RetrogeneDB ID: | retro_ogla_54 | ||
Retrocopy location | Organism: | African rice (Oryza glaberrima) | |
| Coordinates: | 11:11771141..11772881(+) | ||
| 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: | ORGLA03G0062000 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_ogla_54
CCACCAAGCCGTGTGCTTGATAACGCATTGCTGGAGAGCATTCTCCAGTACCTCACGACGGCGCGTGATCGGAACACAGC
ATCACTTGTTTGCCGCTACTGGTACCACGCTGAGGCGGATACACGTCGCAAGCTCTCCATTGGTAACTGTTACGCCATCT
CACCAAGCCATGTCATCGAGCGTTTCCAGGGGCTGAGATCCATCACCCTGAAGGGAAAGCCACGCTTAGCGAACTTCATT
TACTTGCCAAAAGGCTGGGGTGCATATGCATCGCCTTGGGTGGCCGCTTTTGGGCCTGCATACCCGCACCTTGAGTGCAT
CTTCCTCAAGAGGATGACAGTCTTGGACAACGACCTCAGGCTTATTGCACAGTCATTCCCGCAGTTGAAGGAGCTCTCAC
TGATGAACTGCAACAAGTTCACTGCCACCGGCCTCGCTATCATTGCGGAGCAGTGCAAGCATCTCCACGTTCTTGATCTG
ATTAATGACCAAATTGAGGACACAGCAGACGAGCAAGTGGACTGGATCTCTATGTTTCCCCAGCCCAACACACTACTAGA
GTCTCTTGTATTCAGTTGTGTTGACAAGCCCTGCAACTTTGAGTCACTGGAGGCCCTTGTTGCGCGCTCACCGGGTCTAT
GCCGGCTGCGTGTGAATCATCATGTGACAGTGGAGCAGCTGCGCCGCCTCATAGCAATCGCTCCCAATCTCACGCACCTT
GGCACCGGAGTGTTCCGGTCCAAGACTGGTTACCAGACAGGTGAGGCCCCTCCAACGGTGTTTGAACTTGCGACATCTTT
CGCAGCATGCAAGTCACTCATCTCCCTCTCGGGTTTCCAGGATGCCAATCCAGAGTACCTACCTGCGATTTACCCAGTTT
GTGCCAATCTCACATCCCTCAACTTAGGATCTGTGAACATAACAGAGCAACAGCTCACGCCCATCATTCGCCGGTGCAGG
AATCTTCGGACATTTTGTGTTTGCGGCACCGTTGGTGACGATGGCCTTTGTGCTGTGGCTGAGACGTGCTCGGATCTCAG
GCAGCTAAAAGTGTATCCTTTGTTTACTGGGAGTGACTCTGATCTCTCAGTATCAGATGTTGGCCTTGAAGCGATCTCGA
AAGGCTGCCAGAAGCTTGAAACCCTAATATACTATTGTGGAAGCATGACAAATGAGGCAATGATCATTATGTCCAACAAC
TGCCCACACCTTAGAGTCTTCCGCCTCTGCATTTTGAGAACCCACCTCCCAGATAGGATCACCGGGGAACCGATGGATGA
AGGTTTTGGAGCAATTGTGATGAATTGTAAGAAGCTTTCTAGGCTTTCGACCTCTGGTCTGGTCACTGACAAGGCATTTG
CGTACATTGGACAATACGGGAAATCGATCAAAACTCTGTCTGTTGCCTTCTCTGGAAATACTGACATGTCACTCAGATAT
GTGTTTGAAGGATGCACTCAGTTGCAGAAACTTGAGGTCCAGGAATGCCCTTTTGGTGATGAAGGATTGCTGTCTGGTTT
AAGCCATTTTTGCAACATGAGGTTCTTGTGGATGAGCTCTTGCAGAGTAACCATGACAGGCTGTAAATATGTAGCTCAGC
AAATGCCAAATTTGGTGGCTGAAGTGATTAGTGGCCATTCCGGTAATGAAGATGTGACTGCCGATACTGTGGACCATCTG
TATTTATATCGATCTCTTGCAGGACCAAGGGATGACGCCCCTTCATTTGTCAAAATCTTG
ORF - retro_ogla_54 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 52.05 % |
| Parental protein coverage: | 96.35 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | PPDQVLDN-VLETVLQFLDSARDRCAASLVCRSWSRAESATRASVAVRNLLAASPARVARRFPAARRVLL |
| PP..VLDN..LE..LQ.L..ARDR..ASLVCR.W..AE..TR......N..A.SP..V..RF...R...L | |
| Retrocopy | PPSRVLDNALLESILQYLTTARDRNTASLVCRYWYHAEADTRRKLSIGNCYAISPSHVIERFQGLRSITL |
| Parental | KGRPRFADFNLLPPGWAGADFRPWAAAVAAAAFPALASLFLKRITVTDDDLDLVSRSLPASFRDLSLLLC |
| KG.PR.A.F..LP.GW.GA...PW.AA...A..P.L...FLKR.TV.D.DL.L...S.P.....LSL..C | |
| Retrocopy | KGKPRLANFIYLPKGW-GAYASPWVAAFGPA-YPHLECIFLKRMTVLDNDLRLIAQSFP-QLKELSLMNC |
| Parental | DGFSSAGLASIASHCRGLRVLDVVDCEMNDDDDEVVDWVAAFPPGTTDLESLSFECYVRPVSFAALEALV |
| ..F...GLA.IA..C..L.VLD.......D..DE.VDW...FP...T.LESL.F.C...P..F..LEALV | |
| Retrocopy | NKFTATGLAIIAEQCKHLHVLDLINDQIEDTADEQVDWISMFPQPNTLLESLVFSCVDKPCNFESLEALV |
| Parental | ARSPRLTRLGVNEHVSLGQLRRLMANTPRLTHLGTGAFRPGDGPE--DVGLDIEQMASAFASAGRTNTLV |
| ARSP.L.RL.VN.HV...QLRRL.A..P.LTHLGTG.FR...G.............A..FA.......L. | |
| Retrocopy | ARSPGLCRLRVNHHVTVEQLRRLIAIAPNLTHLGTGVFRSKTGYQTGEAPPTVFELATSFAAC---KSLI |
| Parental | SLSGFREFEPEYLPTIAAVSGNLTNLDFSYCPVTPDQFLPFIGQCHNLERLYVLDSVRDEGLQATARTCK |
| SLSGF....PEYLP.I..V..NLT.L.......T..Q..P.I..C.NL....V...V.D.GL.A.A.TC. | |
| Retrocopy | SLSGFQDANPEYLPAIYPVCANLTSLNLGSVNITEQQLTPIIRRCRNLRTFCVCGTVGDDGLCAVAETCS |
| Parental | KLQVLHVLPLNALEDADELVSEVGLTAIAEGCRGLRSTLYFCQSMTNAAVIAISQNCVDLKVFRLCIMGR |
| .L..L.V.PL....D.D..VS.VGL.AI..GC..L....Y.C.SMTN.A.I..S.NC..L.VFRLCI... | |
| Retrocopy | DLRQLKVYPLFTGSDSDLSVSDVGLEAISKGCQKLETLIYYCGSMTNEAMIIMSNNCPHLRVFRLCILRT |
| Parental | HQPDHVTGEPMDEGFGAIVRNCSKLTRLSTSGHLTDRAFEYIGKYAKSLRTLSVAFAGDSNLALQHILQG |
| H.PD..TGEPMDEGFGAIV.NC.KL.RLSTSG..TD.AF.YIG.Y.KS..TLSVAF.G.....L.....G | |
| Retrocopy | HLPDRITGEPMDEGFGAIVMNCKKLSRLSTSGLVTDKAFAYIGQYGKSIKTLSVAFSGNTDMSLRYVFEG |
| Parental | CSKLEKLEIRDCPFGDAGLLSGMHHFYNMRFLWMSGCNLTLQGCKEVARRLPRLVVELINSQPENE--RT |
| C..L.KLE...CPFGD.GLLSG..HF.NMRFLWMS.C..T..GCK.VA...P.LV.E.I.....NE.... | |
| Retrocopy | CTQLQKLEVQECPFGDEGLLSGLSHFCNMRFLWMSSCRVTMTGCKYVAQQMPNLVAEVISGHSGNEDVTA |
| Parental | DGVDILYMYRSLEGPREDVPPFVKIL |
| D.VD.LY.YRSL.GPR.D.P.FVKIL | |
| Retrocopy | DTVDHLYLYRSLAGPRDDAPSFVKIL |
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_54 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 | ORGLA03G0062000 | 1 retrocopy |
retro_ogla_54 ,
|