RetrogeneDB ID: retro_osat_62

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 12:18361453..18362053(+)
• 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_62
AGGGCGTGCTGCGTGGTGGTCGAGTTCCTCGGCGGCGGGACGCTCAAGAAGTACCTGATCGAACACTACCGGAGCAAGCT
CCCCTACGGCGAGGTCGTCCGCCTCGCGCTGTCCATGGCGCGCGGCCTCAGCTTCCTCCACGCCAACAATATCGTCCACC
GCGACGTCAAGACGGAGAACATGCTCTTCCTCGGCGGCGGCGGCGGCGGCGACCTCAAGATCGCCGACTTCGGCGTGGCC
CGCGTGGAGGCGCGCGACCCGAGGGAGATGACCGGCGCGACGGGCACGGTGGGGTACATGGCGCCGGAGGTGCTCGTCGG
GAAGCCGTACAACCGCAAGTGCGACGTGTACAGCTTCGGCATCTGCCTGTGGGAGACGTACTGCTGCGAGATGCCCTTCA
CGTTCGGGCTCAGCGTCGCGGAGGCGTCGGCGGCGGTGGCGCAGCGGGGGATGCGGCCGCCGATCCCGCCGTGCTGCCCG
CCCGCCATGGCGCGCGTCATGGCGAGGTGCTGGGACGCCGACCCGGCGGCGCGGCCGGAGATGGAGGAGGTGGTGCGGAT
GCTGGAGGCGCTCGACACGAGCAATGGCGGCGGGATGGTG

Alignment

ORF - retro_osat_62 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.0 %
• Parental protein coverage: 51.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RACCVVVEYLAGGTLKQYLIKNSRRKLAYKVVVQLALDLARGLSYLHSRKIVHRDVKTENMLLDTQRNLK
          RACCVVVE.L.GGTLK.YLI...R.KL.Y..VV.LAL..ARGLS.LH...IVHRDVKTENML........
Retrocopy RACCVVVEFLGGGTLKKYLIEHYRSKLPYGEVVRLALSMARGLSFLHANNIVHRDVKTENMLFXXXXXXX

Parental  IADFGVARVEAQNPKDMTGATGTLG---YMAPEVLDGKPYNRKCDVYSFGICLWEIYCCDMPYP-DLSFA
          ........V......D....TG..G...YMAPEVL.GKPYNRKCDVYSFGICLWE.YCC.MP....LS.A
Retrocopy XLKIADFGVARVEARDPREMTGATGTVGYMAPEVLVGKPYNRKCDVYSFGICLWETYCCEMPFTFGLSVA

Parental  DVSSAVVHQNLRPDVPRCCPSAFANIMRKCWDANPDKRPDMDEVVQLLEALDTSKGGGMI
          ..S.AV.....RP..P.CCP.A.A..M..CWDA.P..RP.M.EVV..LEALDTS.GGGM.
Retrocopy EASAAVAQRGMRPPIPPCCPPAMARVMARCWDADPAARPEMEEVVRMLEALDTSNGGGMV

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_62 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,