RetrogeneDB ID: | retro_oind_100 | ||
Retrocopy location | Organism: | Rice subsp. indica (Oryza sativa indica) | |
| Coordinates: | AAAA02043581.1:1153..3504(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | BGIOSGA012917 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_oind_100
ATTCAGAGTTTTCCAAAAGTTTCAGGAGGCGATGTTATGCTTTCGAGAGATGCAAATAAAGCTTTGAACGAAGCAGAAAT
TATTGCACAAAAAATGAACGACGAATACGTTTCGATCGAGCATTTAATCTTGGCTATTTTTGATTCAAAAAGTAAAGTTT
CTCAAATTTTAAAAGATCAGGGAGTTACAGGAAAAGGTCTGAAAGCAGCAATCGAAGAACTTCGTAAAGGAGAGAGAGTA
ACTTCTGCTTCTGCCGAAGAAACCTATAACTCATTAAATAAATACGCTAAAAATCTAAACGAATTAGCACGTACAGGAAA
ATTAGACCCGGTTATTGGCCGTGACGAAGAAATTCGTCGTGTATTACAAATTTTAACTCGTCGAACTAAAAACAACCCAA
TGCTTATTGGTGAACCAGGAGTTGGTAAAACCGCCATTGCAGAAGGTTTAGCACATAGAATTGTGGATGGAGACGTTCCT
GAAAACCTGAAAGATAAAATCGTTTTCTCTTTAGATATGGGAGCTTTGATTGCCGGAGCAAAATATAAAGGAGAATTTGA
AGAACGTTTAAAATCGGTTGTAAAAGAAGTTACAGCTGCAGAAGGTGATATCGTATTGTTTATTGACGAAATTCACACGC
TTGTAGGTGCAGGTGGAGGAGAAGGTGCAATGGATGCGGCTAATATCTTGAAACCAGCTTTGGCGCGTGGAGAATTAAGA
GCTATTGGTGCTACAACCCTAGATGAATATCAAAAGTATTTTGAAAAAGACAAAGCGCTTGAAAGACGTTTTCAAAAAGT
ACTAATCGATGAACCGGATACTGAAAGTGCTATTTCAATTTTACGTGGTATCAAAGAAAAATACGAAACGCACCATAAAG
TTCAGATTAAAGACGAAGCAATTATTGCGGCTGTTGAACTTTCGCAAAGATATATTACCAATCGTAGATTACCAGATAAA
GCGATTGATTTAATGGACGAAGCGGCTTCTAAACTGCGTATGGAAATCAATTCAAAACCTGAAGAATTAGATGTTTGGAT
CGTAAAATCATGCAGCTTGAAATCGAAATCGAAGCGATTAAACGTGAAAAAGAAGAAAGTAAGCTGAAAATTTTAGGTAT
GGAATTGGCCAACCTTAAAGAAGAGCGAAACGAAATCTATGCAAAATGGAAACAGGAAAAAGATATCGTTGACGGAATTC
AGGCTGTAAAACACGAAATCGAAGACTTTAAATACGAAGCAGAACGCGCAGAACGTGACGGTGATTACGGAAAAGTAGCC
GAAATTCGTTATGGTAAAATAAAAGAAGCACAAGAACGTCAGGAAACTTTGCAAAAGCAGTTATTGGAATTTCAATCTGG
TAATTCTTTAATTAAAGAAGAAGTTACAAGAGAAGATATTGCCGAAGTTGTAGCAAAATGGACTGGAATACCAGTAACCA
AAATGCTTCAGACAGAAAGAGAAAAACTATTGCATCTTGAAGATGAATTACACAAACGTGTAGTTGGTCAGGAAGAAGCG
ATTGAAGCCGTGAGTGATGCCGTTCGCAGAAGCCGTGCCGGCTTACAGGATATGAAAAAACCTGTTGGATCTTTCTTATT
CTTAGGAACAACCGGAGTTGGTAAAACGGAGCTGGCAAAAGCCTTAGCCGAATATCTTTTCGATGACGAAAATGCGATGA
CTCGTATCGATATGAGCGAATATCAGGAACGTCATAGTGTGAGCCGTTTGGTTGGTGCACCTCCAGGATATGTAGGTTAT
GATGAAGGAGGTCAGTTAACAGAAGCTGTTCGTAGAAAACCTTATTCTGTTGTACTTTTAGACGAGATCGAAAAAGCACA
TCCGGATACTTTCAATATTTTATTGCAGGTTCTGGACGAAGGACGTTTAACAGATAATAAAGGACGTTTGGCCGATTTTA
GAAATACGATTATTATTATGACCTCAAATATGGGAAGTAATATTATTCAGGAGAAATTTGAAAACCTAAAAGGAAGCGTT
GAGGCAGCAACTGAAGCCGCTAAAAACGAAGTTTTAGGATTATTAAAGCAAACTGTTCGTCCTGAGTTTATCAACCGTAT
CGATGAGATTGTAATGTTTACACCGCTTACTGTAGAAAATATTTCAAGAATTGTAAGTTTACAGTTAAAGAGTGTTACTA
AAATGCTGGCTCTGCAAGGTATTACAATGGATGCGACTCCAGAAGCGATTGCTTATCTGGCAGATAAAGGTTACGACCCT
CATTTTGGAGCGAGACCTGTAAAACGTGTAGTTCAGAGAGAAGTCTTAAATCAATTGTCAAAAGAAATTCTGGCAGGGAA
TATTACAACAGATAGTATTATCTTATTAGAT
ORF - retro_oind_100 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 55.5 % |
| Parental protein coverage: | 81.85 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | IQRQPKVLGEDPGSMLGRDLEALIQRARDFKKEYGDSFVSVEHLVLGFAEDKRFGRQLFKDFQITVQSLK |
| IQ..PKV.G.D...ML.RD.......A........D..VS.EHL.L.....K....Q..KD...T...LK | |
| Retrocopy | IQSFPKVSGGDV--MLSRDANKALNEAEIIAQKMNDEYVSIEHLILAIFDSKSKVSQILKDQGVTGKGLK |
| Parental | TAIESIRGKQNVIDQDPEGKYEALDKYGKDLTAMARQGKLDPVIGRDDEIRRCIQILSRRTKNNPVLIGE |
| .AIE..R....V.....E..Y..L.KY.K.L...AR.GKLDPVIGRD.EIRR..QIL.RRTKNNP.LIGE | |
| Retrocopy | AAIEELRKGERVTSASAEETYNSLNKYAKNLNELARTGKLDPVIGRDEEIRRVLQILTRRTKNNPMLIGE |
| Parental | PGVGKTAIAEGLAQRIVQGDVPQALTNRRLIALDMGALIAGAKYRGEFEDRLKAVLKEVTDSDGQTILFI |
| PGVGKTAIAEGLA.RIV.GDVP..L.......LDMGALIAGAKY.GEFE.RLK.V.KEVT...G...LFI | |
| Retrocopy | PGVGKTAIAEGLAHRIVDGDVPENLKDKIVFSLDMGALIAGAKYKGEFEERLKSVVKEVTAAEGDIVLFI |
| Parental | DEIHTVVGAGATNGAMDAGNLLKPMLGRGELRCIGATTLDEYRKYIEKDPALERRFQQVYVDQPSVEDTI |
| DEIHT.VGAG...GAMDA.N.LKP.L.RGELR.IGATTLDEY.KY.EKD.ALERRFQ.V..D.P..E..I | |
| Retrocopy | DEIHTLVGAGGGEGAMDAANILKPALARGELRAIGATTLDEYQKYFEKDKALERRFQKVLIDEPDTESAI |
| Parental | SILRGLRERYELHHGVRISDSALVAAALLSDRYISGRFLPDKAIDLVDESAAKLKMEITSKPTALDE-ID |
| SILRG..E.YE.HH.V.I.D.A..AA..LS.RYI..R.LPDKAIDL.DE.A.KL.MEI.SKP..LD...D | |
| Retrocopy | SILRGIKEKYETHHKVQIKDEAIIAAVELSQRYITNRRLPDKAIDLMDEAASKLRMEINSKPEELDV<LD |
| Parental | RAVIKLEMERLSLTNDTDKASRDRLSRIEAELSLLKEKQKDLTEQWEREKSVMTKIQSIKEEIDRVNVEI |
| R....LE.E...............L.....EL..LKE........W..EK.....IQ..K.EI.....E. | |
| Retrocopy | RKIMQLEIEIEAIKREKEES---KLKILGMELANLKEERNEIYAKWKQEKDIVDGIQAVKHEIEDFKYEA |
| Parental | QQAEREYDLNRAAELKYGSLNALQRQLQTTEKELDEYQSSGKSMLREEVTQDDIAEIVSRWTGIPVSKLK |
| ..AER..D....AE..YG.....Q....T..K.L.E.Q.SG.S...EEVT..DIAE.V..WTGIPV.K.. | |
| Retrocopy | ERAERDGDYGKVAEIRYGKIKEAQERQETLQKQLLEFQ-SGNSLIKEEVTREDIAEVVAKWTGIPVTKML |
| Parental | QSDREKLLYLEEELHKRVVGQDPAVKAVSEAIQRSRAGLSDPNRPIASFMFMGPTGVGKTELAKALAAFM |
| Q..REKLL.LE.ELHKRVVGQ..A..AVS.A..RSRAGL.D...P..SF.F.G.TGVGKTELAKALA... | |
| Retrocopy | QTEREKLLHLEDELHKRVVGQEEAIEAVSDAVRRSRAGLQDMKKPVGSFLFLGTTGVGKTELAKALAEYL |
| Parental | FNTEEAVVRIDMSEYMEKHSVSRLIGAPPGYVGYEEGGQLTEAVRRRPYSIILFDEIEKAHGDVFNVFLQ |
| F..E.A..RIDMSEY.E.HSVSRL.GAPPGYVGY.EGGQLTEAVRR.PYS..L.DEIEKAH.D.FN..LQ | |
| Retrocopy | FDDENAMTRIDMSEYQERHSVSRLVGAPPGYVGYDEGGQLTEAVRRKPYSVVLLDEIEKAHPDTFNILLQ |
| Parental | ILDDGRVTDSQGRKVSFTNSIIIMTSNVGSQFILNMDEE-GGSTDSAYENIKKRVMDAARSVFRPEFMNR |
| .LD.GR.TD..GR...F.N.IIIMTSN.GS..I....E...GS...A.E..K..V........RPEF.NR | |
| Retrocopy | VLDEGRLTDNKGRLADFRNTIIIMTSNMGSNIIQEKFENLKGSVEAATEAAKNEVLGLLKQTVRPEFINR |
| Parental | IDEYIVFKPLEREQINSIVKLQLARVQKRIADRKIKLEVSPGAVEFLGSLGYDPNYGARPVKRVIQQYVE |
| IDE...F.PL..E.I..IV.LQL..V.K..A...I.....P.A...L...GYDP..GARPVKRV.Q..V. | |
| Retrocopy | IDEIVMFTPLTVENISRIVSLQLKSVTKMLALQGITMDATPEAIAYLADKGYDPHFGARPVKRVVQREVL |
| Parental | NELAKGILRGDFKDEDSILVD |
| N.L.K.IL.G.......IL.D | |
| Retrocopy | NQLSKEILAGNITTDSIILLD |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Oryza sativa indica was not studied using RNA-Seq expression data.
Oryza sativa indica was not studied using ChIP-Seq data.
Oryza sativa indica was not studied using EST data.
Oryza sativa indica was not studied using FANTOM5 data.
retro_oind_100 was not experimentally validated.
Retrocopy orthology:
Oryza sativa indica 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 | |
|---|---|---|---|
| Oryza sativa indica | BGIOSGA012917 | 1 retrocopy |
retro_oind_100 ,
|