RetrogeneDB ID: retro_bole_12

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C3:2590386..2591964(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo3g007230
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo8g005850
• Aliases: None
• Description: None

Sequence

>retro_bole_12
ATGGATTCCGATGACTACTACATGGAATCTGGAGAGGAAGATCTTTACAGCGACGGTGCAGATGATTACAACGACGGGGC
TGATCATGATGATGATAAAGATGACACGGGTTTCCTCGGGGATGACGATGACGATTCCTCGATGATCTCCTCGCCTCGCT
CCGATATAAATTATGTCGTTCTCAAGGAAGAAGATATACGTAGAAAACAGGAGAGTGATATTGCACAAGTTTCCATGATA
CTCTCCGTAAGCAAGGTCGAAGCTAGTGTTCTGCTTCTTCACTATCACTGGAATGTTGGTAAAGTTAATGATGAATGGTT
TGCGGATGAGAGGAGGGTTCGGACAAGTGCTGGCTTGGAAGGAGGATCTGTTATTGTTCCATATTCTAAAGGCGGAAAAG
TTGCTTGTGGAATATGCTTTGACTACTTCTGTCCTATAGATATTGTACCGATTCTGTGTGGCCATGCTTTCTGTTCTACA
TGCTGGACAAGTTACATCAGCATAGCCATCAACGATGGCCCAGGATGTTTGATGCAAAAATGTCCTGAGCCATCTTGTCC
AGTTGCTGTTGGTCGAGACATGGTCGAGAAACTGGCTTCCTTTGAAGCCAAGGACAAGTATGATAGGTATTTTCTTAGAT
CTTATGTGGAAGAAAGCAAAAAGACCAAGTGGTGTCCTTCCCCAGGATGTGAGCATGCCATTGAGTTTTCTGCCACCGGG
ACCGGAAGTAGTTACGATGTTTCATGCTTGTGTTCGCATAGCTTCTGCTGGAACTGCACCGAAGACGCTCACCGTCCTGT
GGATTGTGACAGGGTTTCGCAATGGATACGCAAGAACAGCGTTGAAGCTGAAAATACCAAGTGGATACTCGACAATTCCA
AGCCTTGTCCCAAGTGCAAGCGTCCAATTGAAAAGAACCATGGATGCATGCACATGTCATGCACACCACCTTGCAGACAT
CAGTTTTGTTGGCTTTGCCTTGGCGCATGGTCGGAACACGGGGAAGGCACTGGCGGGCCTTATACATGCAACCGGTATTC
GAAGGCTAAGGGACAAGGACTGCATGATGAGGCTGAAATGAAGCGAGAGATGGCAAAGCACTCGCTAGAGAAATACACTC
ATTATTATGAGCGCTGGGCAGGTAATCAAATGTCGAGGCAAAAAGCTATAGGGGATCTACAGAAGTTCCTATCAGTGGAT
GTTATGAAGCTTAGTGACAAACAATGCATACCAGAAACTGAGCTCGGGTTCATCACAGATGCGTGGCTTCAGATCATTGA
ATGCAGAAGGGTGCTGAAATGGACATATGCATACGGGTACTATCTACTTGAATCTGAACAGGAAAAGAGACAGTTTTTCG
AGTATATGCAAGGAGAGGCTGAGTCTGGTCTGGAGAGGCTCCACAAATGCGTTGAGTTGGAATCAGAGGTGTTTCAATAT
CCTGAAGACGCTCCAAAACAAGACTTCAAGGGTTTTCGGACAAAACTAACTACTTTGACCAGTGTAACCAAATCTCACTT
CGAAACTCTGGTGAAAGCTCTGGAGAATGATCTTGCTGATGTTGGATTCGCAAGATAG

Alignment

ORF - retro_bole_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.65 %
• Parental protein coverage: 91.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NDHDMESGEEEDDFYSGETDDYN---DSDGGEPDYGFVEEDVDDSVMIASHRSQVNYVVLKEEDIRRHQK
          .D..MESGEE..D.YS...DDYN...D.D....D.GF...D.DDS.MI.S.RS..NYVVLKEEDIRR.Q.
Retrocopy DDYYMESGEE--DLYSDGADDYNDGADHDDDKDDTGFLGDDDDDSSMISSPRSDINYVVLKEEDIRRKQE

Parental  DDIGQVSMVLSISEVEASILLLHYHWSVSKVHDEWFADEERVRKTVGILDGPVIPTPDDSGELTCGICFE
          .DI.QVSM.LS.S.VEAS.LLLHYHW.V.KV.DEWFADE.RVR...G...G.VI......G...CGICF.
Retrocopy SDIAQVSMILSVSKVEASVLLLHYHWNVGKVNDEWFADERRVRTSAGLEGGSVIVPYSKGGKVACGICFD

Parental  TFPPEEILSVACGHPFCSTCWTGYISTTINGGPGCLMLKCPEPSCPAAVGQDMFEKLASKEDKEKYYRYF
          .F.P..I....CGH.FCSTCWT.YIS..IN.GPGCLM.KCPEPSCP.AVG.DM.EKLAS.E.K.KY.RYF
Retrocopy YFCPIDIVPILCGHAFCSTCWTSYISIAINDGPGCLMQKCPEPSCPVAVGRDMVEKLASFEAKDKYDRYF

Parental  IRSYVEDNRKMKWCPAPGCEHAIDFAA-GTGS-YDVSCLCSHSFCWNCTEEAHRPVDCETVAQWIRKNSA
          .RSYVE...K.KWCP.PGCEHAI.F.A.GTGS.YDVSCLCSHSFCWNCTE.AHRPVDC..V.QWIRKNS.
Retrocopy LRSYVEESKKTKWCPSPGCEHAIEFSATGTGSSYDVSCLCSHSFCWNCTEDAHRPVDCDRVSQWIRKNSV

Parental  ESENMNWILANSKPCPKCKRPIEKNHGCMHMTCTPPCKYEFCWLCLNAWTDHGERTGGFYACNKYEAGKQ
          E.EN..WIL.NSKPCPKCKRPIEKNHGCMHM.CTPPC...FCWLCL.AW..HGE.TGG.Y.CN.Y...K.
Retrocopy EAENTKWILDNSKPCPKCKRPIEKNHGCMHMSCTPPCRHQFCWLCLGAWSEHGEGTGGPYTCNRYSKAKG

Parental  EGRYDEAEKRREMAKNSLERYTHYYERWASNQTSRQKAMVDLEKARSEKLEKLSDIHGTPESQLKCITEA
          .G..DEAE..REMAK.SLE.YTHYYERWA.NQ.SRQKA..DL.K..S....KLSD....PE..L..IT.A
Retrocopy QGLHDEAEMKREMAKHSLEKYTHYYERWAGNQMSRQKAIGDLQKFLSVDVMKLSDKQCIPETELGFITDA

Parental  WLQIIECRRVLKWTYAYGYYL--PDHDKKQFFEYLQGEAESGLERLHKCVEKELEVFLVAE-GPSDDFNH
          WLQIIECRRVLKWTYAYGYYL......K.QFFEY.QGEAESGLERLHKCVE.E.EVF...E..P..DF..
Retrocopy WLQIIECRRVLKWTYAYGYYLLESEQEKRQFFEYMQGEAESGLERLHKCVELESEVFQYPEDAPKQDFKG

Parental  FRTKLTGLTSITKTYFENLVKALENGLADV
          FRTKLT.LTS.TK..FE.LVKALEN.LADV
Retrocopy FRTKLTTLTSVTKSHFETLVKALENDLADV

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_12 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 4 parental genes, and 4 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 ,
Oryza sativa japonica	OS04G0492100	1 retrocopy	retro_osat_31,