RetrogeneDB ID: retro_bole_42

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C2:15144474..15145345(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo4g074280
• Aliases: None
• Description: None

Sequence

>retro_bole_42
ATTCTTTTGGTTTTCGAGTTCATCTCTGTTTTTGCAGCTCTCAACCAAACAAGATGCCTCCACTGACCAAGCAAAGGTCG
GTTAAGATCCCAAAGAACACCCGCGAGAACTATGTGAGGTCTCCAAACCACAATGCTCCGGCTTCATACCCATGGCCGCG
CAAGGACCAAGAGGGTCAGCCAATCCGTATCGACGACCCGATGCTCCTCGATTTTAACTGTGAGGGATGGGATAAGGAGT
CTGCTAAACGTTACAACTCACTCCTCGACATCGAGATCCTCCCCACCCGCTTTGGTCACGCAGACACTCTTGTCCCCCTT
GGTCTCGACACTGATGTCTTTGAAACTCTCCACGCCATGGAGATTGCTCCGCTCTGCTACCAAACGCACGAGCTCTACCC
AGACCTCGTTCGGCAAGTGCTCGCTACAGCTCACATCGGGTATGACGACCCCGCCAAGCCAACATATGAGAGCTGTTCCT
TATCATTCATGGCCGATGGCAAGTTCTGCTCTCTCTCGTTTGACAAGCTCAACGAGATTTATGAGATTTTGGACGAGCGT
AGAGAGGTAGCGGTGATCAACAAATTCTCGCCGACGGATCATTTTTGGGACCTCATTGCGAACGGCACTTTCACATCCTG
CAAGGCGTACCAGCGCAGATCAGAAACCCTACTCTAAGGGTGATTGCGAAGATGGTTTCCAACCTCTTGTTCGCTAAGGA
TCAGACATCGAAGGTCACAAAAGGGGAGCTGCAGATGCTGTACTCGGGGCTTGAGGACGAGGTCCGCAGAGCTAGAGACA
TTCCAGTCCAGACGGTCGACACTAACCCTGGGTACCATCTCATTTGGATGTTCTATACGCGACGGGGCTGC

Alignment

ORF - retro_bole_42 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.5 %
• Parental protein coverage: 80.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VLLVEQPIACSSSFHQFLQMAHTKQSTKRTRATCTSSMPPLQA-QQTSETYPWPR-EQEGEPIDLDSPLL
          .LLV...I.......Q............R...T....M..LQ........YPWPR..QEG.PI..D.P.L
Retrocopy ILLVFEFISVFAALNQTRCLH*PSKGRLRSQRTPARTM*GLQT<HNAPASYPWPRKDQEGQPIRIDDPML

Parental  LDFNCEGWDKGTAARYNALLRVDMLPTRFCHAETLADLGINEDVFETLHAIGIAPLCYTTHELYPDLARQ
          LDFNCEGWDK..A.RYN.LL....LPTRF.HA.TL..LG...DVFETLHA..IAPLCY.THELYPDL.RQ
Retrocopy LDFNCEGWDKESAKRYNSLLDIEILPTRFGHADTLVPLGLDTDVFETLHAMEIAPLCYQTHELYPDLVRQ

Parental  VLATATITYEDSNAPSYANCSFSFMADGEYCSLSLDKLNEIYETTTEPKGVAVAKKFSPSNAFWDCIANG
          VLATA.I.Y.D...P.Y..CS.SFMADG..CSLS.DKLNEIYE...E...VAV..KFSP...FWD.IANG
Retrocopy VLATAHIGYDDPAKPTYESCSLSFMADGKFCSLSFDKLNEIYEILDERREVAVINKFSPTDHFWDLIANG

Parental  NFTPGKAYQ-SQIRNPALRVIAKTISNLLFAKDLTSKVTNGELQALYAGIEDEIRASGSSIPIQKVKTNP
          .FT..KAYQ..QIRNP.LRVIAK..SNLLFAKD.TSKVT.GELQ.LY.G.EDE.R.....IP.Q.V.TNP
Retrocopy TFTSCKAYQ<AQIRNPTLRVIAKMVSNLLFAKDQTSKVTKGELQMLYSGLEDEVRRA-RDIPVQTVDTNP

Parental  GFNSMTMICERRLC
          G.....M...RR.C
Retrocopy GYHLIWMFYTRRGC

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_42 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	Bo4g074280	1 retrocopy	retro_bole_42 ,