RetrogeneDB ID: retro_brap_6

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A09:115985..117434(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra036252
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra037362
• Aliases: None
• Description: None

Sequence

>retro_brap_6
ATGGCGGAGTCTCATTCTCTCAACACTCAGCTCTCGACCCGCACTTCCATCTTCGGTCTGCGTTTATGGATCGTTCTCGG
CGTTTGCGTCGGAGCCGCAATCGTTATTCTCCTCTTCCTCATCTCTCTCTGGTTCATCCACCGAAGAAGCAACAACAAAG
CTCTCGAGTCTCACACCGTCGTCCCCGTAGTCTCCAAGGAGATTCGGGTCGACCCAATTCAACCCGACCCGACCCCCACA
CCCGAGACGACAACAAACCACCGTGAAGACGACAACAAAATCCACATCGACATCGGAAAAGACCACCGTATCTCCTTCCC
GGAGCGCGGCGGTTGGTCCGGGTCAGGGTCCGGGTCAGGACCCGACCAGGCTGCCTGTTCGGGTCCTGAGGTTTCTCATT
TAGGTTGGGGGCATTGGTACACTCTAAGAGAGCTCGAGGTTTCCACCGATGGTTTCTCCGACAAGCACGTGATCGGACAA
GGAGGGTACGGGATTGTCTACCGAGGCGTCCTCGAGGATAAATCGATAGTCGCTATAAAGAATCTTCTCAACAACAGAGG
GCAGGCTGAGAAAGAGTTTAAAGTCGAGGTCGAAGCGATAGGTAGAGTGCGGCACAAGAATCTCGTGAGGCTCCTTGGTT
ACTGCGTCGAAGGAGAGCATAGGATGCTTGTTTACGAGTATGTTGATAACGGGAACTTAGAGCAGTGGCTTCACGGCGAT
GCGTTGGGAGCTAAGAGTCCTCTCACGTGGGAGATTAGAATGAACATCGTTCTCGGGACGGCTAAAGGGTTGATGTATTT
ACACGAAGGTCTTGAACCTAAGGTTGTTCATAGAGATATCAAGTCTAGTAATATCTTGCTCGACAAGCAATGGAACGCGA
AGGTTTCGGATTTTGGTTTAGCTAAGCTATTGGGGTCGGAGATGAGCTACGTGACTACTCGTGTGATGGGTACTTTTGGT
TACGTGGCTCCTGAGTATGCTAGTACGGGGATGTTGAACGAGAGGAGCGATGTTTACAGCTTCGGTGTTCTTGTTATGGA
GATGATATCCGGGAGGAACCCTGTGGATTACAGCAGGCCTGTCGGAGAGGTGAACCTTGTGGAGTGGCTGAAGAGAATGG
TGTCGAATCGTGAAGCGGAAGGGGTTTTGGATCCGAGGCTGGTGGACAAACCGTCTTTGAGGTCGTTGAAGCGTACGCTT
TTGGTGGCTTTGAGATGTGTTGATCCTAATGCTCAGAAGAGACCAAAGATGGGTCATGTCATTCACATGCTTGAGGCTGA
GGACTTGGTGTCGAGAGATGATCGGAGAAACTCCGGCGGCGGCGGGGGAGGAGGTGATCCGAGAAGGTCACCGAGGAAGA
TGAATGTGGCGGAATCAGAGGATGAGAGTGTTAATTCCATTCTGATCAAGAATGACCAGTTAGCTTCGGACAAGGAGGAG
AGTCAGTGA

Alignment

ORF - retro_brap_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.3 %
• 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....LG.....A...L..........R........S..V..P.VSK...EI
Retrocopy LNTQLSTRTSIFGLRLWIV----LGVCVGAAIVILLFLISLWFIHRRSNNKALESHTVV-PVVSK---EI

Parental  VRPPAQQDHHYHP-TQPEIQVDIGKAEHRVVFSDRVSSGESRGTVSASETASYSGSGCVGPEVSHLGWGR
          ...P.Q.D....P.T......D..K.........R.S..E..G..............C.GPEVSHLGWG.
Retrocopy RVDPIQPDPTPTPETTTNHREDDNKIHIDIGKDHRISFPERGGWSGSGSGSGPDQAACSGPEVSHLGWGH

Parental  WYTLRELEAATNGLCEENVIGEGGYGIVYRGILNDGTKVAVKNLLNNRGQAEKEFRVEVEAIGRVRHKNL
          WYTLRELE..T.G.....VIG.GGYGIVYRG.L.D...VA.KNLLNNRGQAEKEF.VEVEAIGRVRHKNL
Retrocopy WYTLRELEVSTDGFSDKHVIGQGGYGIVYRGVLEDKSIVAIKNLLNNRGQAEKEFKVEVEAIGRVRHKNL

Parental  VRLLGYCVEGAYRMLVYDYVDNGNLEQWIHGD-VGDKSPLTWDIRTNIILGMAKGLAYLHEGLEPKVVHR
          VRLLGYCVEG..RMLVY.YVDNGNLEQW.HGD..G.KSPLTW.IR.NI.LG.AKGL.YLHEGLEPKVVHR
Retrocopy VRLLGYCVEGEHRMLVYEYVDNGNLEQWLHGDALGAKSPLTWEIRMNIVLGTAKGLMYLHEGLEPKVVHR

Parental  DIKSSNILLDRQWNAKVSDFGLAKLLFSESSYVTTRVMGTFGYVAPEYACTGMLNEKSDIYSFGILIMEL
          DIKSSNILLD.QWNAKVSDFGLAKLL.SE.SYVTTRVMGTFGYVAPEYA.TGMLNE.SD.YSFG.L.ME.
Retrocopy DIKSSNILLDKQWNAKVSDFGLAKLLGSEMSYVTTRVMGTFGYVAPEYASTGMLNERSDVYSFGVLVMEM

Parental  ITGRNPVDYSRPQGEVNLVEWLKTMVGNRRSEEVIDPKIVEPPSSKALKRLLLVALRCVDPDANKRPKMG
          I.GRNPVDYSRP.GEVNLVEWLK.MV.NR..E.V.DP..V..PS...LKR.LLVALRCVDP.A.KRPKMG
Retrocopy ISGRNPVDYSRPVGEVNLVEWLKRMVSNREAEGVLDPRLVDKPSLRSLKRTLLVALRCVDPNAQKRPKMG

Parental  HIIHMLEAEDLFYRDERR
          H.IHMLEAEDL..RD.RR
Retrocopy HVIHMLEAEDLVSRDDRR

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_6 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 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 ,