RetrogeneDB ID: retro_bole_22

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C9:1236561..1238013(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo9g005960
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo9g003540
• Aliases: None
• Description: None

Sequence

>retro_bole_22
ATGGCGGAGTCTCATTCTCTCAACACGCAGCTCTCGAGTCGCACTTCCATCTTCGGTCTGCGTTTATGGATCGTTCTCGG
CGTTTGCGTCGGAGCCGCAATCGTTATTCTCCTCTTCCTCATCTCCCTCTGGTTCATTCACCGAAGAAGCAACAACAACA
AAGCCCTCGAGTCTCACACCATCGTCCCCGTAGTCTCCAAGGAGATTCGGGTCGACCCAATTCAACCCGACCCGACTCCC
ACACCCGAGTCAACGAACCACCGTGAAGACGACAACAAAATCCACATCGACATCGGAAAAGACCACCGTATCTCCTTCCC
GGAGCGCGGCGGTTGGTCCGGGTCAGGGTCCGGGTCAGGACCCGATCAGGCTGCCTGTTCGGGTCCTGAGGTTTCTCATT
TAGGTTGGGGGCATTGGTACACTTTGAGAGAGCTCGAGGTTTCGACAGACGGATTCTCCGACAAGCATGTGATCGGACAA
GGAGGGTACGGGATCGTGTACCGAGGCGTCCTCGAGGATAAATCGATAGTAGCGATAAAGAATCTTCTCAACAACAGAGG
GCAAGCTGAGAAAGAGTTCAAAGTCGAAGTCGAAGCGATAGGTAGAGTGCGGCACAAGAATCTAGTGAGGCTCCTTGGTT
ACTGCGTTGAAGGAGAGCATAGGATGCTTGTTTACGAGTATGTCGATAACGGGAACTTAGAGCAGTGGCTTCACGGCGAT
GGGTTGGGTTCCAAGAGTCCTCTCACGTGGGAGATTAGGATGAACATCGTCCTCGGGACGGCTAAAGGGTTGATGTATTT
ACACGAAGGTCTTGAGCCTAAGGTTGTTCATAGGGATATTAAATCGAGTAATATCTTGCTCGACAAGCAATGGAACGCGA
AGGTTTCGGATTTTGGTTTAGCTAAGCTCTTGGGGTCGGAGATGAGCTATGTGACTACTCGTGTGATGGGTACTTTTGGT
TATGTGGCTCCTGAGTACGCTAGTACGGGGATGTTGAACGAGAGGAGCGATGTTTATAGCTTCGGTGTTCTTGTTATGGA
GATGATATCCGGGAGGAACCCTGTGGATTACAGCAGGCCTGTCGGAGAGGTGAACCTTGTGGAGTGGCTGAAGAGAATGG
TTTCGAATCGTGAAGCGGAAGGGGTTTTGGATCCGAGGATGGTGGAGAAACCGTCTTTAAGGTCGTTGAAGCGTACGCTT
TTGGTGGCTTTGAGATGTGTTGATCCTAATGCTCAGAAGAGACCAAAGATGGGTCATGTCATTCACATGCTTGAGGCTGA
GGATTTGGTGTCGAGAGATGATCGGAGAAACTCCGGCGGCGGCGGGGGAGGAGGTGATCCGAGAAGGTCACCGAGGAAGA
TGAATGTGGCTGAATCAGAGGATGAGAGTGTTAATTCCATTCTGATTAAGAATGACCAGTTAGCTTCGGAGAAGGAGGAG
GAGAGTCAGTGA

Alignment

ORF - retro_bole_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.13 %
• Parental protein coverage: 93.56 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  INAELSKPTSIFGLKLWVVIGILLGSLIVIALFFLSLCLTSRRRNRKPRHADFASAAVATPPVSKEIQEI
          .N..LS..TSIFGL.LW.V.G...G..IVI.L.FL.......RR................P.VSKEI...
Retrocopy LNTQLSSRTSIFGLRLWIVLGVCVGAAIVI-LLFLISLWFIHRRSNNNKALE---SHTIVPVVSKEIRV-

Parental  VRPPPQQDHHYHPTQPEIQVDIGKAEHRVVFSDRVSSGESRGTVSVSETASYSGSGCVGPEVSHLGWGRW
          ...P.Q.D....P.......D..K.........R.S..E..G..............C.GPEVSHLGWG.W
Retrocopy --DPIQPDPTPTPESTNHREDDNKIHIDIGKDHRISFPERGGWSGSGSGSGPDQAACSGPEVSHLGWGHW

Parental  YTLRELEAATNGLCEENVIGEGGYGIVYRGVLNDGTKVAVKNLLNNRGQAEKEFRVEVEAIGRVRHKNLV
          YTLRELE..T.G.....VIG.GGYGIVYRGVL.D...VA.KNLLNNRGQAEKEF.VEVEAIGRVRHKNLV
Retrocopy YTLRELEVSTDGFSDKHVIGQGGYGIVYRGVLEDKSIVAIKNLLNNRGQAEKEFKVEVEAIGRVRHKNLV

Parental  RLLGYCVEGAYRMLVYDYVDNGNLEQWIHGD-VGDKSPLTWDIRTNIILGMAKGLAYLHEGLEPKVVHRD
          RLLGYCVEG..RMLVY.YVDNGNLEQW.HGD..G.KSPLTW.IR.NI.LG.AKGL.YLHEGLEPKVVHRD
Retrocopy RLLGYCVEGEHRMLVYEYVDNGNLEQWLHGDGLGSKSPLTWEIRMNIVLGTAKGLMYLHEGLEPKVVHRD

Parental  IKSSNILLDRQWNAKVSDFGLAKLLFSESSYVTTRVMGTFGYVAPEYACTGMLTEKSDIYSFGILIMELI
          IKSSNILLD.QWNAKVSDFGLAKLL.SE.SYVTTRVMGTFGYVAPEYA.TGML.E.SD.YSFG.L.ME.I
Retrocopy IKSSNILLDKQWNAKVSDFGLAKLLGSEMSYVTTRVMGTFGYVAPEYASTGMLNERSDVYSFGVLVMEMI

Parental  TGRNPVDYSRPQGEVNLVEWLKTMVGNRRSEEVIDPKIVEPPSSKALKRLLLVALRCVDPDANKRPKMGH
          .GRNPVDYSRP.GEVNLVEWLK.MV.NR..E.V.DP..VE.PS...LKR.LLVALRCVDP.A.KRPKMGH
Retrocopy SGRNPVDYSRPVGEVNLVEWLKRMVSNREAEGVLDPRMVEKPSLRSLKRTLLVALRCVDPNAQKRPKMGH

Parental  IIHMLEAEDLFYRDERR
          .IHMLEAEDL..RD.RR
Retrocopy VIHMLEAEDLVSRDDRR

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_22 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo9g003540	1 retrocopy	retro_bole_22 ,
Brassica rapa	Bra037362	1 retrocopy	retro_brap_6,