RetrogeneDB ID: | retro_ogla_2 | ||
Retrocopy location | Organism: | African rice (Oryza glaberrima) | |
| Coordinates: | 1:17932438..17934706(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ORGLA01G0190900 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ORGLA03G0313900 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ogla_2
ATGGGCGAGGGCGAGTTCGTCGACGTCGAGCGCGGCGTGGTCGCTGAGGGGGCGTTGGACGACGACGCGTCGCCGATCGA
GGAGGTCCGGCTGACGGTTCCGGTCACTGACGACCCGTCCCTTCCGGTGTGGACGTTCCGGATGTGGACACTCGGCCTGC
TCTCGTGCGTGCTCATCAGCTTCCTGAACCAGTTCTTCTCCTACCGCACCGAGCCGCTCATCGTCACCCAGATCACCGTG
CAGGTGGCCTCGCTGCCTCTGGGCCACATCCTCGCCCGCGTGCTGCCGCGCCGCAAGTTCAAGGCCCCCGCGCTGCTCGG
CGGCGGGGAGTGCAGCCTCAACCCGGGGCCCTTCAACATGAAGGAGCACGTGCTCGTCTCCATCTTCGCCAACGCCGGCT
GCGCCTTCGGCAGCGGGTCCGCCTACGCCGTCATGATCGTCGACATCATCCGCGCCTTCTACGGGCGGTCCATCTCCCTC
TTCCCCGCATGGCTCCTCATCACTACCACGCAGGTGCTCGGCTACGGGTGGGCGGGGCTGATGCGCAAGTACGTGGTGGA
GCCGGCGCAAATGTGGTGGCCCGGCACGCTCGTGCAGGTGTCGCTGTTCAGGGCGCTGCACGGGAAGGGGGAAGAGAAGG
AGGAGAATAAGGAGGGCAGCGGCGGCGGGATGTCTCAGGCCAAGTTCTTCCTGATCGCGCTCGCCTGCAGCTTCCTGTGG
TACGCCGTGCCGGGTTACCTGTTCCCGACGCTGACCTCCGTCTCGTGGGTCTGCTGGATCTTCTCCAAGTCCGTCACCGC
GCAGCAGCTGGGCTCCGGCATGAAGGGCCTGGGCCTCGGCGCCTTCACCCTCGACTGGACGGCCGTGTCAGCCTTCCTGT
ACAGCCCGCTGATCTCGCCGTTCTTTGCCACCGCCAACATCTTGGCCGGCTACGTGCTCCTGATGTACGTGGTCGTGCCG
GTGTCGTACTGGGGCCTCGACCTGTACAACGCCCGGAGGTTCCCCATCTTCTCGTCGCACCTGTTCACGGCCACCGGCAG
CACATACGACATCACGGCCATCGTGAACGACCGCTTCGAGATCGACATGGACGGGTACCATCGGATGGGGCGGATCAACA
TGAGCACGTTCTTCGCGCTGTCCTACGGGCTCGGCTTCGCGACGATCGCGGCCACCGTCACGCACGTGGCGCTGTTCCAC
GGGAAGGAGATCTACCGCCGGTTCCGCGCGTCGCAGAGGGACAAGCCCGACGTGCACACGAGGCTGATGAAGAGCTACCG
CGACGTGCCGAGCTGGTGGTTCTACGCGATGCTCGCGCTGTCCATGGCCGTCTCGCTCTTTCTCTGCACCGTCCTCAGGT
CGGCGGTGCAGCTCCCGTGGTGGGGTCTCCTCTTCGCCTGCGCCATGGCCTTCGTGTTCACGCTGCCGATCAGCATCATC
ACGGCCACGACCAACCAGACGCCGGGGCTCAACATCATCACCGAGTACGTCATCGGGCTCATGCTTCCGGGCAAGCCCAT
CGCCAACGTCTGCTTCAAGGCGTACGGCTACATGAGCATGTCGCAGGCCGTGTCCTTCCTGTCCGACTTCAAGCTCGGCC
ACTACATGAAGATACCCCCCAAGTCCATGTTCCTCGTGCAGTTGGTCGGCACGGTGGTCGCCTCCACGGTCAACCTCGTG
GTGGCGTACTGGCTGCTGGGTTCCATCCCCAACATCTGCCAGGACGCGCTCCTCCCGGCGGATAGCCCGTGGACGTGCCC
GAACGACCGCGTCTTCTTCGACGCGTCCGTCATCTGGGGCCTCGTCGGGCCGCGCCGCATCTTCGGGCCACTCGGCAACT
ACGGCGCGCTCAATTGGTTCTTCCTCGCTGGCGCCGTGGGACCCGTCATTGTGTACTTGCTCCACAGGGCGTTCCCCAGC
AAGACCTGGATACCGATGATCAACCTGCCGGTGCTCATCGGAGCGACCTCCTACATGCCGCCGGCAACGGCCGTGAACTA
CAACTCCTGGCTGATCATCGGGATCATCTTCAACTTCTTCGTTTTCCGGTACAGGAAGCTGTGGTGGAAGAGGTACAACT
ACATCCTCTCGGCTGCGCTCGACGCCGGCGTCGCGTTCATGGCGGTGCTGCTCTACTTCTCGCTGTCGATGGAGAACCGG
AGCATCAGCTGGTGGGGTACGGCCGGCGAGCACTGCCCGCTGGCCTCATGCCCTACCGCCAAAGGGATAAACTTGGGCGC
TGATAGCGTCTGCCCTGTTGTGTTATAA
ORF - retro_ogla_2 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 55.48 % |
| Parental protein coverage: | 96.7 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | EGERCPVEEVALVVPETDDPTTPVMTFRAWTLGLASCVVLIFLNTFFTYRTQPLTISGILAQILVLPAGQ |
| .....P.EEV.L.VP.TDDP..PV.TFR.WTLGL.SCV...FLN.FF.YRT.PL....I..Q...LP.G. | |
| Retrocopy | DDDASPIEEVRLTVPVTDDPSLPVWTFRMWTLGLLSCVLISFLNQFFSYRTEPLIVTQITVQVASLPLGH |
| Parental | FMAAVLPSREVR---LLGGRLGSFNLNPGPFNIKEHVIITIFANCGVSYGGGDAYSIGAITVMKAYYKQS |
| ..A.VLP.R......LLGG..G...LNPGPFN.KEHV...IFAN.G...G.G.AY.........A.Y..S | |
| Retrocopy | ILARVLPRRKFKAPALLGG--GECSLNPGPFNMKEHVLVSIFANAGCAFGSGSAYAVMIVDIIRAFYGRS |
| Parental | LSFLCALLIVLTTQILGYGWAGMLRRYLVDPADMWWPSNLAQVSLFRALHEK-EGGDGGKGSSSRGPTRM |
| .S...A.L...TTQ.LGYGWAG..R.Y.V.PA.MWWP..L.QVSLFRALH.K.E.....K..S..G.... | |
| Retrocopy | ISLFPAWLLITTTQVLGYGWAGLMRKYVVEPAQMWWPGTLVQVSLFRALHGKGEEKEENKEGSGGGMSQA |
| Parental | RFFLIFFFASFAYYALPGYLLPILTFFSWACWAWPHSITAQQVGSGYHGLGVGAFTLDWAGISAYHGSPL |
| .FFLI....SF..YA.PGYL.P.LT..SW.CW....S.TAQQ.GSG..GLG.GAFTLDW...SA...SPL | |
| Retrocopy | KFFLIALACSFLWYAVPGYLFPTLTSVSWVCWIFSKSVTAQQLGSGMKGLGLGAFTLDWTAVSAFLYSPL |
| Parental | VAPWSSIANTAAGFVMFIYLIVPLCYWKFDTFDARKFPIFSNQLFTASGQKYDTTKVLTREFDLNVAAYE |
| ..P....AN..AG.V...Y..VP..YW..D...AR.FPIFS..LFTA.G..YD.T......F......Y. | |
| Retrocopy | ISPFFATANILAGYVLLMYVVVPVSYWGLDLYNARRFPIFSSHLFTATGSTYDITAIVNDRFEIDMDGYH |
| Parental | SYGKLYLSPLFAISIGSGFLRFTATIVHVALFHGGDIWRQSRSAMSSAAAKMDVHAKLMRRYKQVPQWWF |
| ..G....S..FA.S.G.GF....AT..HVALFHG..I.R..R........K.DVH..LM..Y..VP.WWF | |
| Retrocopy | RMGRINMSTFFALSYGLGFATIAATVTHVALFHGKEIYRRFRASQRD---KPDVHTRLMKSYRDVPSWWF |
| Parental | LVLLVGSVAVSLVMSFVYREEVQLPWWGMLFAFALAFVVTLPIGVIQATTNQQPGYDIIAQFMIGYALPG |
| ...L..S.AVSL....V.R..VQLPWWG.LFA.A.AFV.TLPI..I.ATTNQ.PG..II....IG..LPG | |
| Retrocopy | YAMLALSMAVSLFLCTVLRSAVQLPWWGLLFACAMAFVFTLPISIITATTNQTPGLNIITEYVIGLMLPG |
| Parental | KPIANLLFKIYGRISTVHALSFLADLKLGHYMKIPPRCMYTAQLVGTVVAGVVNLAVAWWMLGSIDNICD |
| KPIAN..FK.YG..S...A.SFL.D.KLGHYMKIPP..M...QLVGTVVA..VNL.VA.W.LGSI.NIC. | |
| Retrocopy | KPIANVCFKAYGYMSMSQAVSFLSDFKLGHYMKIPPKSMFLVQLVGTVVASTVNLVVAYWLLGSIPNICQ |
| Parental | VEALHPDSPWTCPKYRVTFDASVIWGLIGPARLFGRHGLYRNLVWLFLAGAVLPVPVWLLSRAFPEKKWI |
| ...L..DSPWTCP..RV.FDASVIWGL.GP.R.FG..G.Y..L.W.FLAGAV.PV.V.LL.RAFP.K.WI | |
| Retrocopy | DALLPADSPWTCPNDRVFFDASVIWGLVGPRRIFGPLGNYGALNWFFLAGAVGPVIVYLLHRAFPSKTWI |
| Parental | ALINVPVISYGFAGMPPATPTNIASWLVTGTIFNYFVFKYRKGWWQKYNYVLSAALDAGTAFMGVLIFFA |
| ..IN.PV.......MPPAT..N..SWL..G.IFN.FVF.YRK.WW..YNY.LSAALDAG.AFM.VL..F. | |
| Retrocopy | PMINLPVLIGATSYMPPATAVNYNSWLIIGIIFNFFVFRYRKLWWKRYNYILSAALDAGVAFMAVLLYFS |
| Parental | LQNAHHELKWWGTAVDHCPLASCPTAPGI---AVKGCPV |
| L........WWGTA..HCPLASCPTA.GI...A...CPV | |
| Retrocopy | LSMENRSISWWGTAGEHCPLASCPTAKGINLGADSVCPV |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Oryza glaberrima was not studied using RNA-Seq expression data.
Oryza glaberrima was not studied using ChIP-Seq data.
Oryza glaberrima was not studied using EST data.
Oryza glaberrima was not studied using FANTOM5 data.
retro_ogla_2 was not experimentally validated.
Retrocopy orthology:
Oryza glaberrima 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 glaberrima | ORGLA03G0313900 | 1 retrocopy |
retro_ogla_2 ,
|