RetrogeneDB ID: retro_bole_11

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C3:40136795..40138484(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo3g113310
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo2g165520
• Aliases: None
• Description: None

Sequence

>retro_bole_11
ATGGCGGCAGGAGGAGTTGAAATCTCGAAAGGCTCTGTCGTCGTTGATCGTGTTCGTGATTTTTATCCTCGTCAGGGTGG
TAGGGACGGTGAGAGGCGTCAAACCAAACGACCCAGTGATTCTGATCGCTGGTTGAAAGATGGGCGACGTGATTTGTATC
AAAGAGGAGAAGCCCGAGAGGGAGATGTTGGTCAGAGACACCCTGAGAAGAGGAGGAAGCGTTCTCCAGTTTCACCTGCA
CTTGCTGAGAAGACCATTGTTGATGTGGGTTCTGCTAGGAAGATTTCATCTGAGGATCATGCCGGTGTTCTGAAGTCAAC
AGAGTATGTTTCTGCAGTGTCTGTGACGCCTGTTAAACATCCTTTTGATGATCTTGAGGAGGGCCAGTTGGAGGCCGAGC
AGGTGGTTCAGGCACCCAATATTGCTACGTCTAAGTGGTGTTTGGAATCTCCAAAGGATGAGGCAGTTCATGTTGTCAGG
AATAGCAGATGGAATAGGAGCAGCCTTACTCCTGAGAGCGGTGAATTTCAAGTGGATTCGTCTGATGAACATCGGTCCAA
TTCTTCTGGATCTCGCAGCTTAGAACCCATCAGTGCTCATGAGGATTCAGAGCATGAGTTGGAGGGTCGTATTGACATGG
ATGTTGGTGAAGAAGAATGTTGTGCTTCTGATTTTAACGACTCGGAAGTTGATGAACCAGAGGGAGGCCTGAGCATGCTA
TCTGGCAGTAGAGATGTTAACGAATACCAGAAGCTAAGCAAGATAAATGAAGGAACTTATGGTGTTGTCTACAAAGCCAA
GGACAGAAAGACGGAAGAGATTGTGGCACTTAAAATGATCAAGATGAACATGGAAGACGAATATGGATTCCCATTGACAT
CTTTGAGGGAGATCAACATTCTTTTGTCTTGCAATCACCCGTCGATTGTGAACGTCAAGGAAGTCGTGGTGGGAAACGGT
GACAGTGTTTTCATGGTCATGGAACACTTGGAACACGACTTGAGGGGCGTTATGGACAGGATGAAACAGCCTTTTAGCAC
CAGTGAGGTCAAATGCTTGATGATTCAGCTGTTGGAGGGTTTGAAGTACCTACATAGCAACTGGATCATCCACAGGGATC
TGAAGCCATCTAATCTTCTACTGAACAACAGTGGGGAGCTGAAAATATGCGATTTTGGAATGGCTAGGCAATATGGGAGT
CCTATCAAGCCCTACACGCAGTTGGTTGTCACACAGTGGTACAGGTCCCCGGAGCTTCTTCTAGGAACAAAGGAGTATTC
AACCGCAGTTGATATGTGGTCCATCGGGTGCATTATGGGTGAGTTGCTGTCTCTAAAACCTCTTTTCCGAGGGAAAAGTC
AGAATGACATTGACCAGCTTCAACAGATATTTGCGGTTCTTGGAACACCGAGTGAGACAACTTGGCCTGGATTCACTGCG
CTGCCAGGTTCCAAAGCCAAGTTTCGTAAGCAGCCATACAATTTACTGCGTAAGAAATTTCCTGCTGCATCTTTTACCGG
AGGTCCAGTTCTTTCAGAATTGGGATTTGATTTGTTGAACAGATTATTGAATGTTGACCCTGAGAAGCGACTAACAGTTG
ACGAGGCTCTTAACCACTCCTGGTTCAGTGAAGTACCTCTCCAGAAATCCAAGGAGTTCATGCCTACATTTCCTTCAAAG
CGTAACTGA

Alignment

ORF - retro_bole_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.23 %
• Parental protein coverage: 68.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EYSDNEYFSSDHDELEAEEPASPAQGGMNMLLGSRSVNGFQKLNKINEGTYGIVYRARDEKTKEIVALKK
          .....E...SD....E..EP.....GG..ML.GSR.VN..QKL.KINEGTYG.VY.A.D.KT.EIVALK.
Retrocopy DVGEEECCASDFNDSEVDEP----EGGLSMLSGSRDVNEYQKLSKINEGTYGVVYKAKDRKTEEIVALKM

Parental  IKMKEDKYEEEYGFPLTSLREINILLSCNHPSIVNVKEVVVGGRNDSDVYMVMEHLEHDLKGLMERKKQP
          IKM.....E.EYGFPLTSLREINILLSCNHPSIVNVKEVVVG..N...V.MVMEHLEHDL.G.M.R.KQP
Retrocopy IKMN---MEDEYGFPLTSLREINILLSCNHPSIVNVKEVVVG--NGDSVFMVMEHLEHDLRGVMDRMKQP

Parental  FSTSEVKCLMLQLLEGVHYLHTNWIIHRDLKPSNLLMNNSGELKICDFGMARQYGSPIKPYTQMVITQWY
          FSTSEVKCLM.QLLEG..YLH.NWIIHRDLKPSNLL.NNSGELKICDFGMARQYGSPIKPYTQ.V.TQWY
Retrocopy FSTSEVKCLMIQLLEGLKYLHSNWIIHRDLKPSNLLLNNSGELKICDFGMARQYGSPIKPYTQLVVTQWY

Parental  RPPELLLGAKQYSTAVDMWSIGCIMAELLSQKPLFPGKT--ELDQLQKIFAVLGTPTESIWPGFSSLPNA
          R.PELLLG.K.YSTAVDMWSIGCIM.ELLS.KPLF.GK.....DQLQ.IFAVLGTP.E..WPGF..LP..
Retrocopy RSPELLLGTKEYSTAVDMWSIGCIMGELLSLKPLFRGKSQNDIDQLQQIFAVLGTPSETTWPGFTALPGS

Parental  KAKFPTQSYNLLRKKFPAISFVGGQILSERGFDLLNGLLTLDPEKRLTVEEALNHSWFHEVPLPKSQDFM
          KAKF..Q.YNLLRKKFPA.SF.GG..LSE.GFDLLN.LL..DPEKRLTV.EALNHSWF.EVPL.KS..FM
Retrocopy KAKFRKQPYNLLRKKFPAASFTGGPVLSELGFDLLNRLLNVDPEKRLTVDEALNHSWFSEVPLQKSKEFM

Parental  PTFPPRR
          PTFP..R
Retrocopy PTFPSKR

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_11 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo2g165520	1 retrocopy	retro_bole_11 ,
Brassica rapa	Bra029230	1 retrocopy	retro_brap_13,