RetrogeneDB ID: retro_brap_15

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A06:24152887..24154906(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra024894
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra031010
• Aliases: None
• Description: None

Sequence

>retro_brap_15
ATGAACAAAGTAAAATCGATGGCTAGTCGCCAACAAAACAGACAAATTAGATACGGTATTACAGAACCTATCTCTTTAGT
AGGACCAACGGAGCTTGACGTTATCAAGACAAAAGCCCTAGAGAACTACTTGCAAGACGCTGGATTATACGAAAGCAACG
AGGAAGCTCTTAGAAGAGAAGAAGTTCTTGGGAGACTAGACGAGATTGTCAAAACATGGATTAAAAAAATAAGCCGTGAC
AAAGGGTTAAGCGATGAGACGGTTGAACAAGCGAACGCCAAGATATTCACCTTCGGTTCTTATAGGTTAAAAGTACATGG
ACCTGGTGCTGATATCGACACTCTATGCGTTGGTCCAAGATACGCTACAAGAGAGAATGGTTTCTTTGGAGAGTTACATA
GAATGCTTTCGGAGTTGCCTGAAGTGACAGAGCTCCACTCTGTGCCTGATGCTTATGTTCCTTTAATGGGTTTCAAACTT
AATGGTGTCTCTATTGATCTCCTCTACGCAAAGCTCCCTTTGTGGATTATCCCCGAGGACTTGGATCTATCGCAAGATTC
TATTCTACAGAACGCTGATGAGCAAACTGTTCGAAGCCTCAACGGTTGTAGAGTTACTGACAAGATCTTTCGTCTGGTTC
CTAACATTCAGAGTTTCAGGACGACGTTGAGATGCATTAGGTTTTGGGCTAAGAAGCGTGGTGTATACTCTAACGTATCT
GGCTTTCTTGGTGGTATAAACTGGGCGTTGCTTGTAGCTAGGATCTGTCAGCTTTATCCTAACGCATCACCAAACATGTT
GGTGTCTCGGTTCTTTAGAGTCTACACTCAATGGCGTTGGCCCAATCCTATTCTTCTTTGCTCTATAGATGAAGACGAAG
GATCATCATTAGGTCTTCAAGTTTGGGATCCTAGAAGAAACCCTAAAGACTTGCTGCACAAGATGCCTATCATTACTCCT
GCTTATCCTTGTATGAACTCAAGTTACAACGTCTCCGCGAGTACACTGAGGATTATGACAGGAGAGTTTCAGAGAGGGAG
AGATGTATGCGCGGCTATGGAAGCTGAACAATGGGATACTCTTTTTGAGCCGTTTGGGTTCTTTGAAGCGTATAAGAACT
ATCTTCAGATCAACATCTCTGCTTCTAACGTGGAGGATTTGAAAAAGTGGAGAGGATGGGTTGAGTCACGTTTCAGACAG
CTTACGTTGGTGATTGAGAGACATACTTACGACATGCTTCAGTGCCACCCTCATCCACATGGCTTCCAAGACGATTCAAG
ACCGCTACAGTGTTCTCTATTCATGGGTCTGCAACGTAAAGAGGGAGTGGAAGCAGGAGGAGGCGAGCCGTTTGATATCA
GAAGAACCATTGAGGAGTTTAAACAAACTGTTTACGGTTATATGTTGTGGGTTCATGGGATGGAGGTTAGTGTCAGCCAT
GTAATGAGAAGAAGCATACCGAGCTTTGTGTTTCCTTGTGGAGTTAGACCTTTGGGTAACTTGAAAAGAACGAGGGATAG
CAAAAGCAGTTCAGAGCAAAGAGTTTCTTCTACAGTGAGTTCATCATCTACTATTACTAGTTGTGAAAGAAGAGGTGGGA
AGAAGAGAAAGTTGGGAGGTGATGAGACACTCACCGATCAGTTAAGGAACTCAAAACGTGTTGCAGTTTCAGTGCATGTA
GAGAATGGTGAAGACGGGAGCCCAAACTCATCTGCTGGATCTATTTGTTCAGCTCCTATGAAAGTAGGAGAGAGTCATCC
AGTAGAGAAGATAGACATTCCTCAGGATTCTCATAGTCAAGAAAGTGAGGAGGTTGAAGACAACTTTGGTTTCAGAAATC
AAGTTTCAAGTAAAGATGCATTCTCCAAAGGAGCAGTGGAAGTGGAAGAACTCGAAGATGTTCCAATGCAACGGCCCGTG
GTGATGCCCAAAGCTTCAGTGCAACTGCGGAAACCGATAATCAAGTTGAACTTCACGTCTCTAAGCATGACCAATGCCAA
GAATCTTAGAGCTTGTTGA

Alignment

ORF - retro_brap_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.28 %
• Parental protein coverage: 61.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FFGELQRMLSEMPEVTELHPVPDAHVPLMGFKLNGVSIDLLYAQLPLWVIPKDVDISQDSILQNADEQTV
          FFGEL.RMLSE.PEVTELH.VPDA.VPLMGFKLNGVSIDLLYA.LPLW.IP.D.D.SQDSILQNADEQTV
Retrocopy FFGELHRMLSELPEVTELHSVPDAYVPLMGFKLNGVSIDLLYAKLPLWIIPEDLDLSQDSILQNADEQTV

Parental  RSLNGCRVTDQILRLVPNIENFRTTLRCMRFWAKRRGVYSNVSGFLGGINWALLVARICQLYPNALPNML
          RSLNGCRVTD.I.RLVPNI..FRTTLRC.RFWAK.RGVYSNVSGFLGGINWALLVARICQLYPNA.PNML
Retrocopy RSLNGCRVTDKIFRLVPNIQSFRTTLRCIRFWAKKRGVYSNVSGFLGGINWALLVARICQLYPNASPNML

Parental  ASRFFRVYTQWRWPNPVLLCSMDE---GSLGLQVWDPRRNPKDRLHMMPIITPAYPCMNSSYNVSASTLR
          .SRFFRVYTQWRWPNP.LLCS.DE....SLGLQVWDPRRNPKD.LH.MPIITPAYPCMNSSYNVSASTLR
Retrocopy VSRFFRVYTQWRWPNPILLCSIDEDEGSSLGLQVWDPRRNPKDLLHKMPIITPAYPCMNSSYNVSASTLR

Parental  IMTGEFQRGKDICEAMEANKADWDTLFEPFAFFEAYKNYLQIDISAANVDDLRKWKGWVESRLRQLTLKI
          IMTGEFQRG.D.C.AMEA....WDTLFEPF.FFEAYKNYLQI.ISA.NV.DL.KW.GWVESR.RQLTL.I
Retrocopy IMTGEFQRGRDVCAAMEAEQ--WDTLFEPFGFFEAYKNYLQINISASNVEDLKKWRGWVESRFRQLTLVI

Parental  ERHTYDMLQCHPHPHDFQDASRPLHCSYFMGLQRKQGVPAAEGEPFDIRRTVEEFKHTVNGYMLWIPGME
          ERHTYDMLQCHPHPH.FQD.SRPL.CS.FMGLQRK.GV.A..GEPFDIRRT.EEFK.TV.GYMLW..GME
Retrocopy ERHTYDMLQCHPHPHGFQDDSRPLQCSLFMGLQRKEGVEAGGGEPFDIRRTIEEFKQTVYGYMLWVHGME

Parental  ISVSHIKRRSLPSFVFPGGVRPSHASKGTWDSKRRAEHRVSSTASAATTTTATTTNEASSESKAGSNSPG
          .SVSH..RRS.PSFVFP.GVRP....K.T.DSK...E.RVSST.S...T.T.............G.....
Retrocopy VSVSHVMRRSIPSFVFPCGVRPLGNLKRTRDSKSSSEQRVSSTVSSSSTITSCERRGGKKRKLGGDETLT

Parental  DEKKRKR
          D......
Retrocopy DQLRNSK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Brassica rapa was not studied using RNA-Seq expression data.

ChIP-Seq

Brassica rapa was not studied using ChIP-Seq data.

EST

Brassica rapa was not studied using EST data.

TSS

Brassica rapa was not studied using FANTOM5 data.

Lab

retro_brap_15 was not experimentally validated.

Homology

Retrocopy orthology:

Brassica rapa 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
Brassica oleracea	Bo8g104580	1 retrocopy	retro_bole_26,
Brassica rapa	Bra031010	1 retrocopy	retro_brap_15 ,
Triticum aestivum	Traes_4AL_4A747B462	1 retrocopy	retro_taes_53,