RetrogeneDB ID: retro_osat_2

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 3:36150924..36152043(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OS03G0856700
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OS01G0883800
• Aliases: None
• Description: None

Sequence

>retro_osat_2
ATGAGCATGGTGGTGCAGCAGGAGCAGGAGGTGGTGTTCGACGCGGCGGTGCTGAGCGGGCAGACGGAGATCCCGTCGCA
GTTCATATGGCCGGCGGAGGAGAGCCCCGGGTCGGTGGCGGTGGAGGAGCTGGAGGTGGCGCTGATCGACGTGGGGGCGG
GGGCGGAGAGGTCGTCGGTGGTCCGGCAGGTGGGGGAGGCGTGCGAGAGGCACGGCTTCTTCCTGGTGGTTAACCACGGC
ATCGAGGCGGCGCTGCTGGAGGAGGCGCACCGGTGCATGGACGCCTTCTTCACGCTGCCGCTGGGGGAGAAGCAGCGGGC
GCAGCGGCGCGCGGGGGAGAGCTGCGGCTACGCCAGCAGCTTCACGGGGCGCTTCGCGTCCAAGCTGCCGTGGAAGGAGA
CGCTGTCGTTCCGGTACTCATCGGCTGGAGATGAAGAGGGCGAGGAGGGCGTGGGTGAGTACCTGGTGCGGAAGCTCGGG
GCGGAGCACGGGCGGCGGCTGGGCGAGGTGTACTCGCGCTACTGCCACGAGATGAGCCGCCTGTCGCTGGAGCTGATGGA
GGTGCTCGGGGAGAGCCTGGGCATCGTCGGAGACCGGCGCCACTACTTCCGGCGATTCTTCCAGCGCAACGACTCCATCA
TGCGCCTCAACTACTACCCGGCGTGCCAGAGGCCACTCGACACGCTGGGCACCGGTCCGCACTGCGACCCCACCTCGCTC
ACCATCCTCCACCAGGACCACGTCGGCGGCCTGGAGGTGTGGGCGGAGGGGCGGTGGCGCGCCATCCGCCCTCGCCCCGG
GGCGCTCGTCGTCAACGTCGGCGACACCTTCATGGCGCTCTCCAACGCCAGGTACCGCAGCTGCCTGCACCGGGCGGTCG
TCAACAGCACGGCGCCTCGCCGCTCGCTGGCCTTCTTCCTCTGCCCGGAGATGGACACGGTGGTGCGCCCGCCGGAGGAG
CTGGTCGACGACCACCACCCGAGGGTGTACCCGGACTTCACGTGGCGGGCGCTGCTGGACTTCACGCAGCGCCACTACAG
GGCCGACATGCGCACGCTTCAGGCCTTCTCCGACTGGCTTAATCATCATCGTCACCTGCAACCAACAATATACTCCTAG

Alignment

ORF - retro_osat_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.91 %
• Parental protein coverage: 85.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EPKIPEPFVWPNGDARPASAAELDMPVVDVGVLRDGDAEGLRRAAAQVAAACATHGFFQVSEHGVDAALA
          ...IP..F.WP.....P.S.A.....V....V..........R...QV..AC..HGFF.V..HG..AAL.
Retrocopy QTEIPSQFIWP-AEESPGSVAVEELEVALIDVGAGAERSSVVR---QVGEACERHGFFLVVNHGIEAALL

Parental  RAALDGASDFFRLPLAEKRRARRVPGTVSGYTSAHADRFASKLPWKETLSFGFH---DRAAAPVVADYFS
          ..A......FF.LPL.EK.RA.R..G...GY.S....RFASKLPWKETLSF......D......V..Y..
Retrocopy EEAHRCMDAFFTLPLGEKQRAQRRAGESCGYASSFTGRFASKLPWKETLSFRYSSAGDEEGEEGVGEYLV

Parental  STLGPDFAP-MGRVYQKYCEEMKELSLTIMELLELSLGV---ERGYYREFFADSSSIMRCNYYPPCPEPE
          ..LG.......G.VY..YC.EM..LSL..ME.L..SLG.....R.Y.R.FF....SIMR.NYYP.C..P.
Retrocopy RKLGAEHGRRLGEVYSRYCHEMSRLSLELMEVLGESLGIVGDRRHYFRRFFQRNDSIMRLNYYPACQRPL

Parental  RTLGTGPHCDPTALTILLQDDVGGLEVLVDGEWRPVSPVPGAMVINIGDTFMALSNGRYKSCLHRAVVNQ
          .TLGTGPHCDPT.LTIL.QD.VGGLEV...G.WR...P.PGA.V.N.GDTFMALSN.RY.SCLHRAVVN.
Retrocopy DTLGTGPHCDPTSLTILHQDHVGGLEVWAEGRWRAIRPRPGALVVNVGDTFMALSNARYRSCLHRAVVNS

Parental  RRERRSLAFFLCPREDRVVRPPPSAATPQH---YPDFTWADLMRFTQRHYRADTRTLDAFTRWL
          ...RRSLAFFLCP..D.VVRPP.......H...YPDFTW..L..FTQRHYRAD.RTL.AF..WL
Retrocopy TAPRRSLAFFLCPEMDTVVRPPEELVDDHHPRVYPDFTWRALLDFTQRHYRADMRTLQAFSDWL

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_2 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Leersia perrieri	LPERR01G34060	1 retrocopy	retro_lper_3,
Oryza barthii	OBART01G39570	1 retrocopy	retro_obar_12,
Oryza meridionalis	OMERI01G36440	1 retrocopy	retro_omer_11,
Oryza glaberrima	ORGLA01G0334700	1 retrocopy	retro_ogla_32,
Oryza sativa japonica	OS01G0883800	1 retrocopy	retro_osat_2 ,
Setaria italica	Si001573m.g	1 retrocopy	retro_sita_29,