RetrogeneDB ID: retro_bole_36

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C1:13524607..13525327(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo9g037340
• Aliases: None
• Description: None

Sequence

>retro_bole_36
GAGGTGAAAAGAGGCAATGCAAGCAACGTAAGGAACCTCTTACTCGGTGATAAGAACAAGTACAGATCAATGTGGATAAG
GACGTGCTCGTCTCTCTGGATGCTCGGAGGAGTTTTCTTTATAATCTACATGGGACATCTCTACATATGGGCTATGGTTG
TTGGCATACAGATATTCATGGCGAAAGAGCTCTTCTTTCTTCTCAGAAGAGCTCACGAGGAGCGTCGCTTGCCTGGCTTC
AGGCTCTTGAACTGGCACTTCTTCTTCACGGCTATGTTGTTTGTCTATGGACGCATACTTCAGCAGCAGCTGGTCAACAC
TGTTTCTTCGGATAGGTTTATCTACAAGCTTGTTAGTGGTTTGATCAAGTACCAGATGGTCATCTGCTACTTCTTGTACA
TTGCTGGTTTCATGTGGTTTATACTTACGTTGAAGAAGAAGATGTATAAGTATCAGTTTGGGCAGTACGCTTGGACGCAT
ATGATACTTATCGTTGTGTTTACTCAGTCTTCTTTCACTGTGGCTAATATTTTCGAAGGGATCTTTTGGTTTCTTCTTCC
GGCTGCGCTGATTGCTATGAACGATGTGGCGGCTTACTTCTTTGGTTTCTATTTTGGGAAGACTCCTTTGATAAAGCTGT
CTCCGAAGAAGACGTGGGAAGGTTTCATTGGAGCATCGGTGGCAACTACAATCTCTGCGTTTCTTGTAAGTAACCATCTT

Alignment

ORF - retro_bole_36 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.58 %
• Parental protein coverage: 57.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EVLDGDKVNASPLLVNDRNKYKSFMVRTYSTLWMIAGFVMVVYMGHLYITAMVLVIQIFMAKELFNLLRK
          EV..G...N...LL..D.NKY.S...RT.S.LWM..G.....YMGHLYI.AMV..IQIFMAKELF.LLR.
Retrocopy EVKRGNASNVRNLLLGDKNKYRSMWIRTCSSLWMLGGVFFIIYMGHLYIWAMVVGIQIFMAKELFFLLRR

Parental  APEDKCLPGIKQLNWHFFFTAMLFVYGRILSQRLANTVTADQFLYRLVSGLIKYHMAICYFLYIIGFMWF
          A.E...LPG...LNWHFFFTAMLFVYGRIL.Q.L.NTV..D.F.Y.LVSGLIKY.M.ICYFLYI.GFMWF
Retrocopy AHEERRLPGFRLLNWHFFFTAMLFVYGRILQQQLVNTVSSDRFIYKLVSGLIKYQMVICYFLYIAGFMWF

Parental  ILTLKKKMYKYQFGQYAWTHMILIVVFTQSSFTVANIFEGIFWFLLPASLIIINDIFAYIFGFFFGRTPL
          ILTLKKKMYKYQFGQYAWTHMILIVVFTQSSFTVANIFEGIFWFLLPA.LI..ND..AY.FGF.FG.TPL
Retrocopy ILTLKKKMYKYQFGQYAWTHMILIVVFTQSSFTVANIFEGIFWFLLPAALIAMNDVAAYFFGFYFGKTPL

Parental  IKLSPKKTWEGFIGASVTTIISAFVLANVL
          IKLSPKKTWEGFIGASV.T.ISAF...N.L
Retrocopy IKLSPKKTWEGFIGASVATTISAFLVSNHL

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_36 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	Bo9g037340	1 retrocopy	retro_bole_36 ,