RetrogeneDB ID: retro_ogla_11

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: ADWL01005748.1:1015..2854(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORGLA02G0346900
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA04G0062900
• Aliases: None
• Description: None

Sequence

>retro_ogla_11
ATGGTGAGACGTCTCCTTGTCATTCTCCTCCAAGCTCTGACCGGCCTCCTCGTGATTCTCGCCCTGTGGATCGTCTCCCA
CCTCGCCGGCGACCGTCCGCCGCCGGGGCCGGTGGTCTGCGCCGCCAACGGGACGTCCGGCTGCACGCTGACGAACATCT
ACGGCTCCTTCTCTGACCGCGCCATCTGCCGCGCCGCCAACGTCACGTACCCGCGCACCGAGGTGGAGCTCGTCGCGGCG
GTGGCGGCGGCGGTGGCGGCGGGGCGGAAGGTGAAGGTCGCCACCAGGTACTCCAACAGCTTCCCGCGGCTGGCGTGCCC
CGGCGGCGAGGACGGCACCGTCATCAGCACGCGGTGGCTGGATCGTGCGGTGCGCGTCGACGCAGCGCGGCGGCTGATGA
CGGTGGAGAGCGGCATGGTGATGCGTGACTTGATTAGGGAGGCCGCCGCGGCGGGGCTCGCGCTGCCGCACTCGCCGTAC
TGGTCGGGCCTCACGATCGGCGGCGTGCTCGCCACGGGCGCGCACGGGAGCTCGCTGTGGGGGAAGGGGAGCGCCGTGCA
CGAGTACGTGGTGGGGATGAGGATCGTGACGCCGGCGCCGGCGAGCGAGGGGTTCGCGGCGGTGAGGGAGCTCGCCGCTG
GCGACCCGGACCTCGACGCGGCCAAGGTCTCCCTCGGCGTCCTCGGCGCCATCTCCCAGGTCACCCTCGCGCTGCAGCCG
CTGTTCAAGCGGTCGGTGGCGTTCGTGACCCGCAACGACTCTGACGTCGCCGACACGGTCGCCGCGTGGGGCCGCCTCCA
CGAGTTCGGCGACGTGGCGTGGCTGCCGCGGCGGCGCGTGGCCGTGTACCGCGTGGACGACCGCGTCGACGTCGCGACGC
CCGGCGACGGCCGCAGCGACTACCCGGCGTTCCGGCCGACGCCGACGATACCCCTCGTCGCCAGCAGGCTCGCGGAGGAG
TGGCTGGAGGAGAGATCAGGCAGCGACGCCGCCCGGTGCGCGGCGTCGCGCGTGATGCCGGCGACGCTCGAGCACCTCAA
CTACGGGCTCACCAACGACGGCGAGGCCTTCACGGGGTACCCGGTGGTGGGCTACCAGCACCGCATCCAGGCGTCGAGCT
CGTGCACGGGCGCCATGGAGGACGACGGGCTCATCCCCACCTCCACCTGCCTCTGGAACGGCCGCCTCCGGGGACACCTC
TTCTACAACTCCGGCTTCAGCATCGCGCTGTCGCGCGCGCGGGCGTTCGTCGCCGACGTCGCGCGGCTCCGCGACCTCAA
CCCGGCGGCGTTCTGCCAGATCGACTCCAAGATGGGCCTGCTGATGCGCTACGTCGCGGCCTCGTCGGCGTACCTCGGCA
AGGCGGAGGACTCGGTGGACTTCGACGTCACCTACTACCGGAGCTACGCCCGCGGCGCGCCGCGCGCGCACGCCGACGTG
TTCGACGAGGTCGAGCAGATGGCGCTGCGCAAGCACGGCGGCGTGCCGCACTGGGGCAAGAACCGCAACTACGCCTTCGA
CGGCGCCATCGCCAGGTACCCCAACGCCGGCGAGTTCATGAGGGTGAAGGACAGGTTCGACCCCGACGGCGTCTTCTCCA
GCGAGTGGAGCGACCAGGTGCTCGGCGTCGGCGGGGCGAGCCCGGTCATCGTCGGCGACGGCTGCGCCATGGAGGGGCTC
TGCGTGTGCTCCGACGACTCGCACTGCGCGCCGGAGAAGGGCTACTTCTGCCGGCCGGGGAAGGTGTTCACGGCGGCGAG
GGTGTGCTCGCCGTCGCCGCGAGACGCTGCGAATGGCGGCGACGACGACGACGAAATATCGGACGTTGGCGATGAGTAG

Alignment

ORF - retro_ogla_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.57 %
• Parental protein coverage: 91.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RYIVAIVVEILRGLLVILLLGFVLHLAGGDRHPPPGPIACARGGTSGGCTVTNIYGSFPDRAACRAAGVA
          R....I....L.GLLVIL.L..V.HLAG.DR.PPPGP..CA..GTSG.CT.TNIYGSF.DRA.CRAA.V.
Retrocopy RRLLVILLQALTGLLVILALWIVSHLAG-DR-PPPGPVVCAANGTSG-CTLTNIYGSFSDRAICRAANVT

Parental  YPRTEEELVAAVAAAAAAGRKAKAATRYSNSFPRLACPGGGEGEGGVTISTRWLNRTVRVDAARRLMTVE
          YPRTE.ELVAAVAAA.AAGRK.K.ATRYSNSFPRLACPG...GE.G..ISTRWL.R.VRVDAARRLMTVE
Retrocopy YPRTEVELVAAVAAAVAAGRKVKVATRYSNSFPRLACPG---GEDGTVISTRWLDRAVRVDAARRLMTVE

Parental  GGMVLRDLIREAAAAGLALPHSPYWSGVTVGGALATGAHGSSLWGKGSAVHEYVVGMRIVTPAPASEGFA
          .GMV.RDLIREAAAAGLALPHSPYWSG.T.GG.LATGAHGSSLWGKGSAVHEYVVGMRIVTPAPASEGFA
Retrocopy SGMVMRDLIREAAAAGLALPHSPYWSGLTIGGVLATGAHGSSLWGKGSAVHEYVVGMRIVTPAPASEGFA

Parental  VVRELAADDPDLDAAKVSLGVLGIISQVTLALEPQFKRSVKFVKRDDADIAEKVAVWGRLHEFGDMVWLP
          .VRELAA.DPDLDAAKVSLGVLG.ISQVTLAL.P.FKRSV.FV.R.D.D.A..VA.WGRLHEFGD..WLP
Retrocopy AVRELAAGDPDLDAAKVSLGVLGAISQVTLALQPLFKRSVAFVTRNDSDVADTVAAWGRLHEFGDVAWLP

Parental  GQRQVIYREDNRVNISTPGDGLNDYFGFRAQPTLSMVGARVIDEWLEENPMYTDTARCLASRAVTKMFDL
          ..R...YR.D.RV...TPGDG..DY..FR..PT...V..R...EWLEE.....D.ARC.ASR........
Retrocopy RRRVAVYRVDDRVDVATPGDGRSDYPAFRPTPTIPLVASRLAEEWLEERSG-SDAARCAASRVMPATLEH

Parental  LAYGFTNDGATFTGYPVVGYQHRIQSSGSCMGSLEEKDDGLLLTTTCPWDRRTRGVFAYNVAFTVPLSRA
          L.YG.TNDG..FTGYPVVGYQHRIQ.S.SC.G..E..DDGL..T.TC.W..R.RG...YN..F...LSRA
Retrocopy LNYGLTNDGEAFTGYPVVGYQHRIQASSSCTGAME--DDGLIPTSTCLWNGRLRGHLFYNSGFSIALSRA

Parental  PAFVADVSRLRDLDPAAFCQIDAKMGVLVRYVAASSAYLGKAEDSVDFDVTYYRSRARGAPRAHADVFDE
          .AFVADV.RLRDL.PAAFCQID.KMG.L.RYVAASSAYLGKAEDSVDFDVTYYRS.ARGAPRAHADVFDE
Retrocopy RAFVADVARLRDLNPAAFCQIDSKMGLLMRYVAASSAYLGKAEDSVDFDVTYYRSYARGAPRAHADVFDE

Parental  VEQMALRGHGGVPHWGKNRNAAFDGAIARYPNAGEFLRVKDRFDPEGVFSSEWSDRVLGVGGASPAIVGD
          VEQMALR.HGGVPHWGKNRN.AFDGAIARYPNAGEF.RVKDRFDP.GVFSSEWSD.VLGVGGASP.IVGD
Retrocopy VEQMALRKHGGVPHWGKNRNYAFDGAIARYPNAGEFMRVKDRFDPDGVFSSEWSDQVLGVGGASPVIVGD

Parental  GCAMEGLCVCSDDSHCAPELGYSCRPGKVFTEARVCS-LLRDAADG
          GCAMEGLCVCSDDSHCAPE.GY.CRPGKVFT.ARVCS...RDAA.G
Retrocopy GCAMEGLCVCSDDSHCAPEKGYFCRPGKVFTAARVCSPSPRDAANG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryza glaberrima was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza glaberrima was not studied using ChIP-Seq data.

EST

Oryza glaberrima was not studied using EST data.

TSS

Oryza glaberrima was not studied using FANTOM5 data.

Lab

retro_ogla_11 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA015276	1 retrocopy	retro_oind_24,
Oryza glaberrima	ORGLA04G0062900	1 retrocopy	retro_ogla_11 ,