RetrogeneDB ID: retro_bole_4

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C1:15627730..15629128(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo1g053510
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo7g064600
• Aliases: None
• Description: None

Sequence

>retro_bole_4
ATGTTACCCGTGAGAGAAGGTCTTCAGAAACAGGTTAAGATTCTTATTGGATTAGGGTTTGGGGGTTACCGGGGTTTCCA
CTCTAGATTCGCTAGCCCTAACGGGTTTCTCGAGCCCGCGAGCTCCGATTTGCTTCTGAGCAACGAAAGGAGGAACCTTT
CTGTCCTCGGTGCTCTCTCTCGAACTTTCTCTGTTCCTTCTGTGTCCGGTCCGGCGTTTCAGGTCTGTGGTTATCACATT
GATCTCTTGCTCTCGGACGCGAGTTTGAGATCGGTGGGTGAATCAATGGCGAGTCTTGGTGGTTCAAAGTCCTTGTTTTT
AGATCGCCGTTTTGATCCTTCCGTTTCTGGTGTGATGGTGTGTGGAGATGGTCGTAGCCGTGGAAGGATCAGTATGAGAC
TCACAGGAAGAGATCACGGGGATAATAACTCTACGGTCTACGGCTACTTTGCTTATCGAGCTGCTAAGAAATGGATTGCT
TTCAATCCTAAAACTGGAGGGTTAGGGTTTAGAGGCTTACACAGCTCACTGTTGAGCCGCTTTTCAGTTGGGAATGCGCC
TGATGTCTCGTTTGATAGCTCTCCCGCCGAGGAGCTGGCTAAAGGCTCTTCGGATTCTGTAGCGGATAAGCTTTGTGTTA
AGCCGTTGAAGCTTGTCTCCGGGTCTTGCTACCTACCTCATCCTGATAAAGAGGCGACGGGAGGAGAGGATGCTCACTTT
ATCTGCGCAGAGGAGCAAGCTTTGGGTGTTGCAGATGGTGTGGGAGGTTGGGCAGAGCTTGGCATCGATGCGGGTTACTA
CTCTCGTGAGCTTATGTCTAACTCTGTGAACGCAATCCATGACGAGCCTAAAGGATCGATCGATCCTGCCAGAGTATTGG
AGAAGGCTCATACTAGTACAAAGTCACAAGGGTCTTCAACGGCTTGCATCATAGCGTTGACGGACCAGGGACTTAACGCG
ATCAACCTAGGGGACAGCGGGTTCATGGTGGTCCGTGAAGGGCATACCGTTTTCCGCTCTCCCGTTCAACAGCATGACTT
CAACTTCACGTATCAGCTGGAGAGTGGGAGCAACGGCGATTTGCCAAGCTCAGGTCAGATGTTCACGGTCGCTGTAGCTC
CCGGAGACGTGATAATAGCTGGAACAGACGGATTATTCGACAATTTGTACAACAACGAGATCACAGCGATAGTGGTTCAA
GCGGTGAGAGCTGGAACAGATCCTCAGGTGACAGCACAGAAGATTGCAGCTTTGGCGAGGCAAAGAGCACAGGACAAGAA
CAGACAGACTCCATTCTCTACAGCAGCGCAAGATGCTGGGTTCAGATACTATGGAGGTAAGCTTGATGATATTACAGTTG
TAGTCTCTTATGTGGCGGCTTCGAAGGAAGAAGGGTGA

Alignment

ORF - retro_bole_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.39 %
• Parental protein coverage: 60.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LKCLKLVSGSYYLPHPEKEATGGEDAHFICDEEQAIGVADGVGGWAEVGVNAGLFSRELMSYSVAAIREL
          .K.LKLVSGS.YLPHP.KEATGGEDAHFIC.EEQA.GVADGVGGWAE.G..AG..SRELMS.SV.AI...
Retrocopy VKPLKLVSGSCYLPHPDKEATGGEDAHFICAEEQALGVADGVGGWAELGIDAGYYSRELMSNSVNAIHDE

Parental  AKGSSIDPLMVLERAHSQTRAQGSSTACIIALTDKGLHAINLGDSGFTVVRDGTTVFQSPVQQHGFNFTY
          .KGS.IDP..VLE.AH..T..QGSSTACIIALTD.GL.AINLGDSGF.VVR.G.TVF.SPVQQH.FNFTY
Retrocopy PKGS-IDPARVLEKAHTSTKSQGSSTACIIALTDQGLNAINLGDSGFMVVREGHTVFRSPVQQHDFNFTY

Parental  QLGCGDSGGDMPHSGQVFMIDVEAGDVIVAGTDGVYDNLYNEDITGVVVSSVRAGLDPKGTAQKIADLAR
          QL..G.S.GD.P.SGQ.F...V..GDVI.AGTDG..DNLYN..IT..VV..VRAG.DP..TAQKIA.LAR
Retrocopy QLESG-SNGDLPSSGQMFTVAVAPGDVIIAGTDGLFDNLYNNEITAIVVQAVRAGTDPQVTAQKIAALAR

Parental  ARAVDKKRQSPFATAAQEAGYRYYGGKLDDITALVSYV
          .RA.DK.RQ.PF.TAAQ.AG.RYYGGKLDDIT..VSYV
Retrocopy QRAQDKNRQTPFSTAAQDAGFRYYGGKLDDITVVVSYV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Brassica oleracea was not studied using RNA-Seq expression data.

ChIP-Seq

Brassica oleracea was not studied using ChIP-Seq data.

EST

Brassica oleracea was not studied using EST data.

TSS

Brassica oleracea was not studied using FANTOM5 data.

Lab

retro_bole_4 was not experimentally validated.

Homology

Retrocopy orthology:

Brassica oleracea 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 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,