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 summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | Bra035212 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>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
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 |
Brassica rapa was not studied using RNA-Seq expression data.
Brassica rapa was not studied using ChIP-Seq data.
Brassica rapa was not studied using EST data.
Brassica rapa was not studied using FANTOM5 data.
retro_brap_34 was not experimentally validated.
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 ,
|