RetrogeneDB ID: retro_oind_24

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 4:14763808..14765647(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA016194
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA015276
• Aliases: None
• Description: None

Sequence

>retro_oind_24
ATGGTGAGACGTCTCCTTGTCATTCTCCTCCAAGCTCTGACCGGCCTCCTCGTGATTCTCGCCCTGTGGATCGTCTCCCA
CCTCGCCGGCGACCGTCCGCCGCCGGGGCCGGTGGTCTGCGCCGCCAACGGGACGTCCGGCTGCACGCTGACGAACATCT
ACGGCTCCTTCTCCGACCGCGCCATCTGCCGCGCCGCCAACGTCACGTACCCGCGCACCGAGGAGGAGCTCGTCGCGGCC
GTGGCGGCGGCGGTGGCGGCGGGGCGGAAGGTGAAGGTCGCCACCAGGTACTCCAACAGCTTCCCGCGGCTGGCGTGCCC
CGGCGGCGAGGACGGCACCGTCATCAGCACGCGGTGGCTGGACCGCGCGGTGCGCGTCGACGCGGCGCGGCGGCTGATGA
CGGTGGAGAGCGGCATGGTGATGCGTGACCTGATCAGGGAGGCCGCCGCGGCGGGGCTCGCGCTGCCGCACTCGCCGTAC
TGGTCGGGCCTCACGATCGGCGGCGTGCTCGCCACGGGCGCGCACGGGAGCTCGCTGTGGGGGAAGGGGAGCGCCGTGCA
CGAGTACGTGGTGGGGATGAGGATCGTGACGCCGGCACCGGCGAGCGAGGGGTTCGCGGCGGTGAGGGAGCTCGCCGCCG
GCGACCCGGACCTCGACGCGGCCAAGGTCTCCCTCGGCGTCCTCGGCGCCATCTCCCAGGTCACCCTCGAGCTGCAGCCG
CTGTTCAAGCGGTCGGTGGCGTTCGTGACCCGCAACGACTCGGACGTCGCCGACACGGTCGCCGCGTGGGGCCGCCTCCA
CGAGTTCGGCGACGTGGCGTGGCTGCCGCGGCGGCGCGTGGCCGTGTACCGCGAGGACGACCGCGTCGACGTCGCGACGC
CCGGCGACGGCCGCAGCGACTACCCGGCGTTCCGGCCGACGCCGACGCTACCCCTCGTCGCCAGCAGGCTCGCGGAGGAG
TGGCTGGAGGAGAGATCAGGGAGCGACGCCGCCCGGTGCGCGGCGTCGCGCGTGATGCCGGCGACGCTCGAGCACCTCAA
CTACGGGCTCACCAACGACGGCGAGGCCTTCACGGGGTACCCGGTGGTGGGCTACCAGCACCGCATCCAGGCGTCGAGCT
TGTGCACGGGCGCCATGGAGGACGACGGGCACATCCCCACCTCCACCTGCCTCTGGAACGGCCGCCTCCGGGGACACCTC
TTCTACAACTCCGGCTTCAGCATCGCGCTGTCGCGCGCGCCGGCGTTCGTCGCCGACGTCGCGCGGCTCCGCGACCTCAA
CCCGGCGGCGTTCTGCCAGATCGACTCCAAGATGGGCCTGCTGATGCGCTACGTCGCGGCGTCGTCGGCGTACCTCGGCA
AGGCGGAGGACTCGGTGGACTTCGACGTCACCTACTACCGGAGCTACGCCCGCGGCGCGCCGCGCGCGCACGCCGACGTG
TTCGACGAGGTCGAGCAGATGGCGCTGCGCAAGCACGGCGGCGTGCCGCACTGGGGCAAGAACCGCAACTACGCCTTCGA
CGGCGCCATCGCCAGGTACCCCAACGCCGGCAAGTTCATGAGGGTGAAGGACAGGTTCGATCCCGACGGCGTCTTCTCCA
GCGAGTGGAGCGACCAGGTGCTCGGCGTCGGCGGGGCGAGCCCGGTCATCGTCGGCGACGGCTGCGCCATGGAGGGGCTC
TGCGTGTGCTCCGACGACTCGCACTGCGCGCCGGAGAAGGGCTACTTCTGCCGGCCGGGGAAGGTGTTCACGGCGGCGAG
GGTGTGCTCGCCGTCGCCGCGAGGCGCTGCGAATGGCGGCGACGACGACGACGAAATATCGGACGTTGGCGATGAGTAG

Alignment

ORF - retro_oind_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.24 %
• 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  YPRTEEELVAAVAAAAAAGRKAKAATRYSNSFPRLACPGGVEGEGGVAISTRWLNRTVRVDAARRLMTVE
          YPRTEEELVAAVAAA.AAGRK.K.ATRYSNSFPRLACPG...GE.G..ISTRWL.R.VRVDAARRLMTVE
Retrocopy YPRTEEELVAAVAAAVAAGRKVKVATRYSNSFPRLACPG---GEDGTVISTRWLDRAVRVDAARRLMTVE

Parental  GGMVLRDLIREAAAAGLALPHSPYWSGVTVGGALATGAHGSSLWGKGSAVHEYVVGMRIVTPAAASEGFA
          .GMV.RDLIREAAAAGLALPHSPYWSG.T.GG.LATGAHGSSLWGKGSAVHEYVVGMRIVTPA.ASEGFA
Retrocopy SGMVMRDLIREAAAAGLALPHSPYWSGLTIGGVLATGAHGSSLWGKGSAVHEYVVGMRIVTPAPASEGFA

Parental  VVRELAADDPDLDAAKVSLGVLGIISQVTLALEPQFKRSVKFVKRDDADIAEKVAVWGRLHEFGDMVWLP
          .VRELAA.DPDLDAAKVSLGVLG.ISQVTL.L.P.FKRSV.FV.R.D.D.A..VA.WGRLHEFGD..WLP
Retrocopy AVRELAAGDPDLDAAKVSLGVLGAISQVTLELQPLFKRSVAFVTRNDSDVADTVAAWGRLHEFGDVAWLP

Parental  GQRQVIYREDNRVNISTPGDGLNDYFGFRAQPTLSMVGARVIDECLEENPMYTDTARCLASRAVTKMFDL
          ..R...YRED.RV...TPGDG..DY..FR..PTL..V..R...E.LEE.....D.ARC.ASR........
Retrocopy RRRVAVYREDDRVDVATPGDGRSDYPAFRPTPTLPLVASRLAEEWLEERSG-SDAARCAASRVMPATLEH

Parental  LAYGFTNDGATFTGYPVVGYQHRIQSSGSCMGSLEEKDDGLLLTTTCPWDRRTRGVFAYNVAFTVPLSRA
          L.YG.TNDG..FTGYPVVGYQHRIQ.S..C.G..E..DDG...T.TC.W..R.RG...YN..F...LSRA
Retrocopy LNYGLTNDGEAFTGYPVVGYQHRIQASSLCTGAME--DDGHIPTSTCLWNGRLRGHLFYNSGFSIALSRA

Parental  PAFVADVSRLRDLDPAAFCQIDAKMGVLVRYVAASSAYLGKAEDSVDFDVTYYRSRARGAPRAHADVFDE
          PAFVADV.RLRDL.PAAFCQID.KMG.L.RYVAASSAYLGKAEDSVDFDVTYYRS.ARGAPRAHADVFDE
Retrocopy PAFVADVARLRDLNPAAFCQIDSKMGLLMRYVAASSAYLGKAEDSVDFDVTYYRSYARGAPRAHADVFDE

Parental  VEQMALRGHGGVPHWGKNRNAAFDGAIARYPNAGEFLRVKDRFDPEGVFSSEWSDRVLGVGGASPAIVGD
          VEQMALR.HGGVPHWGKNRN.AFDGAIARYPNAG.F.RVKDRFDP.GVFSSEWSD.VLGVGGASP.IVGD
Retrocopy VEQMALRKHGGVPHWGKNRNYAFDGAIARYPNAGKFMRVKDRFDPDGVFSSEWSDQVLGVGGASPVIVGD

Parental  GCAMEGLCVCSDDSHCAPELGYFCRPGKVFTEARVCS-LLRDAADG
          GCAMEGLCVCSDDSHCAPE.GYFCRPGKVFT.ARVCS...R.AA.G
Retrocopy GCAMEGLCVCSDDSHCAPEKGYFCRPGKVFTAARVCSPSPRGAANG

Legend:

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

Expression

RNA-Seq

Oryza sativa indica was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza sativa indica was not studied using ChIP-Seq data.

EST

Oryza sativa indica was not studied using EST data.

TSS

Oryza sativa indica was not studied using FANTOM5 data.

Lab

retro_oind_24 was not experimentally validated.

Homology

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.

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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,