RetrogeneDB ID: retro_bole_13

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C2:2583765..2585412(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo2g010610
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo5g007100
• Aliases: None
• Description: None

Sequence

>retro_bole_13
ATGGACTCCGATGATGACATGCTCGATGCCTACGATGAGGAATCAGGAGAGTATGATCTTTACAGCGACGTTGATGATGA
ACACGGCCATGGTGGTGAAGATGATTCCGATTACATTCTTGAGGAAGTCGTGGACGATTCTATAACTCATGGCTCTCAGA
TTAATTACGTCGTACTCAAGGAAGAAGACATCCGGAAACGACAGGAGGATGAGATCAAACAACTTTCTACGGTCCTCTCC
ATAACCAACGCAGAAGCTAGCGTTCTGCTTCTCCACTACCGCTGGAACGTTAGTAAACTTACTGACGAATGGTTTGCCGA
CGAGGACAAAGTTCGGAGAACTGTTGGCGTATTGGAGGGAGGAGGAGGATCTGTTGTTGTCGTTGAAAATCATCGAAAAG
TTAAATGCGGAATATGCTTTGACAAATTTCGTCGTAAAAAGATTGTACCCGTAGCATGCGGTCATACTTTCTGTTCTACA
TGCTGGAACGGTTACATCACCACAGCAATCAACGACGGCTCGGGATGCTTGATGCAAAAGTGTCCCGAGCCGTCTTGTCA
CCTTGCTATCGGCGGCGACATGGTCGAGAAGCTGGTTTCCGAGGAAGACCTGAGAAAATACCGGTTGTATTTTCTCAGGT
CTTATATCGAAGAAAGCAAGAAGATGAAGTGGTGCCCCGCTCCCGGATGCGAGGGCGCGGTCGATTTTTCCGCGAGCGGG
ACGAGTATTAACTACGATGTTTCGTGCTCGTGCTCGCATAGATTCTGCTGGAACTGCAACGAGGACGCTCACAGCCCCGT
GGACTGCGACACGGTTTCGCAGTGGATACTCAAGAACAGCGCGGAAGCGGAGAATACGGCGTGGATACTCGCTAACTCGA
AGGCTTGCCCCAAGTGCAAGCGGCCGATCGAGAAGAACCACGGATGCATGCACATGACGTGCGGTCCGCCTTGCAAGCAT
GAGTTTTGTTGGCTTTGCCTCGGCGCGTGGAGAGATCACGGGGACCGCACGGGCGGGTTTAATGCGTGCAACAAGTACGA
GAAGGATAAGAAACAAGGACTGTACGATGACGTTGAGAAGAAGCGACAGATGGCGAAGAGCTCGTTGGAGAGGTACACTC
ATTACTACGAACGATGGGCGAGCAATGAAAAGTCGAGGGGGAAAGCTTTCGGAGATCTACAGGTGTTCTTAACGGAGAAG
ATTGCGAAGCTTAGTGTGATTCAGTGCATACCGGAGACTCAGCTGACGTTCGTCACAGATGCGTGGCTTCAGATCATCGA
ATGCAGACGGGTGCTGAAATGGACGTATGCGTATGGGTACTATCTACCTGAATCTGAGCGTGAGAAGCGGTGTTTTTTCG
AGTACGTGCAAGGGGAGGCCGAGTCTGGTTTGGAGAGGCTCCACAAATGCGTTGAGACGGAGGTGTTTCAGGGTGCTGAA
GAGCGGTCGGAACTAGAGTTTACCGCTTTCCGGGAGAAATTATCTAATTTGACCAGCGTGACGAAGAGACACTTTGAAAC
TCTGGTGAAAGCTCTGGAGAATGGTCTCGCTGATGTCGAGTCTCAAGCGGCTTGCAACAAAGAAACAGAATCATTAAAAA
CAGAAATAAAAAGCAAAGAAACAACGTCTAAAAAAAGGCGGACGTGA

Alignment

ORF - retro_bole_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.12 %
• Parental protein coverage: 96.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDSEDDLLGAHDMESGEDDFYSGGGSDDDYNETDGDEPDYGFVEEDVDDSVMIASHRSQINYVVLKEEDI
          MDS.DD.L.A.D.ESGE.D.YS....DD.......D..DY...EE.VDDS.....H.SQINYVVLKEEDI
Retrocopy MDSDDDMLDAYDEESGEYDLYSD--VDDEHGHGGEDDSDY-ILEEVVDDSI---THGSQINYVVLKEEDI

Parental  RRLQMDDIGRVSMVLSISEAEASILLLHYHWSVSKVHDEWFADEERVRKAVGILER---PVVSTLDGGEL
          R..Q.D.I...S.VLSI..AEAS.LLLHY.W.VSK..DEWFADE..VR..VG.LE.....VV........
Retrocopy RKRQEDEIKQLSTVLSITNAEASVLLLHYRWNVSKLTDEWFADEDKVRRTVGVLEGGGGSVVVVENHRKV

Parental  TCGICFEPFQREEVVSLACGHPFCSTCWTGYISTTINDGPGCLMLKCPEPSCPAAVGQDMFEKFASKEDK
          .CGICF..F.R...V..ACGH.FCSTCW.GYI.T.INDG.GCLM.KCPEPSC..A.G.DM.EK..S.ED.
Retrocopy KCGICFDKFRRKKIVPVACGHTFCSTCWNGYITTAINDGSGCLMQKCPEPSCHLAIGGDMVEKLVSEEDL

Parental  EKYYKYFLRSYIEDNRKMKWCPAPGCENAIEFTA-GTS-NYDVSCSCSRSFCWNCTEEAHRPVDCHTVAQ
          .KY..YFLRSYIE...KMKWCPAPGCE.A..F.A.GTS.NYDVSCSCS..FCWNC.E.AH.PVDC.TV.Q
Retrocopy RKYRLYFLRSYIEESKKMKWCPAPGCEGAVDFSASGTSINYDVSCSCSHRFCWNCNEDAHSPVDCDTVSQ

Parental  WIRKNSAESENMNWILANSKPCPKCKRPIEKNHGCMHMTCTPPCKYEFCWLCLNAWTAHGERTGGFYACN
          WI.KNSAE.EN..WILANSK.CPKCKRPIEKNHGCMHMTC.PPCK.EFCWLCL.AW..HG.RTGGF.ACN
Retrocopy WILKNSAEAENTAWILANSKACPKCKRPIEKNHGCMHMTCGPPCKHEFCWLCLGAWRDHGDRTGGFNACN

Parental  RYESAKQEGLYDEAEKRREMAKNSLERYTHYYERWASNQTSRQKAVEDLQKAQLEKLEKLSDIQCTPESQ
          .YE..K..GLYD..EK.R.MAK.SLERYTHYYERWASN..SR.KA..DLQ....EK..KLS.IQC.PE.Q
Retrocopy KYEKDKKQGLYDDVEKKRQMAKSSLERYTHYYERWASNEKSRGKAFGDLQVFLTEKIAKLSVIQCIPETQ

Parental  LKFITEAWLQIIECRRVLKWTYAYGYYLP--DHDKKQFFEYLQGEAESGLERLHKCVEKELEVFLNAEGS
          L.F.T.AWLQIIECRRVLKWTYAYGYYLP.....K..FFEY.QGEAESGLERLHKCV..E.EVF..AE..
Retrocopy LTFVTDAWLQIIECRRVLKWTYAYGYYLPESEREKRCFFEYVQGEAESGLERLHKCV--ETEVFQGAEER

Parental  SD-NFNHFRTKLTGLTSITKTYFENLVKALENGLADVDTTQGASSKSTSSKSSKTK
          S...F..FR.KL..LTS.TK..FE.LVKALENGLADV...Q.A..K.T.S.....K
Retrocopy SELEFTAFREKLSNLTSVTKRHFETLVKALENGLADVE-SQAACNKETESLKTEIK

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_13 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G05890	1 retrocopy	retro_atha_22,
Brassica oleracea	Bo5g007100	1 retrocopy	retro_bole_13 ,
Brassica oleracea	Bo8g005850	1 retrocopy	retro_bole_12,
Brassica rapa	Bra015463	1 retrocopy	retro_brap_11,
Oryza sativa japonica	OS04G0492100	1 retrocopy	retro_osat_31,