RetrogeneDB ID: retro_brap_20

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A09:3252376..3252853(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra035862
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra032519
• Aliases: None
• Description: None

Sequence

>retro_brap_20
ATGACGACTACCAACGAACCAGAGTTTGCCACGGCTGTGGCGGTTGCGACAAAGAACAGAACGTTCAAGAAGTTCTCATT
CAGAGGGTTCAACGTCGAAGCTCTTCTCAAAATGTCCACATATGATCTCTCTAAGCTTTTCAACGCTCGTGTGAGAAGGA
GATTCTATAGAGGGCTAAAGAAGAAGCCTCTGATTCTGATCAAGAAGCTACGCAAGGCGAAGAAAGAAGCAAAGGATGAG
AAGCCTGAACTGGTGAAGACGCATCTAAGGAACATGATCATTGTCCCTGAGATGATTGGAAGTGTTGTTGGAGTGCACAA
CGGTAAGAAGTTTAACGAGGTTGTGATTAAACCTGAGATGATTGGTCATTATCTTGCTGAGTTTTCGATGACTTGTAAGA
AAGTTGATCACTATAGACCACGTATCTGTGGTTGTGGTTGTTACCGTAATTCCACCAGGTTTATTCCTCTGAGGTGA

Alignment

ORF - retro_brap_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.58 %
• Parental protein coverage: 97.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EPE--VAAAGVPKKRTFKKFAFKGVDLDALLDMSTDDLVKLFPSRIRRRFSRGLTRKPMALIKKLRKAKR
          EPE...A.A...K.RTFKKF.F.G....ALL.MST.DL.KLF..R.RRRF.RGL..KP..LIKKLRKAK.
Retrocopy EPEFATAVAVATKNRTFKKFSFRGFNVEALLKMSTYDLSKLFNARVRRRFYRGLKKKPLILIKKLRKAKK

Parental  EAPQGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKHGRP---G
          EA...EKPE.V.THLRNMIIVPEMIGS..GV.NGK.FN.V.IKPEMIGHYLAEFS...K.V.H.RP...G
Retrocopy EA-KDEKPELVKTHLRNMIIVPEMIGSVVGVHNGKKFNEVVIKPEMIGHYLAEFSMTCKKVDHYRPRICG

Parental  VGATHSS-RFIPLK
          .G....S.RFIPL.
Retrocopy CGCYRNSTRFIPLR

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_20 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G04270	1 retrocopy	retro_atha_20,
Brassica rapa	Bra032519	1 retrocopy	retro_brap_20 ,
Arabidopsis lyrata	fgenesh2_kg.1__358__AT1G04270.1	1 retrocopy	retro_alyr_8,
Medicago truncatula	MTR_1g070450	1 retrocopy	retro_mtru_46,
Solanum tuberosum	PGSC0003DMG400007336	1 retrocopy	retro_stub_80,
Solanum lycopersicum	Solyc02g082000.2	1 retrocopy	retro_slyc_75,
Triticum aestivum	Traes_2AL_52D3F9AF41	1 retrocopy	retro_taes_67,