RetrogeneDB ID: retro_bole_45

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C2:20038762..20039510(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo1g071100
• Aliases: None
• Description: None

Sequence

>retro_bole_45
GATATAACTCTGATACTAGGACTGAAACCCTCACCCTCGGGTGCTCCGGATGGATTTATTTGGAACCACACAAAATCAGG
GGTATACTCCGTCAAAACAGGCTATGACCTTATACGGTCACACAAGTCAAGTCATTCACGAGAAGGTGCTTCGGAACCGA
GTATCACAGGCCTTCAGAGCCATGCATGGAAGATCCAGGCCCCCAACAAAATGAAGCATTTTTTGTGGCAAGCAGTCTCC
GGTTGTGTGGCAACGGCCGAAAGACTCATGTATAGACACCTGGGCACCGATAGGAGTTGTCCTAGATTTGCTGGCCCAGT
GGAGTCGATTAATCATCTTCTATTTGAATGCCCCCCCGCCCTTCAGGTTTGGGCTTTATCGGACTATCCGTCCCTTCCGG
GTTACTTCCCGAGTACATCTATCTATCAAAACATGAACTTCCTTTTCTGGAAGCGAAAAGAGGTGGCTCCGTCGAGTCCA
CAATTCGATATTTTCCCTTGGATCTGCTGGTTCATTTGGAAAGCTAGAAACGATAAGTTATTCAATGGGAAAGATGTTTC
ACCCATGGATACCCTTCGTCATGCCTCCAATGAGGCTGAATGTTGGAAAAAAGCTAATGAAAAGGAGGAAGAGGAGGATG
GCCGTGACGACCCGCTATCCTCGGAAACTATGATGTTGCCTCCTTGGATATCCCGAATCCCTACCTGCCAAATTGATGCT
TCATGGATCAACAATGGCAGGGTCAGTG

Alignment

ORF - retro_bole_45 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.3 %
• Parental protein coverage: 88.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DASDILGLKVEASSMSFNFVKLSKSDSAGIVRNVESMGKNEKEEEMIQRSEKSERKGTKSHVWKIKAPSK
          D...ILGLK...S.....F...........V..........K..............G..SH.WKI.AP.K
Retrocopy DITLILGLKPSPSGAPDGFIWNHTKSGVYSVKTGYDLIRSHKSSHSREGASEPSITGLQSHAWKIQAPNK

Parental  MKHFLWQVISGCVATAERLTYRPMSTDMICPRCAGPVESINHLLFECPQALQVWALSDYMSLPGYFPSTS
          MKHFLWQ..SGCVATAERL.YR...TD..CPR.AGPVESINHLLFE...ALQVWALSDY.SLPGYFPSTS
Retrocopy MKHFLWQAVSGCVATAERLMYRHLGTDRSCPRFAGPVESINHLLFEXXXALQVWALSDYPSLPGYFPSTS

Parental  IYQNMNFLFWFWERKEVAPLGPQFDTFP--CWYIWKARNDKLFNGKDVSPIDTLQHASLEADCWRKANEK
          IYQNMNFLFW...RKEVAP..PQFD.FP..CW.IWKARNDKLFNGKDVSP.DTL.HAS.EA.CW.KANEK
Retrocopy IYQNMNFLFW--KRKEVAPSSPQFDIFPWICWFIWKARNDKLFNGKDVSPMDTLRHASNEAECWKKANEK

Parental  EEANEDHDDPLL-QRLRQCPLGYPE-LPVKLMHHGSIMAASV
          EE.....DDPL....L..C.LGYPE.LP.KLM.HGS.MA.SV
Retrocopy EEEEDGRDDPLS>RKL*CCLLGYPESLPAKLMLHGSTMAGSV

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_45 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo1g071100	7 retrocopies	retro_bole_38, retro_bole_45 , retro_bole_49, retro_bole_53, retro_bole_66, retro_bole_68, retro_bole_73,