RetrogeneDB ID: retro_bole_14

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C2:9909656..9911207(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo2g034110
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo3g019490
• Aliases: None
• Description: None

Sequence

>retro_bole_14
ATGGTGAAAGAGAGGCTCAACGAGTTACCAGATGAACTGATCGTGACGATACTCTCAAAGCTTCCGACGTTTAAAGAAAG
CGTTGCAACACGTCTCATATCAAGACGGTACGAGGATCCTTGGAACCTTGCGCAGGACGTCACGCTTGAAGATAACGATG
AGGAGAGTGTCATGACGTTTCTCTATGGATATTTTTTGTCTAACGATGCTCCAGCTCTACAGAGGTTGCGTCTCAAGCTT
ACCCGGAAACATTCGGCTTCAGACATCGACTTTTGGGTTCAAACCGCGGTTAACCGAAACGTGAGAAAGCTGAGATTCGA
CTTGTCTGGTGGAACCCTAGAACTGCCGAGTTGCTTGAGCACATGCACAACCCTAAAATCGTTGATACTACGTGACGTAC
TTATCGAGGCTGTTCCTTGGGGTTTTCGTTTGCCATCTCTCAGAAGTCTACACCTTTTCTCGGTTAACTTCTCGATTGGT
GATTCCGTTGCAAATCTTTTAAAAATCTGCCCCCATCTTGAATATTTGGTTTTAAACCAAATCAGATATGATGTGGACCA
TGTGGATACTGAGTTTGCTCCACTTCGGTTCTTCTTATCATCACTCAAAAGTCTTCACCTTTGCCCGGTTATATTCTCCG
GCAAAAATCCCGTTACACGTTTTTTACGTAGCTGTCCGGTTCTTGAAACTTTGGTTATAAACGAAATCAAATGTGCCTAC
GAGATGTTCGAGGTTGTTTTTCCACCAAGATCTTGTCTGTCATCATCACTCAAAACCCTACACCTTTTTTCGGTTAACTT
CTCGAGTGATGAATCTGTTGTAAAGCTTTTAGAAAATTGTAAGGCTCTTGAAGACTTGGTCATAACCCGAACCAGAGATG
ACAATGTGTGGTTATTCAATATCACCGTGCCTACTCTCAAGAGCTTATCTATTAATAACGCGAAGGTGAAACGCGCCGAT
GCTCCTGGGTTTGTTATAAATGCTCCTAATTTGGAGAGATTGAGCATTAAGGATACCGTCAGTAACTTTCTAATGTTTGG
ATATATGCCCGAGGTGACCACGGCAAATATTGAGGCTGTTTGTGACCAATCTGAAAATTTTATAGGGTCTCTTACCTTCA
TCCAACATCTGTCTCTCTGTTCTCCAACGTCAAAGACTCCATATACTAGCGGCACTGTCTTCTTCTTCCTCGAACATCTA
GAGCTATGTACGTGTTCTGCTAGATGGGCGAAACTACTTGGCTCTATACTCAATGACGCTCCAAGACTTCAGTCTATCAA
GCTTAAGTCGAAATGTAGCGCTCCTTTCAAGCGTCCGTTGGAACTCTGGACCGAACCAACAGTTGTTCCAGAATGTTTAC
TGAAGCATCTTGAGATCTTGGAATGGAGAGAATATGATGGCACAGAGCAAGAGAGGAAAGTGGCTGCGTACATACTAGGA
AACGCTACTTGTCTAAAGATGGCTACATTCTCGACAAGGTGCGGAGACAAATGTACAGAGTTGAAGAAAATGTCCAGAGT
TTCAGAGATATGTCAGTTAGTGTTTGAGTAA

Alignment

ORF - retro_bole_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.84 %
• Parental protein coverage: 65.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SPSLKSLHLLSVNFSGDESFSKLIQRCPVLEDLVINKTRDDNVTIFNINAPSLRSLSIDNSTGERTYVEE
          S.SLK.LHL.SVNFS.DES..KL...C..LEDLVI..TRDDNV..FNI..P.L.SLSI.N....R.....
Retrocopy SSSLKTLHLFSVNFSSDESVVKLLENCKALEDLVITRTRDDNVWLFNITVPTLKSLSINNAKVKRA---D

Parental  NHGFVINAPSLEKMNFKDTFSNCLVFEHMPEVIEANIHVICGQPENFIGSLTSICHLSLCSLSSETPYPS
          ..GFVINAP.LE....KDT.SN.L.F..MPEV..ANI...C.Q.ENFIGSLT.I.HLSLCS..S.TPY.S
Retrocopy APGFVINAPNLERLSIKDTVSNFLMFGYMPEVTTANIEAVCDQSENFIGSLTFIQHLSLCSPTSKTPYTS

Parental  GTTFPYLEHLELCTRCAGWANLLVCILKDAPTLKYLKLKSQHGAHYNHPMILWKEPTADPECLSTHLEIM
          GT.F..LEHLELCT..A.WA.LL..IL.DAP.L...KLKS...A....P..LW.EPT..PECL..HLEI.
Retrocopy GTVFFFLEHLELCTCSARWAKLLGSILNDAPRLQSIKLKSKCSAPFKRPLELWTEPTVVPECLLKHLEIL

Parental  EWRQYEGTEQERSMAAYILANATCLKTATFSTRCGDKHHNMLRKLKNLNRVSE
          EWR.Y.GTEQER..AAYIL.NATCLK.ATFSTRCGDK....L.K.........
Retrocopy EWREYDGTEQERKVAAYILGNATCLKMATFSTRCGDK-CTELKKMSRVSEICQ

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_14 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	Bo3g019490	1 retrocopy	retro_bole_14 ,