RetrogeneDB ID: retro_bole_30

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C9:47270253..47271459(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo9g160030
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo9g118840
• Aliases: None
• Description: None

Sequence

>retro_bole_30
ATGATCTCCTTGAATCTATCAGCTTCCCTAAACCCGGGTCTCACCCGGATCCGGCAAAACCCTACCCGTTTCTCCGCTCT
CCACGCCGCCGCCGCCGCCGATAAACCCTTCAGCTGCCAATACCCACTAAGCCTTCCACAGATCCCCAATCTCCAGATTC
GCGAAAAACCCTTCCTTTCAATCACCAAAAGATCCAGATCCGTCCCCGCCGCCGCGAATCCAGACGGCGGAGAGTCCGAG
TCCGAGGAAGCTGCCAAGAAGGAGAAGAAAGCGAAGAATCTCCAGCTAGGGATAGTCTTCGGTCTCTGGTACTTCCAGAA
CATCGTCTTCAACATCTTCAACAAGAAGGCTCTCAACGTCTTCCCTTACCCCTGGCTCCTCGCTTCCTTCCAGCTCTTCG
CCGGCTCCGTCTGGATGCTCGTCTTGTGGTCGTTCAAGCTCTACCCTTGCCCTAAAATCTCCAAGCCGTTCATCGTCGCT
CTCCTCGGACCCGCGCTGTTCCACACAGTAGGACACATCTCTGCTTGCGTCTCCTTCTCCAAAGTCGCTGTCTCCTTCAC
CCACGTGATCAAATCGGCCGAGCCTGTCTTCTCTGTGATTTTCTCGTCTTTCTTGGGAGACACGTATCCGTTAGCTGTTT
GGTTGTCGATTCTACCGATAGTTATGGGTTGTTCTTTAGCTGCGGTTACTGAAGTGTCGTTCAACTTGGGTGGCTTATCT
GGAGCTATGATTAGTAACGTTGGGTTTGTTTTAAGGAACATTTACTCTAAAAGGAGTCTACAGAGTTTTAAAGAGATTGA
TGGGTTGAATCTGTACGGTTGCATCAGTATACTCTCTCTGGTTTATCTGTTTCCTGTTGCGGTTTTCGTTGAAGGGTCGC
AGTGGGTTCAGGGCTACCATAAAGCTATTGCTTCTGTTGGGAAACCGTGGACGTTTTACTTTTGGGTTTTGCTCTCTGGT
GTCTTCTACCATTTATACAACCAGTCTTCTTACCAGGCGCTTGATGAGATTAGTCCTTTGACTTTCTCTGTTGGGAACAC
GATGAAGAGGGTGGTGGTGATTGTCTCCACTGTTTTGGTGTTTAGGAACCCTGTTAGGCCTCTCAATGCTCTTGGATCAG
CTATCGCGATTTTCGGTACTTTCTTGTATTCTCAGGCGACTGCCAAGAAGAAGAAGATTGAAGCTGGAGATGATAAGAAG
AATTGA

Alignment

ORF - retro_bole_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.69 %
• Parental protein coverage: 78.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DDDAAETKSEAAKKLKIGIYFATWWALNVVFNIYNKKVLNAYPYPWLTSTLSLAAGSLMMLISWAVGIVE
          ....A..K...AK.L..GI.F..W...N.VFNI.NKK.LN..PYPWL.....L.AGS..ML..W......
Retrocopy ESEEAAKKEKKAKNLQLGIVFGLWYFQNIVFNIFNKKALNVFPYPWLLASFQLFAGSVWMLVLWSFKLYP

Parental  TPKTDFDFWKTLFPVAVAHTIGHVAATVSMSKVAVSFTHIIKSGEPAFSVLVSRFLLGETFPTSVYLSLI
          .PK....F...L...A..HT.GH..A.VS.SKVAVSFTH.IKS.EP.FSV..S.F.LG.T.P..V.LS..
Retrocopy CPKISKPFIVALLGPALFHTVGHISACVSFSKVAVSFTHVIKSAEPVFSVIFSSF-LGDTYPLAVWLSIL

Parental  PIIGGCALSALTELNFNMTGFMGAMISNLAFVFRNIFSKKGMKG-KSVSGMNYYACLSMLSLLILTPFAI
          PI..GC.L.A.TE..FN..G..GAMISN..FV.RNI.SK......K...G.N.Y.C.S.LSL..L.P.A.
Retrocopy PIVMGCSLAAVTEVSFNLGGLSGAMISNVGFVLRNIYSKRSLQSFKEIDGLNLYGCISILSLVYLFPVAV

Parental  AVEGPQMWIDGWQKALSDVGP--QFVGWVAAQSVFYHLYNQVSYMSLDQISPLTFSVGNTMKRISVIVSS
          .VEG.Q.W..G..KA...VG....F..WV....VFYHLYNQ.SY..LD.ISPLTFSVGNTMKR..VIVS.
Retrocopy FVEGSQ-WVQGYHKAIASVGKPWTFYFWVLLSGVFYHLYNQSSYQALDEISPLTFSVGNTMKRVVVIVST

Parental  IIIFRTPVQPVNALGAAIAILGTFLYSQA
          ...FR.PV.P.NALG.AIAI.GTFLYSQA
Retrocopy VLVFRNPVRPLNALGSAIAIFGTFLYSQA

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_30 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00062p00036220	1 retrocopy	retro_atri_14,
Brassica oleracea	Bo9g118840	1 retrocopy	retro_bole_30 ,
Musa acuminata	GSMUA_Achr7G03380_001	1 retrocopy	retro_macu_2,
Populus trichocarpa	POPTR_0001s44610	1 retrocopy	retro_ptri_19,
Physcomitrella patens	PP1S70_177V6	1 retrocopy	retro_ppat_10,
Arabidopsis lyrata	scaffold_802017.1	1 retrocopy	retro_alyr_24,
Theobroma cacao	TCM_030978	1 retrocopy	retro_tcac_18,