RetrogeneDB ID: retro_bole_8

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C6:16562894..16565006(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo6g064270
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo01031s010
• Aliases: None
• Description: None

Sequence

>retro_bole_8
ATGATGGCCAGGACGATTGACTTTGCGCAAGGATGGAGAAGTATGCAGATTGGTATCACTAAGCTGGAAAAGCATGTGGA
AGGACTTCCTGGGCACTCACTTAATAGTGAGCAATATATAAACCTTTACACGACTGTCTACGTTATGTGCACCCAGAAAC
CTCCTCATGATCACGCAGAGAAGCTTTACAACAAGTACCGTGAAGTAGTTGAGGAATATACTAAGTCGACAGTTTTGCCT
GCTCTAAGGAAGACCTATGACGATGAATATATGTTGCTGCGAGTGCTTCTTGAAAGATGTTCTATCCATAAAAAGATGGT
TAGACGCCTATCCAGGATCTTCCACTATGTTGACCGTTACTTCGTTGTTCGCAACTCACTCCTATCTCTAGAAGAAGTTG
GATTAGCATGCTTCGTTGACATGGTTTATAACACGTTGCAACTCAGGGTCAGAGAAGCTGTGATAGCTATAGTTGATAAA
GAACGAGAAGGTGATGATACTGGTATTGATAGGGCGTTACTTGAAAACGTTAAAGACATTTATGTAGAGATTGGAATGGG
TAAGATGAAAAGATACGAACAAGATTTGGAGAGCTTCATGCTTGAAGGTACAGCGTCTTACTATTCTCGCAAGGCATCAA
GATGGATTCAAGAATATTCTTACTTTGATTACATTCGGAAGTCTGAAGAATGTGTAAAGAAGGAGAAGAAGAGAGTGTCT
CACTACCTTTACGCAAGCAGTGAGCCAAAGCTGGTTAAAATAGTAGAGCATGAGTTGTTTGTAGTGTATGCCAACAAGCT
TCTTGAGAAAAAGCACTCAGAGTTCAGGGAAATTGCGGGAGGCTTGGAACCTATAACAAACATATTCAAGCAGCATGTTG
AAGACACAGATGGTCAAGACACGGCTGCAATCAGAAAAGTGATTGAGGTACATGATAAGTACATAGTCTATGTCACAAAG
TGTCTCGAGAATCAAACCATCTTTCACAAGTCCTTGAAAGAGGCATTTAAGTTTTTTTGTAGCAAAGCAGTGTCTGGAAG
CTCTTTAAGTGATGAATCACTGGCAACAATTTGTGACAGAATTATAATTCTCAAGAAATGGGCAAGTGAGGAGCTGAGTG
ATGAAGCTATTGAGAAGGTGGTCAAGTTTCTTGCGTATATAAGTGATGACAAGGATCTTTTTGCAGAGTTTTACAAGAAG
AAGCTGGCACGTAGGCTGCTATTGAATCGTGATGCTAGTGATGATCATGAGAGAGGAATCATTACAAAGCTCAAACAACA
GTTTGGTGGGAATTTTACTTATAAGATGGAGGGAATGGTGACAGATTTGACATTGTCAAGACAAAACCAAAACAGCTTCG
ATGAGTATGTAGCCAATAACCCTGCTGCAAAACCAGGGATTGATTTGAGCGTCACTCTTCTTACAACTAGTGTTTGGCCA
AGTTACAAAACGTTTGACGTGAATCTACCTAGTGAAATGGTCAAGTGTGTTGAAATTTTCAAAGTGTTTTATGAAACCAA
ACACAAACGTAGGAAACTTACTTGGCTCCACTCACTAGAAACTTGTCACATCAACGGAAAGTTCGATCAAAAGCCCATTG
ATTTGATCGTGTCGACTCACCAGGCTGCTGTGCTTCTGCTTTTTAACACAAGGGACAAACTGAACTACACTGACATCCAA
ACTCAACTGAACCTACGCCATGAAGATCTTGTGTGGGTGCTTCATTCCTTGTCATGTGCTAAATACAAGGTTCTTATCAA
GGAGCCAGCCACAGAGACTGTCTCCAAGACTGATGTTTTTGAAGTCAACTCCAAATTTACCTCTAGAACGGGCGGAGTAA
AGATTCCTCTCTCTCATGTTGATGAACGGAAGAAAGTTGTTGAATATGTTAATAACGACAGGCGCTATGCAATTGAGGCT
TCTATTGTCAGGATCATGAAGGGCAAGAAAGTATTGGGACATGAACAACTTGTTTCTGAATGTGTCAAGCAACTTAGTGG
GATGTTCAAGCCTGATGTTAAAGCGATTAAAACACGTATAGAGGAATTAATAGCAAGAGATTATTTGGAGAGGGACAAGA
TGAATCCTAACATGTTTAGGTACTTGGCTTAG

Alignment

ORF - retro_bole_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.35 %
• Parental protein coverage: 54.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QEQVLIRKVIELHDKYMVYVVECFQNHTLFHKALKEAFEIFCNKTVAGSS-SAELLATFCDNI--LKKGG
          Q....IRKVIE.HDKY.VYV..C..N.T.FHK.LKEAF..FC.K.V.GSS.S.E.LAT.CD.I..LKK..
Retrocopy QDTAAIRKVIEVHDKYIVYVTKCLENQTIFHKSLKEAFKFFCSKAVSGSSLSDESLATICDRIIILKKWA

Parental  SEKLSDEAIEDTLEKVVKLLAYISD-KDLFAEFYRKKLARRLLFDRSANDDHERSILTKLKQQCGGQFTS
          SE.LSDEA.....EKVVK.LAYISD.KDLFAEFY.KKLARRLL..R.A.DDHER.I.TKLKQQ.GG.FT.
Retrocopy SEELSDEA----IEKVVKFLAYISDDKDLFAEFYKKKLARRLLLNRDASDDHERGIITKLKQQFGGNFTY

Parental  KMEGMVTDLTLARENQTSFEEYLGNNPAANPGIDLTVTVLTTGFWPSYKSFDINLPSEMVKCVEVFKGFY
          KMEGMVTDLTL.R.NQ.SF.EY..NNPAA.PGIDL.VT.LTT..WPSYK.FD.NLPSEMVKCVE.FK.FY
Retrocopy KMEGMVTDLTLSRQNQNSFDEYVANNPAAKPGIDLSVTLLTTSVWPSYKTFDVNLPSEMVKCVEIFKVFY

Parental  ETKTKHRKLTWIYSLGTCHLNGKFDHKPIELVVSTYQAAVLLLFNTTDKLSYNDILTQLNLSHEDLVRLL
          ETK.K.RKLTW..SL.TCH.NGKFD.KPI.L.VST.QAAVLLLFNT.DKL.Y.DI.TQLNL.HEDLV..L
Retrocopy ETKHKRRKLTWLHSLETCHINGKFDQKPIDLIVSTHQAAVLLLFNTRDKLNYTDIQTQLNLRHEDLVWVL

Parental  HSLSCARYKILTKEPSTKTVSQTDSFEFNAKFTDRMRRIKIPLPPVDERKKVVEDVDKDRRYAIDAAIVR
          HSLSCA.YK.L.KEP.T.TVS.TD.FE.N.KFT.R....KIPL..VDERKKVVE.V..DRRYAI.A.IVR
Retrocopy HSLSCAKYKVLIKEPATETVSKTDVFEVNSKFTSRTGGVKIPLSHVDERKKVVEYVNNDRRYAIEASIVR

Parental  IMKSRKVLGHQQLVSECVEQLSRMFKPDIKAIKKRMEDLITRDYLERDKENPNMFRYLA
          IMK..KVLGH.QLVSECV.QLS.MFKPD.KAIK.R.E.LI.RDYLERDK.NPNMFRYLA
Retrocopy IMKGKKVLGHEQLVSECVKQLSGMFKPDVKAIKTRIEELIARDYLERDKMNPNMFRYLA

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_8 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo01031s010	1 retrocopy	retro_bole_8 ,
Prunus persica	PRUPE_ppa001948mg	1 retrocopy	retro_pper_19,
Theobroma cacao	TCM_004565	1 retrocopy	retro_tcac_22,