RetrogeneDB ID: retro_bole_2

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C7:35853247..35855116(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo7g093270
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo3g001500
• Aliases: None
• Description: None

Sequence

>retro_bole_2
ATGATTACTGCGATGCCCCCAGAAGAATCAGGAAGAAGTAGTTACTTGCCCCGCAAGCGACATCTCGAAAACCCTTCCGA
AGAACAGAGCAAAAGATCGAGACTTTACCAAAACGCAAACGTTATCCCTCACGGTTGGCTAGATTGTCCACGTTTCGGCC
ACGAGATCGGTCCCATCATCCCATCAAAAGTCCCTCTCAGCGAATCTTACAACGACCACCTCCCTCCCGACAAACGATAC
ACTTTTAAACAGCTGCTAACCAACAACAAAAGGAACAAGCTCGGTCTAGTGATCGATCTCACCAACACAACTCGTTACTA
CAACCCTAGCACAGAGCTGCTAAGAAGGGAAGGGATCGAGTACGTTAAGATTCGTTGCAGCGGTCGTGACTCTGTCCCTG
ATAACGTCTCCGTGAACACATTCGTCCACGAGGTGAATCAGTTTGAGAGACGTAACTTCTCGAAAAAGTCTGTTCTCGTT
CACTGTACGCATGGTCATAACCGCACAGGGTTCATGGTTGTTCATTACCTTATGAGGTCTAGTACCTTGATGAGCGTTAC
TCAGGCTCTTAAAACGTTTTACGATGCTCGTCCCCCAGGAATCTATAAATCGGATTACATCGACGCTCTTTACAGTTTCT
ATCACGAAACAAAGCCCGAGAGTGCTGTTTGCCCACAAACTCCCGAGTGGAAGCGGTCTGAAGAAAACGAGTCTTTATCT
GTATCATTATCACCGTGTGTCCCTTTAGTGATCAAGAAGATGTCAAACGACGACGTTTTGGGGGACGAGATACCTTACGG
TCAAGAGAAGTGTTACCAGGAGTTTTGCTACGAGATGCTGAATATTAAGATAGAAGGAAGATCTTCGTCTCTGCAGTTTC
CCGGCTCGCATCCTGTGTCTTTAGACAGGGAAGGGTTCCAACTCTTGAGGCGGAGGTACTACTACGCCACGTGGAAGGCG
GACGGGACGCGTTACATGATGCTATTGACTAGAGAAGGGTGTTACTTAATAGACAGAAAGTTTAGATTCAGAAGGGTACA
GATGCGGTTCCCTTGCAAGCCTCACGAGGCTAAAGTGCATGACTACACTCTGCTCGATGGAGAGATGGTTGTAGATAACT
TCCTTGACGGACAAGGAAAGCCTCGCCAGGCGAGGAGGTACCTCGTCTACGACATGGTAGCAGTCAACGGCGAATCACTC
GCTGACCGTCCTTTCAGTGAGAGATGGAGTGTTATCGATAGAGAAGTGATCAGACCACGTAACGACGAGAAGAAAGTTAC
AAAAGGTTACAGATACGAGATGGAGCCTTTCGGCGTACGTATAAAAGCCTTTTGCCTACTATCTTCCGTGGAGAAGAAGG
TGTTCAACGAGCTGATACCTTCGCTCTCTCACGACTCCGACGGGATCATACTCCAAGGCTGGGACGAGCCTTACGTCTAC
CAGAGGAACCAAGCCTTGCTCAAGTGGAAGTTTCTAGACACCATCGACTTTTTGTTCGAGGTGGGGAGGGACGGGCGTTA
CATGCTGTTCTTGTGTGAAAACGGGAGGAACAAGCTTATGGAGGGGCATACGGTTGAGTTTAGAGGCGACGGTTGGGAGG
AACCGGGGAGGTATAGTGGGAAGCTTTTGGAGTGTTTTTGGGATAAGGAGGATAAGGTTTGGGTGCCTATGAGGGTTAGA
GTTGATAAGTCTCAGCCGAATGGTATGGGAACGTTCCGTGGGGTGATGAAATCTATTAATGATGGTATAACTAAGGAGGT
TTTGTTGAAGGAGATTAAAGAAATTGTTAGGCTTCCTATGTACGTTGAGCGTATTCGTGTAGATACTCTAGCTGCGGAAC
GGCGTAGGCATGGGAACCGCAGGGGGTGA

Alignment

ORF - retro_bole_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.02 %
• Parental protein coverage: 54.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IVTMSNDDILGDEIPHYQEEAYRKFCYKMLMMSIGGRGCA-QFPGSHPVSLDRESLQLLRQRYYYATWKA
          I..MSNDD.LGDEIP..QE..Y..FCY.ML...I.GR....QFPGSHPVSLDRE..QLLR.RYYYATWKA
Retrocopy IKKMSNDDVLGDEIPYGQEKCYQEFCYEMLNIKIEGRSSSLQFPGSHPVSLDREGFQLLRRRYYYATWKA

Parental  DGTRYMMLLTIDGCYLIDRSFKFRRVQMRFPCRHSSGGMPDQVHHFTLLDGEMVIDNPMNEKGQAR--RR
          DGTRYMMLLT..GCYLIDR.F.FRRVQMRFPC........D.....TLLDGEMV.DN.....G..R..RR
Retrocopy DGTRYMMLLTREGCYLIDRKFRFRRVQMRFPCKPHEAKVHD----YTLLDGEMVVDNFLDGQGKPRQARR

Parental  YLVYDLVAINGESVVERTFCERWNMVVHEVIKGRDVDKQRNHCYRYDLEPFGVRMKGFYLLSTVE-KLLK
          YLVYD.VA.NGES...R.F.ERW.....EVI..R...K.....YRY..EPFGVR.K.F.LLS.VE.K...
Retrocopy YLVYDMVAVNGESLADRPFSERWSVIDREVIRPRNDEKKVTKGYRYEMEPFGVRIKAFCLLSSVEKKVFN

Parental  GTIPSLSHEADGLIFQGWDDPYVPRTHKGLLKWKYAEMNSVDFLFEMGEEDEGCRMLFLFERGKKKLMDG
          ..IPSLSH..DG.I.QGWD.PYV......LLKWK.......DFLFE.G....G..MLFL.E.G..KLM.G
Retrocopy ELIPSLSHDSDGIILQGWDEPYVYQRNQALLKWKF--LDTIDFLFEVGR--DGRYMLFLCENGRNKLMEG

Parental  YTVEFR-DG-SDPSSYNGKIVECSWDKEKKVWVSMRIRVDKTTPNDINTARKVIKSINDNITEEVLLQEI
          .TVEFR.DG...P..Y.GK..EC.WDKE.KVWV.MR.RVDK..PN...T.R.V.KSIND.IT.EVLL.EI
Retrocopy HTVEFRGDGWEEPGRYSGKLLECFWDKEDKVWVPMRVRVDKSQPNGMGTFRGVMKSINDGITKEVLLKEI

Parental  REIIRLPMYADRIRMDLRAAGR
          .EI.RLPMY..RIR.D..AA.R
Retrocopy KEIVRLPMYVERIRVDTLAAER

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_2 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	Bo3g001500	1 retrocopy	retro_bole_2 ,
Brassica rapa	Bra005691	1 retrocopy	retro_brap_27,