RetrogeneDB ID: retro_osat_31

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 9:22220409..22221987(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OS09G0559000
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OS04G0492100
• Aliases: None
• Description: None

Sequence

>retro_osat_31
ATGGAGTCCGGCTACAGCGACGTCGACGACGACTACTTCGGCGACTCCGACGAGGATTATGGCGACGACGGCGATTACAT
GGATGACGATGGCGACGACTATGGTGGGCAGGTGGTCGAGGAAACGGAGGCGCCGGCGATGGAGAAGACGTACGTTGTTC
TAACCGAGGACGACGTACGCGCGCGGCAGGAGGAGGACATTGCCAAGGTGTGCGAGGTGCTCTCGCTCTCGCCGGGCGCC
GCCGCCGTCCTCCTCCGGCTGTACAGGTGGAGGGCCGTCCTGCTCCAGGAGGAGTGGTTCCTGGACGAGCGCCGCATACG
CGACGCCGCCGGCCTCCTGCCGGCGGACGGCGGCGGCGGCGAGGTGCCCGCGCGGGTCAACCGGCGGCGGCTCACCTGCG
CCATCTGCTTCGACGTGTTCGACACCGGCGGGATGAGGTCGGCGGGGTGCTCCCACTTCTACTGCGTCTCCTGCTGGCGC
GGGTACGTCCGCGCGGCGGTGGGCGACGGCGCGCGGTGCCTGTCGCTCCGGTGCCCGGATCCGTCGTGCCCGGCGGCCGT
CGTGCGCGAGCTGGTCGACGCGGTGGCCGACGGCGAGGACAGGGAGCGGTTCGGCTGGTTCGCGCTCCGGTCGTACGTGG
AGGAGAGCGCCGGGATGAGGTGGTGCCCGGGGCCCGGGTGCAGCCGCGCCGTGGAGTTCGTGGGCGGCGGCGACGGCGAG
GAGAGCAGCGAGGTGTTCTGCTCGTGCGGGCACGGGCTGTGCTGGCGGTGCGGCGAGGAGGCGCACCGGCCGGTGTCGTG
CAAGACGGTGGCGAAGTGGGTGGAGAAGAACAGCTCGGAGTCGGAGACGGCGACGTGGCTGCTCGCCCACACAAAGCACT
GCCCCAAGTGCCGGCTGCCGATCGAGAAGAACCTCGGGTGCATGCACATGACATGCCGGCCGCCGTGCCTCCACGAGTTC
TGCTGGATCTGCCTCAAGCCATGGCACGGCCACGCGGCGTGCTCCCGGTACCAGCCCAACGGCACGGTGGTGGCGCTGGC
CGGCGCCAACGCCGACGACGAGCGGCGGCGGCAGGCCAAGGCGTCCCTGGACAGGTACCTCTACCACTACGAGCGGTGGG
ACGCCAACCTCAAGTCGCTGCGCGTGGCGCTCCGCGACATGGAGAGCCTGGAGCGGTCGGAGCTGGAGGCGATGGCCTCG
GCGGCGGGCGTGCCGGCGACGGAGATGGGCTTCGTGACGGAGGCGTACGAGCAGGTCGGCGAGGGGCGGCGGGTGCTCGG
CTGGGCGCACGCCTACGGCTACTACCTCGACCCGGACCGCGACTTCACCAAGCGGCAGCTGTTCGAGTACCTGCAGGAGG
ACGCCAACGCGTCGCTGGAGCGGCTGCACGGCTGCGCCGAGAGGGAGAGGAGGGAGCTCTTCGCCGCCGGCGCCGACGAC
AAGGCCGCCGTCGACTTCGACAAGTACAGGGCGTACAGGGAGAAGCTCGCCGGGCTCACCAGGGTGACGCGGCAATACTT
TGGGAACCTCGTCAAAGCGTTCGAGACCGACCTGGCCGAGGTCTCCTCCTCTAGTTAA

Alignment

ORF - retro_osat_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.12 %
• Parental protein coverage: 83.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NDRELTCGICFENCPRTSMSAAACGHPFCSACWRGYISTSINDGPGCLMLRCPDPSCTAAVGQDMINSLA
          N.R.LTC.ICF.......M..A.C.H..C..CWRGY......DG..CL.LRCPDPSC.AAV........A
Retrocopy NRRRLTCAICFDVFDTGGMRSAGCSHFYCVSCWRGYVRAAVGDGARCLSLRCPDPSCPAAVVRELVDAVA

Parental  DDEDREKYGRYLRRSYIEDNRKTKWCPAPGCEYAVEFVM---GSGSYDVNCNCSYGFCWNCTEEAHRPVD
          D.EDRE..G....RSY.E......WCP.PGC..AVEFV....G..S..V.C.C..G.CW.C.EEAHRPV.
Retrocopy DGEDRERFGWFALRSYVEESAGMRWCPGPGCSRAVEFVGGGDGEESSEVFCSCGHGLCWRCGEEAHRPVS

Parental  CATVSKWILKNSAESENMNWILANSKPCPKCKRPIEKNQGCMHITCTPPCKFEFCWLCLGPWSEHGERTG
          C.TV.KW..KNS.ESE...W.LA..K.CPKC..PIEKN.GCMH.TC.PPC..EFCW.CL.PW..HG....
Retrocopy CKTVAKWVEKNSSESETATWLLAHTKHCPKCRLPIEKNLGCMHMTCRPPCLHEFCWICLKPW--HGHAAC

Parental  GFYACNRYEAARQEGAYDESERRREMAKNSLERYTHYYERWAANQSSRQKALGDLLSLQNDKLEKLSDIQ
          ..Y..N....A......D..ERRR..AK.SL.RY...YERW.AN..S...AL.D..SL....LE......
Retrocopy SRYQPNGTVVALAGANADD-ERRRQ-AKASLDRYLYHYERWDANLKSLRVALRDMESLERSELEAMASAA

Parental  SQPESQLKFIIEAWLQIVECRRVLKWTYAYGFYL-PEHEHAKRQFFEYLQGEAESGLERLHQCAEKELQV
          ..P.....F..EA..Q..E.RRVL.W..AYG.YL.P.....KRQ.FEYLQ..A...LERLH.CAE.E...
Retrocopy GVPATEMGFVTEAYEQVGEGRRVLGWAHAYGYYLDPDRDFTKRQLFEYLQEDANASLERLHGCAERERRE

Parental  YLEAESPSK---DFNDFRT---KLAGLTSVTRNYFENLVRALETGLNDVGPST
          ...A....K...DF...R....KLAGLT.VTR.YF.NLV.A.ET.L..V..S.
Retrocopy LFAAGADDKAAVDFDKYRAYREKLAGLTRVTRQYFGNLVKAFETDLAEVSSSS

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_31 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G05890	1 retrocopy	retro_atha_22,
Brassica oleracea	Bo5g007100	1 retrocopy	retro_bole_13,
Brassica oleracea	Bo8g005850	1 retrocopy	retro_bole_12,
Brassica rapa	Bra015463	1 retrocopy	retro_brap_11,
Oryza sativa japonica	OS04G0492100	1 retrocopy	retro_osat_31 ,