RetrogeneDB ID: retro_brap_22

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A01:10913813..10915217(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra038489
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra012095
• Aliases: None
• Description: None

Sequence

>retro_brap_22
ATGTTACCCGTGAGAGAAGGTCTTCAGAAACAGGTTAAGATTCTGATTGGATTAGGGTTTGGGGGTTACCGGGGTTTCCA
CTCTAGATTCGCTAGCCCTAACGGCTTTCTCGAGCCCGCGAGCTCCGATTTGCTTCTGAGCAACGAAAGGAGGAACCTTT
CTGTCCTCGGCGCTCTCTCTCGAACTTTCTCCGTTCCTTCTGTCTCCGGTCCGGCGTTTCAGGTCTGTGGCTATCACATT
GATCTTTTGCTCTCGGACGCGAGTTTGAGGTCGGTGGGTGAATCAATGGCGAGTCTTGGTGGTTCAAAGTCCTTGTTTTT
AGATCCCTTGGTTTCTGGTGTGACGGTGTGTGGAGATGGTCATAGCCGTGGAAGAGTCAGTATGAGACTCAGAGGAAGAG
ACCACGGGGATAATAACAACTCTACGGTCTACGGCTACTTTGCTTACCGAGCTGCTAAGAAATGGATTGCTTTCAATCCT
AAAACTGGAGGGTTAGGGTTTAGAGGCTTGCACAGCTCACTGTTGAGCCGCTTTTCAGCTGGGAATGCGCCTGATGTCTC
GTTTGATAGCTCTCCCGCCGAGGAGCAGGTTAAAGGTTCTTCTTCGGATTCTGTAGCGGATAAGCTTTGTGTTAAGCCGT
TGAAGCTCGTCTCCGGGTCTTGCTACCTACCGCATCCTGATAAAGAGGCGACGGGAGGAGAGGATGCTCACTTTATCTGC
GCAGAGGAGCAAGCGTTGGGTGTTGCAGATGGTGTGGGAGGTTGGGCGGAGCTTGGTATCGATGCGGGTTACTACTCTCG
TGAGCTTATGTCTAACTCTGTGAACGCAATCCAAGACGAGCCTAAAGGATCGATTGATCCTGCAAGAGTATTGGAGAAGG
CTCATACTAGTACAAAGTCGCAAGGGTCTTCAACGGCTTGCATCATAGCGTTGACGGACCAGGGACTTAACGCGATCAAC
CTAGGGGACAGCGGGTTCATGGTGGTCCGTGAAGGGCATACCGTTTTCCGCTCCCCCGTTCAACAGCATGACTTCAACTT
CACGTATCAGCTGGAGAGTGGGAGTAACGGCGATTTGCCAAGCTCGGGTCAGGTGTTCACGGTTGCTGTAGCTCCTGGAG
ACGTGATAATAGCTGGAACAGACGGATTATTCGACAATTTGTACAACAACGAGATCACAGCCATAGTGGTTCAAGCGGTG
AGAGCCGGAACAGATCCTCAGGTGACAGCACAGAAGATTGCAGCTTTGGCGAGGCAAAGAGCGCAGGACAAGAACAGACA
GACTCCATTCTCTACGGCAGCGCAAGATGCTGGATTCAGATACTATGGAGGTAAGCTTGATGACATTACAGTTGTAGTCT
CTTATGTGGCGGCTTCGAAAGAAGTAGGGAAAACATTGAAATGA

Alignment

ORF - retro_brap_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.68 %
• Parental protein coverage: 65.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AHELSTSQDSELSPTTTSLKCLKLVSGSCYLPHPEKEATGGEDAHFICDEEQAIGVADGVGGWAEVGVNA
          A.E......S.........K.LKLVSGSCYLPHP.KEATGGEDAHFIC.EEQA.GVADGVGGWAE.G..A
Retrocopy AEEQVKGSSSDSVADKLCVKPLKLVSGSCYLPHPDKEATGGEDAHFICAEEQALGVADGVGGWAELGIDA

Parental  GLFSRELMSYSVAAIRELAKGSSIDPLMVLEKAHSQTRAQGSSTACIIALTDKGLHAINLGDSGFTVVRD
          G..SRELMS.SV.AI....KGS.IDP..VLEKAH..T..QGSSTACIIALTD.GL.AINLGDSGF.VVR.
Retrocopy GYYSRELMSNSVNAIQDEPKGS-IDPARVLEKAHTSTKSQGSSTACIIALTDQGLNAINLGDSGFMVVRE

Parental  GTTVFQSPVQQHGFNFTYQLGCGDSGGDMPRSGQVFMIDVEAGDVIVAGTDGVYDNLYNEDITGVVVSSV
          G.TVF.SPVQQH.FNFTYQL..G.S.GD.P.SGQVF...V..GDVI.AGTDG..DNLYN..IT..VV..V
Retrocopy GHTVFRSPVQQHDFNFTYQLESG-SNGDLPSSGQVFTVAVAPGDVIIAGTDGLFDNLYNNEITAIVVQAV

Parental  RAGLDPKGTAQKIADLARARAVDKKRQSPFATAAQEAGYRYYGGKLDDITALVSYV
          RAG.DP..TAQKIA.LAR.RA.DK.RQ.PF.TAAQ.AG.RYYGGKLDDIT..VSYV
Retrocopy RAGTDPQVTAQKIAALARQRAQDKNRQTPFSTAAQDAGFRYYGGKLDDITVVVSYV

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_22 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT5G66720	1 retrocopy	retro_atha_16,
Brassica oleracea	Bo7g064600	1 retrocopy	retro_bole_4,
Brassica rapa	Bra012095	1 retrocopy	retro_brap_22 ,