RetrogeneDB ID: retro_osat_81

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 5:9265766..9266724(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OS03G0638800
• Aliases: None
• Description: None

Sequence

>retro_osat_81
CCCAAGGCGGCGTGGGAGATCGACCTCTCGAGGCTGCGTATCCGCCAGGGCGCTCCCGTCAAGCACGGCTTCCGCGGCTC
GCTGTTCCGCGCGGACTACGATGGCCGCGACGTCGCCGTGAAGCTCCTCGACTGGGGGAAGGAGGGGTTCTCGACGCCCG
AGCAGATCGCCCACCTGCGCGCGTCGCTCAGGGGCGTGGCCGAAGCCTGGCACAAGATCGACCACCCCAACATCACCAAG
TTCGTCGGCGCATCCATGGCCACCGCCGACCTCAACATCCCACAAGGCCAGAGCACCGCGCCGCCGCTGCCGCCGCCGCC
ACCGGACACACCATGCTGCGTCGTGGTCGAGTACCTCACCGGAGGGACTCTGAAGAGCTATCTCATCAAGCACATGGAGC
GCAAGCTCGCCTACAAGGACGCGTCCGCTTCGCGCTGTCAATGGCGAGAGGGCTGAGCTACCTGCACTCGAGGAAGATCG
TGCACCGCGACGTCAAGACCGACAACATGCTCCTCGACGGCGAGCTCAACCTCAAGATAGCCGACTTCGGGGTGGCGCGC
ATCGAGGCGTCGGACCCGAGGGAGATGACCGGGGTGATGTGGACGCTGGGCTACATGGCCCCGAGGTGCTCGTCGGGGAG
CCGTACAACCGCAAGTGCGACGTGTACAGCTTCGGGATCTGCCTGTGGGAGATCTACTGCTGCGAGATGCCGTTCATGGA
CCTCAGCCTGGCCGACGTCTCGTCGGCGGTCGTCCACAAGGACCTGCGGCCGGAGATCCCGCGGTGCTGCCCGCGCGACA
TGGCGCTCATCATGCGGCGTTGCTGGCACGCCAACCCGGCGGCGCGGCCGGAGATGGAGGAGGTGGTGGGGATGCTGGAG
GCGCTGGACATGAAGAAAGGCCGTGGCATGGTGCCATTAGGGGAGACCGCCGGTTGCTTCTGCATCTCCCTCAGGCGC

Alignment

ORF - retro_osat_81 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.04 %
• Parental protein coverage: 83.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PKEDWEIDLAKLEIRY--VIAQGTYGTVYRGTYDGQDVAVKLLDWGEDGFATEAETAALRTSFKQEVAVW
          PK..WEIDL..L.IR.......G..G...R..YDG.DVAVKLLDWG..GF.T....A.LR.S.......W
Retrocopy PKAAWEIDLSRLRIRQGAPVKHGFRGSLFRADYDGRDVAVKLLDWGKEGFSTPEQIAHLRASLRGVAEAW

Parental  HKLSHPNVTKFVGASMGTTDLKIPTNNSNAGARTNLPARACC-VVVEYLAGGTLKQYLIKNSRRKLAYKV
          HK..HPN.TKFVGASM.T.DL.IP...S.............C.VVVEYL.GGTLK.YLIK...RKLAYK.
Retrocopy HKIDHPNITKFVGASMATADLNIPQGQSXXXXXXXXXPDTPCCVVVEYLTGGTLKSYLIKHMERKLAYKD

Parental  V-VQLALDLARGLSYLHSRKIVHRDVKTENMLLDTQRNLKIADFGVARVEAQNPKDMTGATGTLGYMA-P
          ..V..AL..ARGLSYLHSRKIVHRDVKT.NMLLD...NLKIADFGVAR.EA..P..MTG...TLGYMA.P
Retrocopy A<VRFALSMARGLSYLHSRKIVHRDVKTDNMLLDGELNLKIADFGVARIEASDPREMTGVMWTLGYMA<P

Parental  EVLDGKPYNRKCDVYSFGICLWEIYCCDMPYPDLSFADVSSAVVHQNLRPDVPRCCPSAFANIMRKCWDA
          EVL.G.PYNRKCDVYSFGICLWEIYCC.MP..DLS.ADVSSAVVH..LRP..PRCCP...A.IMR.CW.A
Retrocopy EVLVGEPYNRKCDVYSFGICLWEIYCCEMPFMDLSLADVSSAVVHKDLRPEIPRCCPRDMALIMRRCWHA

Parental  NPDKRPDMDEVVQLLEALDTSKGGGMIPDGQSSGCLCFTKAR
          NP..RP.M.EVV..LEALD..KG.GM.P.G...GC.C....R
Retrocopy NPAARPEMEEVVGMLEALDMKKGRGMVPLGETAGCFCISLRR

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

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

EST

Oryza sativa japonica was not studied using EST data.

TSS

Oryza sativa japonica was not studied using FANTOM5 data.

Lab

retro_osat_81 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza sativa japonica 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_27126	1 retrocopy	retro_hvul_82,
Oryza sativa japonica	OS03G0638800	2 retrocopies	retro_osat_62, retro_osat_81 ,
Oryza sativa japonica	OS06G0636600	1 retrocopy	retro_osat_5,