RetrogeneDB ID: retro_bole_71

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C9:39692017..39692974(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo9g059040
• Aliases: None
• Description: None

Sequence

>retro_bole_71
GGGAACATAGGATATGCAATAGCTCCAATGATTGCACGAGGTATGATGCTAGGTCAAGACCAACCCATGATTCTGCATTT
ACTTGATATAGAACCAGCTTCAAAATCACTAGAAGCTGTGAAGATGGAGCTTCAAGATTCAGCCTTCCCTCTCCTCCACG
GCGTCTTCGCGACAACAAATATTGACGAAGCATGTAAAGGTGTGAATATCGCAATAATGATCGGCGGATTCGCAAGAAAA
GAAGGCATGGAAAGAAGAGATGTGATGTCAAAAAATGCGGTGATATTTAAAGCTCAAGCTTCAGCTCTAGAGCGATATGC
ATCAGATGATTGCAAGGTTCTCGTTGTAGCAAACCCAGCGAACACAAATGCCCTGATTTTAAAAGAGTTTGCACCGTCGA
TCCCGGAAGAAAACATCACTTGCCTGACACGTCTCGATCATAACCGAGCTCAAGCTCGCCTCGCAGAGAAGCTAAGTGTT
CCCGTCAGCAGCGTGAAGAACGTGATCGTCTGGGGAAACCACTCTTCAACTCAGTATCCAGACAGCAATCATGCAACGGT
CTCTACAAAGACCGGAGATCAACCGGTGAACGAACTACTTGTCGCTGATCAGAAATGGCTGAAGAACGAGTTTATTACAG
AAGTTCAGCAACGTGGTGCAGAGATTCTAAGGGCACGGAGACAGTCGAGTGCTTTATCAGCTGCTAGCGCAGCTTGTGAC
CATATTCATGATTGGTTTCTTGGAACACCTAAAGGGAATTGGGTTTCTATGGGTGTTTGTTCTGATGGCTCTTACGGTAT
ACCACCTGGTTTGGTTTACTCGTTTCCGGTTATCTGCGAGAAAGGGAGTTGGAAGATCGTACAAGGACTAAATATTGACG
AGTTCTCCAGAGAGAAAATGGATGACTCTGCAAGAGAGCTAGCTGAAGAGAAGGCTTTAGCTTATTCATGTCTGAAT

Alignment

ORF - retro_bole_71 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.16 %
• Parental protein coverage: 95.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GQIGYALVPMIARGIMLGADQPVILHMLDIPPAAEALNGVKMELIDAAFPLLKGVVATTDAVEGCTGVNV
          G.IGYA..PMIARG.MLG.DQP.ILH.LDI.PA...L..VKMEL.D.AFPLL.GV.ATT...E.C.GVN.
Retrocopy GNIGYAIAPMIARGMMLGQDQPMILHLLDIEPASKSLEAVKMELQDSAFPLLHGVFATTNIDEACKGVNI

Parental  AVMVGGFPRKEGMERKDVMSKNVSIYKSQAAALEKHAAPNCKVLVVANPANTNALILKEFAPSIPEKNIT
          A.M.GGF.RKEGMER.DVMSKN..I.K.QA.ALE..A...CKVLVVANPANTNALILKEFAPSIPE.NIT
Retrocopy AIMIGGFARKEGMERRDVMSKNAVIFKAQASALERYASDDCKVLVVANPANTNALILKEFAPSIPEENIT

Parental  CLTRLDHNRALGQVSERLSVPVSDVKNVIIWGNHSSSQYPDVNHASVKTSSGEKPVRE-LVKDDEWLNGE
          CLTRLDHNRA.....E.LSVPVS.VKNVI.WGNHSS.QYPD.NHA.V.T..G..PV.E.LV.D..WL..E
Retrocopy CLTRLDHNRAQARLAEKLSVPVSSVKNVIVWGNHSSTQYPDSNHATVSTKTGDQPVNELLVADQKWLKNE

Parental  FITTVQQRGAAIIKARKLSSALSAASSACDHIRDWVLGTPEGTFVSMGVYSDGSYNVPAGLIYSFPVTCR
          FIT.VQQRGA.I..AR..SSALSAAS.ACDHI.DW.LGTP.G..VSMGV.SDGSY..P.GL.YSFPV.C.
Retrocopy FITEVQQRGAEILRARRQSSALSAASAACDHIHDWFLGTPKGNWVSMGVCSDGSYGIPPGLVYSFPVICE

Parental  NGEWSIVQGLPIDEASRKKMDLTAEELKEEKDLAYSCLS
          .G.W.IVQGL.IDE.SR.KMD..A.EL.EEK.LAYSCL.
Retrocopy KGSWKIVQGLNIDEFSREKMDDSARELAEEKALAYSCLN

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_71 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo9g059040	1 retrocopy	retro_bole_71 ,