RetrogeneDB ID: retro_bole_32

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C8:30831814..30833224(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo8g091290
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo7g104100
• Aliases: None
• Description: None

Sequence

>retro_bole_32
ATGACGAGGGAGATCGAACCACAGTCACTGCAAAAGCTGAGTCTCAAATCAGTAAAGCGAGCTCTTGATCTTTTCTCCCC
CGCTCATGATCAACTCGCTCCGCCTGATCCGGAAAGCAAAAAGATTCGGCTTTCTCACAAGTTTCAAGTTGCATTTGGAG
GTGTAGAGCCCGTGAGTAAGCAGTCTATACGTAGAGCTGAATATAATAATGAGCAGATAGCTTCATCCAACGCCCTTGCC
GCCCTTCCAGGTCCAGAAGGAGCCAAACAGGGCAAAGCTTTAGTTGTCGGTCCTACTTTACCGCCAAGAAGCTTGAACGA
CAACACCGTTCACGCAGGCAAAAGCACCACGATTCTTCCTGCATTCGGATCCTCATCTGAAAGAAACCTGTCAACTTGTG
CTTTAATGCCTAGTCGATGGCCCCGTCCAGAGTGGCATGCACCATGGAAGAATTACAGGGTGATCCAGGGGCACTTGGGG
TGGGTTAGATCTGTTGCATTTGACCCAAGAAATGAATGGTTTTGCACTGGTTCAGCTGATCGTACCATTAAGGTATGGGA
TGTAGCGAGTGGAGTTCTGAAGCTCACACTTACTGGACATATTGGGCAAGTACGAGGCCTTGCTGTATGCAACAAAGATG
CCTACATGTTCTCTGCTGGTGATGACAAGCAAGTCAAATGCTGGGACCTTGAGCAGAATAAGGTTATCCGATCTTATCAT
GGCCATCTCTCTGGCGTCTACTGTTTAGCTCTTCATCCAACTCTGGACGTTTTACTAACCGGAGGGCGAGACTCTGTCTG
CAGGGTGTGGGATATCCGTACGAAGATGCAGAATTTTGCACTCTCGGGACATGACAAAGACGTTTGTTCCGTCTTCACCC
GTCCAACCGACCCTCAAGTTGTTACCGGATCTCATGATTCCACCATTAAATTTTGGGACCTTCGATATGGTAGAACAATG
ACAACTCTAACGAATCATAAGAAAGCTGTCAGAGCAATGGCGCTCCATCCAACAGAGAATGCTTTTGTTTCTGCATCGGC
TGATAACATCAACAAGTTTAGCCTTCCTAAGGGAGAGTTTTGCCACAACATGCTTTCTCAGCAAAGAGCCATAATCAACG
CAGTGACTGTGAATGAGGATGGTGTAATGGTCACTGGAGGTGATAATGGAAGCTTATGGTTCTGGGATTGGAAGAGTGGT
CACAGTTTCCAACAGGCAGAAGCTATTGTACAGCCTGGTTCGCTGGAGAGTGAAGCTGGTATATATGCAGCGTGTTACGA
TCAGACGGGTTCAAGGCTGGTAACGTGTGAGGCAGACAAGACCATAAAGATGTGGAAGGAAGACGAGAACGCTACTCCTG
AAACCCATCCTCTTAACTTCAGACCTCCCAAAGAGATCAGACGCTTCTGA

Alignment

ORF - retro_bole_32 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.65 %
• Parental protein coverage: 97.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IEPQSLKKLSIKSLKRALDLFSPVHGQFPPPDAEAKKIRLSHKMKVAFGGVEPVS-QPPRQPDRGNEQTG
          IEPQSL.KLS.KS.KRALDLFSP.H.Q..PPD.E.KKIRLSHK..VAFGGVEPVS.Q..R.....NEQ..
Retrocopy IEPQSLQKLSLKSVKRALDLFSPAHDQLAPPDPESKKIRLSHKFQVAFGGVEPVSKQSIRRAEYNNEQIA

Parental  TSSAL-ALPVPEGSKSTQKGVTENALVVGPTFQPKGLNSIGT-SGKSTTIIPANVSSYERNFSTSALMER
          .S.AL.ALP...G......G....ALVVGPT..P..LN......GKSTTI.PA..SS.ERN.ST.ALM..
Retrocopy SSNALAALP---GPEGAKQG---KALVVGPTLPPRSLNDNTVHAGKSTTILPAFGSSSERNLSTCALM--

Parental  IPSRWPRPEWHAPWKNYRVIQGHLGWVRSVAFDPSNEWFCTGSADRTIKIWDVATGVLKLTLTGHIEQVR
          .PSRWPRPEWHAPWKNYRVIQGHLGWVRSVAFDP.NEWFCTGSADRTIK.WDVA.GVLKLTLTGHI.QVR
Retrocopy -PSRWPRPEWHAPWKNYRVIQGHLGWVRSVAFDPRNEWFCTGSADRTIKVWDVASGVLKLTLTGHIGQVR

Parental  GLAVSNRHTYMFSAGDDKQVKCWDLEQNKVIRSYHGHLSGVYCLALHPTLDVLLTGGRDSVCRVWDIRTK
          GLAV.N...YMFSAGDDKQVKCWDLEQNKVIRSYHGHLSGVYCLALHPTLDVLLTGGRDSVCRVWDIRTK
Retrocopy GLAVCNKDAYMFSAGDDKQVKCWDLEQNKVIRSYHGHLSGVYCLALHPTLDVLLTGGRDSVCRVWDIRTK

Parental  MQIFALTGHDNTVCSVFTRPTDPQVVTGSHDTTIKFWDLRYGKTMTTLTHHKKSVRAMTLHPKENAFASA
          MQ.FAL.GHD..VCSVFTRPTDPQVVTGSHD.TIKFWDLRYG.TMTTLT.HKK.VRAM.LHP.ENAF.SA
Retrocopy MQNFALSGHDKDVCSVFTRPTDPQVVTGSHDSTIKFWDLRYGRTMTTLTNHKKAVRAMALHPTENAFVSA

Parental  SADNTKKFSLPKGEFYHNMLSQQKTIINAMAVNEDGVMVTGGDNGSIWFWDWKSGHSFQQSETIVQPGSL
          SADN..KFSLPKGEF.HNMLSQQ..IINA..VNEDGVMVTGGDNGS.WFWDWKSGHSFQQ.E.IVQPGSL
Retrocopy SADNINKFSLPKGEFCHNMLSQQRAIINAVTVNEDGVMVTGGDNGSLWFWDWKSGHSFQQAEAIVQPGSL

Parental  ESEAGIYAACYDQTGSRLVTCEADKTIKMWKEDENATPETHPVNFKPPKEIRRF
          ESEAGIYAACYDQTGSRLVTCEADKTIKMWKEDENATPETHP.NF.PPKEIRRF
Retrocopy ESEAGIYAACYDQTGSRLVTCEADKTIKMWKEDENATPETHPLNFRPPKEIRRF

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_32 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	Bo7g104100	1 retrocopy	retro_bole_32 ,
Prunus persica	PRUPE_ppa005183mg	1 retrocopy	retro_pper_26,