RetrogeneDB ID: retro_bole_29

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C2:51985413..51987462(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo2g166120
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo6g066460
• Aliases: None
• Description: None

Sequence

>retro_bole_29
ATGGCTTCTTTCGCTAAAGACACACAAGTGAAGCTTCCAAGACCAACGCGAGTCAAGAACAAGACTCCAGCACCGCTCCA
AATCACCGCAGAGCAGCTCCTAACAGAAGCTCGAGAGAGACAAGAGTCTCAGATCCTGCCACCTCAGCAGAACATCACTG
ACTCAACAGAGCTTTCTGACTACAGACTCCGCCTTCGTAAGGAGTATGAAGACCGTATCCGCCGCCCAGGACCATCTACA
CAAGTCTTTGTAAACTACGCACGTTGGGAAGAGTCTCAAAAGGATTATGTACGTGCTAGAAGCGTGTGGGAACGTGCCTT
GGCACGTGATTACAAGAACCATGCACTCTGGCTCAAGTACGCAGACTTCGAGATGAAGAACAAGTTCCTCAACTCAGCTA
GAAATGTTTGGGACCGAGCCGTCACGGTTCTCCCGCGCGTGGACCAGTTTTGGTACAAGTACATACACATGGAGGAGATG
CTTGGGAACATCTCCGGAGCTAGAGATATATTCGAGCGGTGGATGAAGTGGTCACCTGATCAACAAGGCTGGCTCTCGTT
TATCAACTTCGAGCTTCGGTATCAAGAAACAGCACGTGCGAGAGATGTCTACGAGAGGTTTGTCCTTTCTCACCCCAAAC
CTTCTTCTTACATCCAATACGCAAAGTTTGAGGCGAAGGGAGGTGAAGTCGCACGCGCGAGGGACGTGTACGAACGCGCC
GTGAAGAATCTTGGAGACGACGAAGACCTCTTTGTGGCCTTTGCTGAGTTCGAAGAGCGTTGCAACGAAGTGGAACGAGC
TAGGGTGATCTACAAGTTTGGTCTTGATCGTGTCGGAAGAGGAGAGGAGCTGTACAGAAAGTTTGTAGCGTTTGAGAAAC
AGTACGGGGACAAGGAAGGGATCGATGACGTCATTGTCGGGAGGAGAAGGGTTGAGTACGAGGAGCAAGTGAGGAAGAGC
CCTCTGAACTATGATGCGTGGTTTGATTACGTTAGGTTAGAGGAAGAGGAGGCTTCTTCCGTGGGAGACAAGGAAAGGGT
CAGAGAAGTTTACGAGAGGGCTATTGCTAACGTTCCACCGGCTAATGAGAAGCGTTACTGGAGGAGATACATTTATCTGT
GGATTAACTATGCTTTGTATGAGGAGATTGAAGCTGAAGATGTGGAGCGTGCACGTCAAGTATACAGAGAATGTCTGAAG
CTTGTCCCACACGCAAGCTTCTCTTTTGCTAAAATATGGCTATTGGCTGCACAGTTTGAGATCAGGCAACTGAATCTCAA
GGGTTGTCGGAAGTTACTTGGGAATGCAATTGGTATAGCTCCAAACAAAGATAAGATCTTCAAAAAGTATATCGAGATGG
AACTTCAGCTGGGAGAGATTGATAGATGCAGGAGACTATACGAGAGGTATCTTGTATGGTCTCCTGATAATTGCTACGTG
TGGTGCAAGTTTGCTGAGTTTGAGAGTTCACTCGAGGAAATAGAAAGAGCAAGAGGTATATTCGAGCTTGCGGTATCTCA
GACTACACTTGACTTGCCCGAGTTGGTATGGAAAGGTTACATCGATTTTGAGATGTCACAAGGGGAGGTAGAGAGGAGGC
GTGCTTTGTATGAGCGACTCTTGGAACGTACGAAGCATTACAAGGTGTGGGTTAGTTTTGCAAAGTATGAAGCTGGTGAA
CAAGATGAAGATGAGGAAGAAGATGGTATTGAACGCAAACAAGAGTGCATCAGACGCACTAGAGCGGTTTTTGACCGAGC
CTACGTGTATTACAAAGACGTTATACCGGAGATGAAGGAAGAAAGGGCAAAGCTGTTGGAGGATTGGTTTAATATGGAGG
TGGGATTTGGTATGCTCGGGGATGTTAGCATTGTAGAGTCAAAGCTCCCTAAGAAGCTCAAGAAGAGAAAGGCAATAACT
GGAGAAGACGGTTCGGTAGAGTATGTTGAGTACACTGATTATCTCTTCCCTGAAGAGTTGCAGGCTTCGAACCTCAAGAT
TCTTGAAGCTGCGTATAGATGGAAGAAGCAGAAGGTTGATGCTGTGTGA

Alignment

ORF - retro_bole_29 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.95 %
• Parental protein coverage: 85.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KDTEVKLPRPTRVKNKTPAPVQITAEQILREARERQEAEIRPPKQKITDSTELSDYRLRRRKEFEDQIRR
          KDT.VKLPRPTRVKNKTPAP.QITAEQ.L.EARERQE..I.PP.Q.ITDSTELSDYRLR.RKE.ED.IRR
Retrocopy KDTQVKLPRPTRVKNKTPAPLQITAEQLLTEARERQESQILPPQQNITDSTELSDYRLRLRKEYEDRIRR

Parental  ARWNIQVWMKYAQWEESQKDYARARSVWERAIEGDYRNHTLWLKYAEFEMKNKFVNSARNVWDRAVTLLP
          .....QV...YA.WEESQKDY.RARSVWERA...DY.NH.LWLKYA.FEMKNKF.NSARNVWDRAVT.LP
Retrocopy PGPSTQVFVNYARWEESQKDYVRARSVWERALARDYKNHALWLKYADFEMKNKFLNSARNVWDRAVTVLP

Parental  RVDQLWYKYIHMEEILGNIAGARQIFERWMQWSPDQQGWLSFIKFELRYNEIERARSIYERFVLCHPKVS
          RVDQ.WYKYIHMEE.LGNI.GAR.IFERWM.WSPDQQGWLSFI.FELRY.E..RAR..YERFVL.HPK.S
Retrocopy RVDQFWYKYIHMEEMLGNISGARDIFERWMKWSPDQQGWLSFINFELRYQETARARDVYERFVLSHPKPS

Parental  AYIRFAKFEMKGGEVARARHVYERATEKLADDEEAETLFVAFAEFEERCKEPERARFIYKFALDHIPKGR
          .YI..AKFE.KGGEVARAR.VYERA...L.DDE....LFVAFAEFEERC.E.ERAR.IYKF.LD....GR
Retrocopy SYIQYAKFEAKGGEVARARDVYERAVKNLGDDED---LFVAFAEFEERCNEVERARVIYKFGLDRV--GR

Parental  AEDLCKKFVAFEKQYGDKEGIEDAIVGKRRFQYEDEVRKNPLNYDSWFDYVRLEE----TVGNKDRIREI
          .E.L..KFVAFEKQYGDKEGI.D.IVG.RR..YE..VRK.PLNYD.WFDYVRLEE.....VG.K.R.RE.
Retrocopy GEELYRKFVAFEKQYGDKEGIDDVIVGRRRVEYEEQVRKSPLNYDAWFDYVRLEEEEASSVGDKERVREV

Parental  YERAIANIPPAEEKRYWQRYIYLWINYALYEEIETEDVERTRDVYRECLKLIPHSKFSFAKIWLLAAQFE
          YERAIAN.PPA.EKRYW.RYIYLWINYALYEEIE.EDVER.R.VYRECLKL.PH..FSFAKIWLLAAQFE
Retrocopy YERAIANVPPANEKRYWRRYIYLWINYALYEEIEAEDVERARQVYRECLKLVPHASFSFAKIWLLAAQFE

Parental  IRQLNLAGARQILGNAIGKAP-KDKIFKKYIEIELQLGNIDRCRKLYERYLEWSPENCYAWSKYAELERS
          IRQLNL.G.R..LGNAIG.AP.KDKIFKKYIE.ELQLG.IDRCR.LYERYL.WSP.NCY.W.K.AE.E.S
Retrocopy IRQLNLKGCRKLLGNAIGIAPNKDKIFKKYIEMELQLGEIDRCRRLYERYLVWSPDNCYVWCKFAEFESS

Parental  LAETERARAIFELAISQPALDMPELLWKAYIDFEIAEGELERTRALYERLLDRTKHYKVWVSFAKFEASA
          L.E.ERAR.IFELA.SQ..LD.PEL.WK.YIDFE...GE.ER.RALYERLL.RTKHYKVWVSFAK.EA..
Retrocopy LEEIERARGIFELAVSQTTLDLPELVWKGYIDFEMSQGEVERRRALYERLLERTKHYKVWVSFAKYEAG-

Parental  VEQEEDEEEED-QEETDAIERKKECIRRARAIFERANSYYKDSAPELKEE
          .EQ.EDEEE.........I.R......RA...........K.....L.E.
Retrocopy -EQDEDEEEDGIERKQECIRRTRAVFDRAYVYYKDVIPEMKEERAKLLED

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_29 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT5G41770	1 retrocopy	retro_atha_18,
Brassica oleracea	Bo6g066460	1 retrocopy	retro_bole_29 ,
Triticum aestivum	Traes_7DL_41F6E8FC4	1 retrocopy	retro_taes_37,