RetrogeneDB ID: retro_osat_13

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 9:22804745..22805972(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OS09G0571100
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OS08G0206950
• Aliases: None
• Description: None

Sequence

>retro_osat_13
ATGAACAAGTGCAGGTCTAGCAGTAGCAGTAGCAATAGCAGGGCCTTGTATGCTCTCCTCCTCACTTCTCTTATACTAAC
AGTAATAATATTGTACCTCCCGCCTCCACCTGATCCTCTTTCCCAATCCCAATTCGAATTCGACCAACTAAAGCTTGACG
ATCATCCGCCGCCACCGCAGCTGCACCGCCGCAGGACGAAGCGGTGCGCCGAGCACCTCAGGTGGGCGGCCTCCCTCGCC
TCTCAACACAATGCCACCCTCCTGCTCACCGTCGATCGCAACCAGGCCGCCGGCTGCGCCAACTTCACCACCATCCAGAA
GGCGGTGGACGCGGTGCCCGACTACGCCGCCACACGCACGCTCATCGCCGTGGACGCCGGCATCTACAGGGAGAAGGTGG
TGGTGTGGTCCAACAAGACGGCCCTCACGCTGCACGGCCGCGGCAACCTCAACACCACCGTCGCCTGGAACGCCACCTCC
AACTCCACCGGCGGCAGCACCGTGTACAGCGCCACCTTCACCGTCCTCGCCCCCGCCTTCGTCGCCTACAACATCACCTT
CCAGAACACGTCGCCCCCGCCCGAGCCCGGGGACGCAGGGGGGCAGGCGGTGGCGCTGAGGGTGGCCGGCGACGAGGCGG
CGTTCCACTGGTGCGGGGTGTACAGCGCGCAGGACACGCTGCTGGACGAGTCCGGGCGGCACCTGTTCCGCGGCTGCTAC
ATCGAGGGCTCCATCGACTTCATCTTCGGCAACGCACGATCCCTCTACGTGGGTTGCACCATAAGCTCCGTGGCCATGGC
GAGCGCGACGGGGAATAAGGAAGTGACGGGGAGCGTGACGGCGCAGGGGAGGGCGTCGGCGGCGGAGAGGACGGGGTTCG
CGTTCGTGCGGTGCAGCGTGGTGGGGACGGGGCAGGTGTGGCTGGGGAGGGCGTGGGGGCCGTACGCGACGGTGGTGTTC
GCGGAGACGTACCTCGGCGACGTGGTGGCGGCGGAGGGGTGGAACGACTGGGGCGACCCCGGCAGGCGGCAGCAGGTGTG
GTTCGCGGAGTACGCGTGCTGGGGCCCCGGATCCGCCACCGCCGCCACCGGCAGGGTGTCCTACGCGCGGCAGCTTGACC
AGCGCCAGGCCGCGCCCTTCATGGACGTCTCCTACATCGACGCCAACCAGTGGGCGCTGCCACCGTCGACGCCGGAACTC
TACGGATCGAGATATACTCCCAGCTAG

Alignment

ORF - retro_osat_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.18 %
• Parental protein coverage: 74.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GCCNFTTVQAAVNAVPSFSKKRNVVWINKGIYYEKVTVPATKPNITFQGQGFDLTAISWNDTANSSHG-T
          GC.NFTT.Q.AV.AVP.....R.......GIY.EKV.V...K...T..G.G...T...WN.T.NS..G.T
Retrocopy GCANFTTIQKAVDAVPDYAATRTLIAVDAGIYREKVVVWSNKTALTLHGRGNLNTTVAWNATSNSTGGST

Parental  FYSGSVSVFATGFVAKNISFINVAPIPRPGDVGAQAVALRIGGDQAAFWGCGFFGAQDTLHDDRGRHYFK
          .YS....V.A..FVA.NI.F.N..P.P.PGD.G.QAVALR..GD.AAF..CG...AQDTL.D..GRH.F.
Retrocopy VYSATFTVLAPAFVAYNITFQNTSPPPEPGDAGGQAVALRVAGDEAAFHWCGVYSAQDTLLDESGRHLFR

Parental  ECFIQGSIDFIFGDARSLYENCRVISIADPVPAGVRTITGSVTAHARESVDDNTGYSFVNCSIGGTGRIW
          .C.I.GSIDFIFG.ARSLY..C...S.A.....G....TGSVTA..R.S....TG..FV.CS..GTG..W
Retrocopy GCYIEGSIDFIFGNARSLYVGCTISSVAMASATGNKEVTGSVTAQGRASAAERTGFAFVRCSVVGTGQVW

Parental  LGRAWRPYSTVVFAYTSMSDIIASEGWNDWNDPSRDQTVFYGEYRCTGDGA--NLSDRVPYAQKLSDVQV
          LGRAW.PY.TVVFA.T...D..A.EGWNDW.DP.R.Q.V...EY.C.G.G.......RV.YA..L...Q.
Retrocopy LGRAWGPYATVVFAETYLGDVVAAEGWNDWGDPGRRQQVWFAEYACWGPGSATAATGRVSYARQLDQRQA

Parental  LPYLNTSFIDGDRWLKP
          .P....S.ID...W..P
Retrocopy APFMDVSYIDANQWALP

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_13 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza glaberrima	ORGLA08G0054200	1 retrocopy	retro_ogla_15,
Oryza sativa japonica	OS08G0206950	1 retrocopy	retro_osat_13 ,
Sorghum bicolor	Sb07g006050	1 retrocopy	retro_sbic_44,