RetrogeneDB ID: retro_bole_9

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C1:26779500..26780907(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo1g090400
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo5g041260
• Aliases: None
• Description: None

Sequence

>retro_bole_9
ATGCCTTCCGTTCAAATGCGTTCGTCTCCGTCTGTTTCACCGCCGAGGACGGTTACTGATCTCAAGCAGCGAGTCATCGC
CTGTCTCAACCGTCTGTCCGATCGCGACACTCAATCTCTAGCCGCCGCAGAGCTCGACTCAATCGCTCTCAACCTCTCAC
CGGAGGCCTTCTCCCTCTTCATAAACTGTCTCCAAACCACAGACTCTTCAGCGAAATCTCCCGTTAGGAAACACTGCGTC
TCGCTCATCTCCTTACTCTCTCGTTCCCATGGAGACTCCCTCGCTCCTCACCTCCCGAAGATGGTCTCCACTATCCTCCG
CCGTCTCCGCGATCCTGATTCCTCCGTCCGCGCCGCTTGCGCAACCGCTTCCGTGGATATGACCACCAACATCACCGAAC
TGCCTTTCTCTGTCCTCGCCGGACCAATGATCGAAGCCTTGATCCACGACTGCGATGCCAACGCGCAGATAGGAGCCGCC
GTGTGCCTTGCGGCGGCTATAGACGCGGCTGATGATCCTGATGTCGAGCAGTTGCAGAAAGCGCTTCCGAAGATCGGGAA
GTTGCTCAAATCGGAAGGTTTCAAGGCGAAACCTGAACTTCTAGGAGCCATAGGAAGCGTAATCGGCGCCATTGGAGGCA
GAAACAGCGACAAGGCGGTTCTGGATTGGCTTTTACCTAACGTGTTGGAGTTTCTAAGCAGCGATGATTGGCATGCGAGG
AAAGCTGCTGCGGAGGCCGTGGCTAGAGTAGCTACGGCTGAAGAAGAGTTAGCTCCTTTGTATAAGAAGGCATGTCTTGC
TCTTCTTGAGAGCAGAAGATTTGATAAGGTTAAGCTTGTTAGGGAGACGATGAATCATACGTTGAGTTTATGGAAGCAAC
TTGGAGATGATTCTCCAGACTCATCTTCCCTCTCCAAATCAGTTTCTACAGGAAAAGGAATCAACACATTGAAAAGCAAA
GAAAATAATCCAAACGTACCAACAAGCTCAAAGTTAAATGATGATGAAGCTGCGGAGTCGAAAGAGAAGCGGCCATTGGG
GACTAGAAGAGTTCTGTTTCCGGCTAAGCCAAAGGTCAAAGAGAATAGATCTAATAAGTCACAAGTTGTTGCTGTTGTTC
AGAGTAGTGATGAAGAAGAGGAGAGTAGTAGTTCTTCTCAGACAAAGAATGCAGAAGAAGAATTGTCTCTGATCAGAAAC
CAGATCACTCAGATCGAAAAACAACAGTCTAGTCTGGTAGATCTCTTTCAGCGATTCATGGAGAGCTCCCAGAACGAAAT
GCAGTCGCTGGGGAGACGAGTGCGTTGTCTAGAGACATCATTCAGTGTACTCTCCACTGATTTGTTAGTGTCTCGCACCA
TAACACAAAATGGCACCCACAAACGAAATGCCCATCTACAGAATTGA

Alignment

ORF - retro_bole_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.81 %
• Parental protein coverage: 53.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PSPPVSSSPNSQSP-SPSDLKQRVIACLNKLADRDTLALATAELDSIARSLTHDSFSSFLSCIHNTDSSC
          PS....SSP....P....DLKQRVIACLN.L.DRDT..LA.AELDSIA..L....FS.F..C...TDSS.
Retrocopy PSVQMRSSPSVSPPRTVTDLKQRVIACLNRLSDRDTQSLAAAELDSIALNLSPEAFSLFINCLQTTDSSA

Parental  KSPVRKQCVAVLSLMSRHHGDSLSPHLAKMVSTVIRRLRDPDSSVRSACAAATADISAHVTAQPFTSVAK
          KSPVRK.CV...SL.SR.HGDSL.PHL.KMVST..RRLRDPDSSVR.ACA.A..D.....T..PF...A.
Retrocopy KSPVRKHCVSLISLLSRSHGDSLAPHLPKMVSTILRRLRDPDSSVRAACATASVDMTTNITELPFSVLAG

Parental  PLIETLIQEGDSNAQIGAALCLAAAVEAAADPDSEQLRMSLPKIGKLLKSEAFKAKAALLSAVGSIITA-
          P.IE.LI...D.NAQIGAA.CLAAA..AA.DPD.EQL...LPKIGKLLKSE.FKAK..LL.A.GS.I.A.
Retrocopy PMIEALIHDCDANAQIGAAVCLAAAIDAADDPDVEQLQKALPKIGKLLKSEGFKAKPELLGAIGSVIGAI

Parental  -GGAGTKPVLDWLVPVLIEFLSSEDWAARKSAAEALGKVATA-EELASQYKKASTAALESRRFDKVKSVR
          .G....K.VLDWL.P...EFLSS.DW.ARK.AAEA...VATA.EELA..YKKA..A.LESRRFDKVK.VR
Retrocopy GGRNSDKAVLDWLLPNVLEFLSSDDWHARKAAAEAVARVATAEEELAPLYKKACLALLESRRFDKVKLVR

Parental  QTMNQALSQWKEVSSGLEEALLSPSRSSTDDGGSIGCFSSVTRSSSIEVGCKSSRPKKATPIMKR
          .TMN..LS.WK...........S....S...G..I....S...........K......A....KR
Retrocopy ETMNHTLSLWKQLGDDSPDS--SSLSKSVSTGKGINTLKSKENNPNVPTSSKLNDDEAAESKEKR

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_9 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	Bo5g041260	1 retrocopy	retro_bole_9 ,