RetrogeneDB ID: retro_brap_34

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A09:13286368..13288651(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra027570
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra035212
• Aliases: None
• Description: None

Sequence

>retro_brap_34
ATGGCAGAAAACGACTTCTCACTTAAAGAGACATGTCCGAAAATCGGCGGTGGAAGATCAACTCCCGGCGGCGAAATGCA
AACGTCATCGTTCGACCTCGTGGAGCGAATGACATTTCTCTACATCCGAGTCGTCAAGGCTCGAGCCTTACCTTCCAACG
ACTCATTCATCGAAGTCACCATCGGAAGCTACAAAGGAAGAACGAAGAACAACACAAACCCTAACCCTAACCCTGAGTTC
CACGAAGTCTTCGCCTTTAACAAGGATCGTCTCCAAGGAAACGTCTTGGACGTTGCTGTGAAGGCCAACGAAGAAGTGAT
TATTGGTAAGTGCAAGTTCGAAGTTGCTGAGATTCCGACGCGTGTCCCTCCGGACAGTCCATTGGCTCCTCAGTGGTATA
GATTAGAAGACATCAACGGGAACAGGTTCGGAGGAGAGGTTATGCTGTCTGTTTGGATGGGGACACAAGCTGATGAAGTG
TTCCCTGAAGCTTGGCATTCAGATTGCGTTACCGTGAATGGAGACAACGCAGTGATCGCACGGTCTAAAGTTTATCTATC
TCCGAGGCTTTGGTATCTGCGTGTGAACATCATCGAGGCTCAAGATTTGGTTCCGTTACAAGGAAACAGAACCAATCCGG
AGATTTTAGTGAAAGGGTTTTTAGGGAACATTGTCGTGAGGAGTCGGGTGTCTCAGACACGAACCTTGAGTCCGGTTTGG
AACGAGGATATGATGTTTGTTGCGGTTGAGCCTTTTGAAGACAGCTTGATACTTAGCTTGGAATGCAAGTTAGGTCAAAA
CGAAGAGTGTTTAGGGAAATGTGAGATAAAGTTATCTCAAGTTGAGAGAAGGGTAATGCCGGATACTGTGCCGGCTATGT
GGTACAACTTGGAACGCGTCGTGGACTCAGTGGTACAGGGATTCGCGGGGAGGATTCATTTGCGGGTTTCGTTGGACGGA
GGTTACCATGTTCTTGACGAGTCTATTCAGTATAGCAGCGATTATAGAGCTTCTGCGAAAATTTTATGGACTCCAGCGAT
CGGTGTGTTGGAGCTTGGTGTCATCAGTGCGTCTGGTTTGATGCCTATGAAGTCACGTGAGGGCCGAGGAACCACTGATG
CGTATTGTGTGGCCAAGTACGGGCAGAAGTGGGTGAGAACGAGGACGATTGTCGATACTTTTAGCCCGAAATGGAACGAG
CAGTATACTTGGGAGGTTTATGATCCTTACACCGTTATCACCATTGGGGTTTTCGACAACATGCATCTATTAGTACCAGG
AAACACGAATGGTCCTAGAGATTCAAGAATCGGTAAGATACGGATACGTTTGTCCACGCTCGAAACGGAACGGATCTACA
CGCATTCGTATCCACTCATTGTTTTGAAACCAGACGGTGTGAAGAAAATGGGTGAAATTCAGCTCGCGGTTCGATTCTCA
TGTACTTCAACGATCGATATGCTTCAGAAATACTCAGAGCCGTTGCTGCCTATGATGCACTACTTAACTCCATTGTCAAT
CTACCAGCTAGACAGTCTTAGGCATCAAGCAACTCATATACTTTGTATGAACCTAGGCCGGACCGAGCCGCCGCTAGGGA
GAGATGTGGTTGAGTATATGCTTGATTTCGGATCCAACATTTGGAGTATCAGAAGAGGAAGAGCGAATTTCGAACGTCTT
GTGACATTCTTCACTGCGTTTCTTGATGCTTGGGTTTGGTTTGATTCGGTTTGCAAATGGAAGAGTCCGGTAACAACGAT
TCTTGCACATTTTATCTTCTTGTTCATTGTGTTTCTCCCTAAGTATTGTGTCACCTCTCTGCTGCTGTACTGCTTTGTGA
TTGGGTTTTATCGGTATCGGTTGAGACCGAGGCATCCTCCTCACATGGATATAAAGCTGTCTAAAGCGGATTCGGCTTTA
CCTGATGAGCTAGACGAGGAGTTTGATGGGTTCCCGAGTGGGAAATCTGCAGATTTGGTGAAGAAAAGGTATGATAGGTT
AAGAGGAATCGCAGGGAGGATGATGATGGTTTTAGGAGACTTGGCTACTCAGGGAGAGAGAGTTAAGAATCTGTTGAGCT
GGAGAGATCCTAGGGCAACGTTTCTGTTTTCGATGTTTTGTTTGGTTGCTTGTGGAGTGATCTTCTTAATCTCCATGAAA
CTGCTGATGACTTTGCTTGCCTTCTACGTCATGAGACACCCTAGGCTCAGGATTTTTGATATTCCTTCGGTTCCTCAAAA
CTTCTTTAGGAGATTGCCTTCAAGAGCTGATAGTATGTTGTGA

Alignment

ORF - retro_brap_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.79 %
• Parental protein coverage: 70.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SVDPFVEVKVGNYKGITRH-FEKRQHPEWNQVFAFAKERMQASVLEVVVKDKDLLKDDYVGFVRFDINDI
          S.D.F.EV..G.YKG.T.........PE...VFAF.K.R.Q..VL.V.VK..........G...F....I
Retrocopy SNDSFIEVTIGSYKGRTKNNTNPNPNPEFHEVFAFNKDRLQGNVLDVAVKANE---EVIIGKCKFEVAEI

Parental  PLRVPPDSPLAPQWYRLEDKKGEKIKGELMLAVWIGTQADEAFSDAWHSDAAMPVDCSPAISAVLRSKVY
          P.RVPPDSPLAPQWYRLED..G....GE.ML.VW.GTQADE.F..AWHSD....V....A..A..RSKVY
Retrocopy PTRVPPDSPLAPQWYRLEDINGNRFGGEVMLSVWMGTQADEVFPEAWHSD-CVTVNGDNAVIA--RSKVY

Parental  HAPRLWYVRVNVVEAQDLVPTEKHRF-PDVYVKAQLGNQVMKTRPCQARTLGAVWNEDFLFVAAEPFEDH
          ..PRLWY.RVN..EAQDLVP....R..P...VK..LGN.V...R..Q.RTL..VWNED..FVA.EPFED.
Retrocopy LSPRLWYLRVNIIEAQDLVPLQGNRTNPEILVKGFLGNIVVRSRVSQTRTLSPVWNEDMMFVAVEPFEDS

Parental  LVLTVEDRVAPGKDEILGRTYIPLNTVEKRADDHMIHSRWYNLERPVIVDVDQLKREKFSMRIHLRVCLE
          L.L..E........E.LG...I.L..VE.R.........WYNLER.V...V.Q........R..L.....
Retrocopy LILSLECKLGQ-NEECLGKCEIKLSQVERRVMPDTVPAMWYNLER-VVDSVVQGFAGRIHLRVSL----D

Parental  GGYHVLDESTHYSSDLRPSARPLWRQPIGVLELGILNAVGLHPMKTREGRGTSDTFCVAKYGQKWVRTRT
          GGYHVLDES..YSSD.R.SA..LW...IGVLELG...A.GL.PMK.REGRGT.D..CVAKYGQKWVRTRT
Retrocopy GGYHVLDESIQYSSDYRASAKILWTPAIGVLELGVISASGLMPMKSREGRGTTDAYCVAKYGQKWVRTRT

Parental  MVDNLCPKYNEQYTWEVFDPATVLTVGVFDNGQLSEKGN----RDVKIGKIRIRLSTLETGRIYTHSYPL
          .VD...PK.NEQYTWEV.DP.TV.T.GVFDN..L...GN....RD..IGKIRIRLSTLET.RIYTHSYPL
Retrocopy IVDTFSPKWNEQYTWEVYDPYTVITIGVFDNMHLLVPGNTNGPRDSRIGKIRIRLSTLETERIYTHSYPL

Parental  LVLHPSGVKKMGELHMAVRFTCVSFANMLYQYSKPLLPKMHYVRPFSVMQQDMLRHQAVNIVAARLGRAE
          .VL.P.GVKKMGE...AVRF.C.S...ML..YS.PLLP.MHY..P.S..Q.D.LRHQA..I....LGR.E
Retrocopy IVLKPDGVKKMGEIQLAVRFSCTSTIDMLQKYSEPLLPMMHYLTPLSIYQLDSLRHQATHILCMNLGRTE

Parental  PPLRKEIIEFMSDTDSHLWSMRKSKANFFRMMTVFSGVIAVGKWFSDICSWRNPITTVLVHVLFLMLVCL
          PPL.....E.M.D..S..WS.R...ANF.R..T.F........WF...C.W..P.TT.L.H..FL..V.L
Retrocopy PPLGRDVVEYMLDFGSNIWSIRRGRANFERLVTFFTAFLDAWVWFDSVCKWKSPVTTILAHFIFLFIVFL

Parental  PELILPTMFLYMFLIGLWNYRFRPRYPPHMNTKISQAEAVHADELDEEFDTFPTTRNPALVRLRYDRLRS
          P........LY.F.IG...YR.RPR.PPHM..K.S.A.....DELDEEFD.FP......LV..RYDRLR.
Retrocopy PKYCVTSLLLYCFVIGFYRYRLRPRHPPHMDIKLSKADSALPDELDEEFDGFPSGKSADLVKKRYDRLRG

Parental  VAGRIQTVIGDLATQGERFQALLSWRDPRATAIYVIFCFLAAMVFFITPIQIVVALAGFYMMRHPRFR-H
          .AGR...V.GDLATQGER...LLSWRDPRAT.....FC..A..V.F.........L..FY.MRHPR.R..
Retrocopy IAGRMMMVLGDLATQGERVKNLLSWRDPRATFLFSMFCLVACGVIFLISMKLLMTLLAFYVMRHPRLRIF

Parental  RLPSVPVNFFRRLPARTDSML
          ..PSVP.NFFRRLP.R.DSML
Retrocopy DIPSVPQNFFRRLPSRADSML

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_34 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Brassica rapa	Bra035212	1 retrocopy	retro_brap_34 ,