro_brap_56 ,