RetrogeneDB ID: retro_bole_61

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C7:37988231..37988757(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo00828s040
• Aliases: None
• Description: None

Sequence

>retro_bole_61
ATCAGCCGAACCAACCACAAAATCAATATGATCATTCAGAATGATATCTCCTCTGGTTGGAGCCACGAGAATCATACAGG
AATCTTCTGGAACTTGGAGGACTGCCCAGTACCTGGTGGTTTACGTCCTGAAATTTTTATTTATTGTTTGGCGGAGACTC
TTTCCACTGGATTCAAGTCGGTCATGGCTTACGGCAAGAAGAGGAGCCTCGCCTTCTATGATCACTTGTTATATGGTTTC
TTTCCCGTCACCTTGGTACCCACAGGTGACAAAGATGAGAGGATCAAGAAAATGTTTAAGGACATTTTCTTATGGGCACT
GGACAGACCCAGAACATCAAAGATCAACCGTAGTGGTGATCACGGAAAGCTTCCCAGACAACATGTATGATGCTGCTTTG
AGTTCAAGAAATTGCGAGCTAGTCTTAGTGGATCCTCATGCAGTTAGTTATGTGAAATCTGTGTGGCTTTTGCAAAGTTT
ATTTGGTGGAGGCAACCCTATCGACCTAAGGGGAAGAAAGAAAGCT

Alignment

ORF - retro_bole_61 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.18 %
• Parental protein coverage: 59.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VNYSRDKINMI-QNDI-SGY---HHTGIFWNMDDCPVPGG----LLDYCFMKTLSTGFKSVMVYGKRRNS
          ......KINMI.QNDI.SG.....HTGIFWN..DCPVPGG.......YC...TLSTGFKSVM.YGK.R..
Retrocopy ISRTNHKINMIIQNDISSGWSHENHTGIFWNLEDCPVPGGLRPEIFIYCLAETLSTGFKSVMAYGKKRSL

Parental  VLYADLLRNTSFPVTLVERGDKDARIKKMFKDIFLWALDRPQTS-RSTVVVITESFPDNMYDALSALSSR
          ..Y..LL....FPVTLV..GDKD.RIKKMFKDIFLWALDRP.TS.RSTVVVITESFPDNMYDA..ALSSR
Retrocopy AFYDHLLYGF-FPVTLVPTGDKDERIKKMFKDIFLWALDRPRTS>RSTVVVITESFPDNMYDA--ALSSR

Parental  NCKLVLVDPHAVSYVNSVWLLPSLFGGDNPIDLRGRKKA
          NC.LVLVDPHAVSYV.SVWLL.SLFGG.NPIDLRGRKKA
Retrocopy NCELVLVDPHAVSYVKSVWLLQSLFGGGNPIDLRGRKKA

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_61 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	Bo00828s040	1 retrocopy	retro_bole_61 ,