RetrogeneDB ID: retro_osat_11

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 1:28891405..28892278(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OS01G0698200
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OS08G0175000
• Aliases: None
• Description: None

Sequence

>retro_osat_11
ATGCAGGTAGCGGCTAGTTCTCCATCGAAAACGTTTTCTCGGCTACGTGCAACGATGAGGCGACCCATGGCTCGCGATTT
TACGGCGACGTTTCTTCTGCTGCTCAGCGTCGCGTCGCTGCTGGTGATCTCGCCGTGCGCGGCCCAGCAGATCAAGACCA
CCGACACGCGGTGGAGCTACCACCTCCCGCTTCCCGACGGCGTCAGCGGCGCCGAGAGCCTCGCCTTCGACGGCAAGGAC
GGCCTCTACACCGGCGTCTCGGACGGCCGCGTGCTCAAGTGGGGAGGCAGCGCCGCCGGCTGGACCACGTTCGCGTACAA
TGCGAACTACCGGAAAATCCCTCTCTGCTCGTCGTCCGAGGTGCCACCGGAGGAGAGGGAGAGCATCTGCGGGCGCCCGC
TGGGGATCCGGTTGTTCAGGAAGACCGGCGAGCTCTACATCGCCGACGCGTACAAGGGGCTGATGAAGGTCGGGCCCGAC
GGCGGCGAGGCCCAGGTGGTCGCGACCGAGGCGGACGGCGTCCCCTTCCACTTCCTCAATGGCCTTGACGTCGACCAAGC
TACGGGTGATGCCTACTTCACCGACAGCAGCAGCACGTACACCCGCAGGTTCAACGGGGAGATCACGATGAACGCCGACG
CGACAGGGCGGCTGCTCAAGTACGACGCGCGGACGCGGCGGGTCACCGTGCTGAAGACCGACCTGCCGTACCCGAACGGC
GTCGCCGTCAGCCGAGACAGGACGCACCTCGTCGTGGCGCACACCGTGCCGTGCCAGGCGTTCCGGTACTGGCTGCGGGG
CACCAAAGCCGGCGAGTACGAGCTCTTCGCCGACCTCCCGGGCTACCCCGACAACGTGAGGCGCGACACCTAG

Alignment

ORF - retro_osat_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.98 %
• Parental protein coverage: 72.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLLAFFLAAPPCAAAQQVKTSHAQFAFHLPLPDGVTGAESLAFDSSNHGPYTGVSDGRVLRWGGAAAGWT
          L..A..L...PCAA.QQ.KT.......HLPLPDGV.GAESLAFD....G.YTGVSDGRVL.WGG.AAGWT
Retrocopy LSVASLLVISPCAA-QQIKTTDTRWSYHLPLPDGVSGAESLAFDGKD-GLYTGVSDGRVLKWGGSAAGWT

Parental  TFAHHENYRKIPMCTTPVAPAEETESMCGRPLGLAFHDRTGDLYIADAYKGLMRVGPRGGEAEVLAAGAD
          TFA...NYRKIP.C.....P.EE.ES.CGRPLG......TG.LYIADAYKGLM.VGP.GGEA.V.A..AD
Retrocopy TFAYNANYRKIPLCSSSEVPPEERESICGRPLGIRLFRKTGELYIADAYKGLMKVGPDGGEAQVVATEAD

Parental  GVPFNFVNGIDVDQATGDVYFTDSSTTYPRRFNSEIMMNADATARLLKYDAATKRVTVLRAGLPYANGVA
          GVPF.F.NG.DVDQATGD.YFTDSS.TY.RRFN.EI.MNADAT.RLLKYDA.T.RVTVL...LPY.NGVA
Retrocopy GVPFHFLNGLDVDQATGDAYFTDSSSTYTRRFNGEITMNADATGRLLKYDARTRRVTVLKTDLPYPNGVA

Parental  VSRDGSHAVVAHTVPCQAFRYWIKGPNAGEYELLADLPGYPDNVRRD
          VSRD..H.VVAHTVPCQAFRYW..G..AGEYEL.ADLPGYPDNVRRD
Retrocopy VSRDRTHLVVAHTVPCQAFRYWLRGTKAGEYELFADLPGYPDNVRRD

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_11 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA028079	1 retrocopy	retro_oind_6,
Oryza glumaepatula	OGLUM08G04830	1 retrocopy	retro_oglu_15,
Oryza meridionalis	OMERI08G04560	1 retrocopy	retro_omer_14,
Oryza punctata	OPUNC08G04420	1 retrocopy	retro_opun_39,
Oryza glaberrima	ORGLA08G0040000	1 retrocopy	retro_ogla_41,
Oryza rufipogon	ORUFI08G05030	1 retrocopy	retro_oruf_9,
Oryza sativa japonica	OS08G0175000	1 retrocopy	retro_osat_11 ,