RetrogeneDB ID: retro_brap_36

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A01:11644257..11644614(-)
• 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_36
CGGAGGCAAAGCCCCAAGAAAGCAGCCAGGAAATCCGCTCCGGCCACCGGCGGAGTGAAGAAGCCACACAGATTCCGTCC
AGGAACGGTGGCATTGAGGGAGATCAGGAAGTACCAGAAGAGCACCGAGCTTCTGATCCGTAAGCTTCCTTTCCAGCGTC
TGGTTCGTGAGATCGCTCAGGATTTCAAGACGGATCTAAGGTTCCAGAGCAGCGCCGTCGCGGCTCTACAGGAAGCAGCC
GAGGCTTACCTCGTTGGGTTGTTTGAAGACACTAATCTTTGCGCGATTCATGCGAAGAGAGTCACTATCATGCCTAAGGA
TATCCAGCTCGCTAGGAGAATCCGTGGTGAAAGAGCT

Alignment

ORF - retro_brap_36 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.28 %
• Parental protein coverage: 87.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RKQLATKAARKSAPTTGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQS
          R.Q...KAARKSAP.TGGVKKPHR.RPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQS
Retrocopy RRQSPKKAARKSAPATGGVKKPHRFRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQS

Parental  HAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
          .AV.ALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
Retrocopy SAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

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_36 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.

---

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,