RetrogeneDB ID: retro_brap_2

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A10:6591018..6592842(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra002942
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra028896
• Aliases: None
• Description: None

Sequence

>retro_brap_2
ATGGACACTGTGATCGGATCAATCGACACGTGCAACCCAACCACCGGCGATATCTGCCGTCCACCAAACGGCACCGTCTC
CACCGTTCAAACCTCTCCTCCCGCTCACTCCACCACCATCAGCCCCTGCGACGCGACCCTCGGCCGCTACCTAGCGAGAC
GCCTCGTCGAGATCGGCGTCACCGACGTCTTCTCCGTCCCCGGAGACTTCAACCTTACGCTCCTCGACCACCTCATCGCC
GAGCCGAGCCTCAAGCTCATCGGCTGCTGCAACGAGCTCAACGCCGGCTACGCCGCCGACGGTTACGCCAGATCCCGCGG
CGTCGGAGCGTGCGTCGTCACCTTCACGGTCGGCGGATTAAGCGTCCTGAACGCGATCGCCGGCGCTTACAGCGAGAATC
TCCCTCTGATCTGCATCGTCGGCGGCCCTAACTCGAACGACTACGGCACGAGTCGGATCCTTCACCATACCATCGGCTTA
CCTGATTTCACTCAAGAGCTCAGATGCTTCCAAGCCGTCACGTGCTATCAAGCTGTGATCAATAACTTGGAAGAGGCTCA
CGAGCTTATCGACACCGCCATCTCCACCGCTTTGAAAGAGAGCAAGCCTGTCTACATCAGCATCAGCTGCAACTTGCCGG
CCATTCCTATGCCGACGTTCAGTCGCCACCCTGTTCCCTTCTCGCTTGCGCCTAAGGTGAGCAACCTGATGGGTTTAGAC
GCGGCGGTGGAGGCGGCTGCTGAGTTCTTGAACAAGGCCGTGAAGCCGGTTCTCGTTGGCGGGCCGAAGATGCGAGTTGC
CAAGGCTGCGGACGCTTTCGTTGAGCTTGCTGATGCTTCTGGGTATGGTGTCGCTGTGATGCCATCTGCTAAGGGGCAGG
TGCCTGAGCATCATAAGCACTTCATTGGCACGTATTGGGGAGCTGTGAGTACTGCGTTTTGCGCTGAGATTGTTGAGTCT
GCTGATGCGTATCTCTTCGCGGGTCCTATCTTTAATGATTACAGCTCCGTTGGGTACTCTCTGCTTCTCAAGAAGGAGAA
GGCAATCATCGTGCAGCCTGATCGGGTTACTATCGGTAACGGACCTGCTTTTGGATGTGTGTTGATGAAGGATTTTCTTA
GCGGTTTAGCTAAACGAATCAAGCATAACAACACCGCTTACGAGAATTACCACAGGATCTTTGTCCCTGAAGGAAAGCCT
CTGAGAGAGAATCCCAAGGAGCCTTTGAGGGTTAATGTGCTGTTTCAACACATTCAGAATCTGCTCTCTTCTGAAACAGC
TGTGCTCGCTGAGACGGGGGATTCTTGGTTCAACTGTCAGAAGCTGAAACTCCCTGAAGGATGTGGTTACGAGTTCCAAA
TGCAGTATGGGTCCATTGGTTGGTCCGTTGGTGCTACTCTAGGCTATGCTCAAGCCATACCAAACAAGCGTGTCATTGCT
TGTATTGGAGACGGTAGTTTCCAGGTTACCGCACAGGATGTGTCGACCATGATAAGGTGTGGGCAGAAGACTATAATCTT
TCTCATCAACAATGGAGGGTACACCATTGAAGTGGAGATCCATGATGGTCCTTACAATGTGATAAAGAACTGGAACTACA
CGGCTTTTGTTGAGGCTATTCACAATGGAGAAGGTAAATGCTGGACTGCAAAAGTGAGGTGCGAGGATGAGCTTGTGAAA
GCGATTAGCACGGCAACGAATGAGGAAAAGGAGAGCTTTTGTTTCATTGAGGTGATAGTGCATAAAGATGATACAAGCAA
GGAGCTTTTGGAGTGGGGATCTAGAGTCTCTGCTGCTAACAGTCGTCCTCCAAATCCTCAGTAG

Alignment

ORF - retro_brap_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDTKIGSIDACKPTNGDVGSPPSGAVATIHDSAPSSALSVGSSEATLGRHLARRLVQAGVTDIFSVPGDF
          MDT.IGSID.C.PT.GD...PP.G.V.T...S.P..........ATLGR.LARRLV..GVTD.FSVPGDF
Retrocopy MDTVIGSIDTCNPTTGDICRPPNGTVSTVQTSPPAHSTTISPCDATLGRYLARRLVEIGVTDVFSVPGDF

Parental  NLTLLDHLIAEPELKNIGCCNELNAGYAADGYARSRGVGACVVTFTVGGLSVLNAIAGAYSENLPVICIV
          NLTLLDHLIAEP.LK.IGCCNELNAGYAADGYARSRGVGACVVTFTVGGLSVLNAIAGAYSENLP.ICIV
Retrocopy NLTLLDHLIAEPSLKLIGCCNELNAGYAADGYARSRGVGACVVTFTVGGLSVLNAIAGAYSENLPLICIV

Parental  GGPNSNDFGTNRILHHTIGLPDFSQELRCFQTVTCHQAVVNNLEDAHEQIDKAISTALKESKPVYISISC
          GGPNSND.GT.RILHHTIGLPDF.QELRCFQ.VTC.QAV.NNLE.AHE.ID.AISTALKESKPVYISISC
Retrocopy GGPNSNDYGTSRILHHTIGLPDFTQELRCFQAVTCYQAVINNLEEAHELIDTAISTALKESKPVYISISC

Parental  NLAATPHPTFIRDPVPFSLTPRLSNKMGLEAAVEATLEFLNKAVKPVMVGGVKLRVAKASDAFVDLADAS
          NL.A.P.PTF.R.PVPFSL.P..SN.MGL.AAVEA..EFLNKAVKPV.VGG.K.RVAKA.DAFV.LADAS
Retrocopy NLPAIPMPTFSRHPVPFSLAPKVSNLMGLDAAVEAAAEFLNKAVKPVLVGGPKMRVAKAADAFVELADAS

Parental  GYAMAVMPSAKGLVPEHHPHFIGTYWGAVSTPFCSEIVESADAYIFAGPIFNDYSSVGYSLLLKKEKAIV
          GY..AVMPSAKG.VPEHH.HFIGTYWGAVST.FC.EIVESADAY.FAGPIFNDYSSVGYSLLLKKEKAI.
Retrocopy GYGVAVMPSAKGQVPEHHKHFIGTYWGAVSTAFCAEIVESADAYLFAGPIFNDYSSVGYSLLLKKEKAII

Parental  VHPDRVTIANGQTFGCVLMSDFFTELAKRVKRNETAYENYHRIFVPEGKPLTCKPKEPLRVNAMFQHIQK
          V.PDRVTI.NG..FGCVLM.DF...LAKR.K.N.TAYENYHRIFVPEGKPL...PKEPLRVN..FQHIQ.
Retrocopy VQPDRVTIGNGPAFGCVLMKDFLSGLAKRIKHNNTAYENYHRIFVPEGKPLRENPKEPLRVNVLFQHIQN

Parental  MISSETAVIAETGDSWFNCQKLKLPKGCGYEFQMQYGSIGWSVGATLGYAQAVPEKRVLAFIGDGSFQVT
          ..SSETAV.AETGDSWFNCQKLKLP.GCGYEFQMQYGSIGWSVGATLGYAQA.P.KRV.A.IGDGSFQVT
Retrocopy LLSSETAVLAETGDSWFNCQKLKLPEGCGYEFQMQYGSIGWSVGATLGYAQAIPNKRVIACIGDGSFQVT

Parental  AQDVSTMLRNGQKTIIFLINNGGYTIEVEIHDGPYNVIKNWNYTGLVDAIHNGEGKCWTAKVRYEEELVE
          AQDVSTM.R.GQKTIIFLINNGGYTIEVEIHDGPYNVIKNWNYT..V.AIHNGEGKCWTAKVR.E.ELV.
Retrocopy AQDVSTMIRCGQKTIIFLINNGGYTIEVEIHDGPYNVIKNWNYTAFVEAIHNGEGKCWTAKVRCEDELVK

Parental  AIKTATTEKKDSLCFIEVIVHKDDTSKELLEWGSRVAAANGRPPNPQ
          AI.TAT.E.K.S.CFIEVIVHKDDTSKELLEWGSRV.AAN.RPPNPQ
Retrocopy AISTATNEEKESFCFIEVIVHKDDTSKELLEWGSRVSAANSRPPNPQ

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_2 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT4G33070	1 retrocopy	retro_atha_21,
Brassica oleracea	Bo2g001320	1 retrocopy	retro_bole_3,
Brassica rapa	Bra028896	1 retrocopy	retro_brap_2 ,
Arabidopsis lyrata	fgenesh2_kg.7__814__AT4G33070.1	1 retrocopy	retro_alyr_26,