RetrogeneDB ID: retro_oind_87

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 5:22225593..22226763(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA017602
• Aliases: None
• Description: None

Sequence

>retro_oind_87
ATTTGTGAGGTACAACAATTATTAGGAAATAATCGAGTTAGAGCTGTAGCTATGAGTGCTACAGATGGGTTGATGAGAGG
AATGGAAGTGATTGACACGGGAGCTCCTCTCAGTGTTCCTGTCAGTGGAGCTACTCTTGGACGAATTTTCAACGTTCTTG
GGGAGCCTGTTGACAATTTGGGTCCTGTAGATACTAGTGCAACATTCCCTATTCATAGATCCGCGCCCGCCTTTATCGAG
TTAGATACGAAATTATCCATCTTTGAAATTGGTATTAAGGTGGTCGATCTTTTAGCTCCTTATCGGCGTGGAGGAAAAAT
CGGACTATTTGGGGGAGCTGGAGTAGGTAAAACAGGACTCATCATGGAATTAATCAACAATATTGCTAAAGCTCACGGGG
GCGTATCCGTATTTGGCGGAGTAGGGGAACGGACTCGTGAAGGAAATGATCTTTATATGGAAATGAAGGAATCTGGAGTA
ATTAATGAAAAAAATCTTGAGGAATCAAAGGTAGCTCTAGTCTATGGCCAAATGAATGAACCGCCAGGAGCTCGTATGAG
AGTTGGTTTGACTGCCCTAACTATGGCAGAATATTTCCGAGATGTTAATAAGCAAGACGTGCTTCTATTCATCAATAATA
TCTTTCGTTTTGTTCAAGCAGGATCGGAGGTATCTGCCTTATTAGGGAGAATGCCCTCTGCAGTGGGTTATCAACCTACT
CTTAGTACAGAAATGGGTTCTTTGCAAGAAAGAATTACTTCTACTAAAAAGGGATCTATAACTTCGATCCAAGCGGTTTA
TGTACCTGTGGACGATTTGACCGACCCTGCTCCTGCTACAACATTTGCACATTTGGATGCTACTACCGTACTTTCCAGAG
GATTAGCTTCCAAAGGGATTTATCCTGCAGTAGATCCTTTAGATTCAACCTCAACTATGTTACAACCTCGGATCGTTGGC
AACGAACATTATGAAACTGCGCAAAGAGTTAAGCAAACTTTACAACGTTACAAAGAACTTCAGGACATTATCGCAATTCT
TGGGTTGGATGAATTATCGGAGGAGGATCGTTTAACTGTAGCAAGAGCACGAAAAATTGAGCGCTTCTTATCACAACCGT
TTTTTGTGGCAGAAGTTTTTACCGGTTCTCCGGGAAAGTATGTTGGTCTT

Alignment

ORF - retro_oind_87 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.4 %
• Parental protein coverage: 72.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLEVAQHLGENMVRTIAMDGTEGLVRGQRVLNTGSPITVPVGRATLGRIMNVIGEPIDEKGDITTNHFLP
          ..EV.Q.LG.N.VR..AM..T.GL.RG..V..TG.P..VPV..ATLGRI.NV.GEP.D..G...T....P
Retrocopy ICEVQQLLGNNRVRAVAMSATDGLMRGMEVIDTGAPLSVPVSGATLGRIFNVLGEPVDNLGPVDTSATFP

Parental  IHREAPAFVEQATEQQILVTGIKVVDLLAPYQRGGKIGLFGGAGVGKTVLIMELINNVAKAHGGFSVFAG
          IHR.APAF.E..T...I...GIKVVDLLAPY.RGGKIGLFGGAGVGKT.LIMELINN.AKAHGG.SVF.G
Retrocopy IHRSAPAFIELDTKLSIFEIGIKVVDLLAPYRRGGKIGLFGGAGVGKTGLIMELINNIAKAHGGVSVFGG

Parental  VGERTREGNDLYREMIESGVIKLGDKQSESKCALVYGQMNEPPGARARVGLTGLTVAEHFRDAEGQDVLL
          VGERTREGNDLY.EM.ESGVI.......ESK.ALVYGQMNEPPGAR.RVGLT.LT.AE.FRD...QDVLL
Retrocopy VGERTREGNDLYMEMKESGVINXXXLE-ESKVALVYGQMNEPPGARMRVGLTALTMAEYFRDVNKQDVLL

Parental  FIDNIFRFTQANSEVSALLGRIPSAVGYQPTLATDLGGLQERITTTKKGSITSVQAIYVPADDLTDPAPA
          FI.NIFRF.QA.SEVSALLGR.PSAVGYQPTL.T..G.LQERIT.TKKGSITS.QA.YVP.DDLTDPAPA
Retrocopy FINNIFRFVQAGSEVSALLGRMPSAVGYQPTLSTEMGSLQERITSTKKGSITSIQAVYVPVDDLTDPAPA

Parental  TTFAHLDATTVLSRQISELGIYPAVDPLDSTSRMLSPHVLGEDHYNTARGVQKVLQNYKNLQDIIAILGM
          TTFAHLDATTVLSR.....GIYPAVDPLDSTS.ML.P...G..HY.TA..V...LQ.YK.LQDIIAILG.
Retrocopy TTFAHLDATTVLSRGLASKGIYPAVDPLDSTSTMLQPRIVGNEHYETAQRVKQTLQRYKELQDIIAILGL

Parental  DELSEDDKLTVARARKIQRFLSQPFHVAEVFTGAPGKYVEL
          DELSE.D.LTVARARKI.RFLSQPF.VAEVFTG.PGKYV.L
Retrocopy DELSEEDRLTVARARKIERFLSQPFFVAEVFTGSPGKYVGL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryza sativa indica was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza sativa indica was not studied using ChIP-Seq data.

EST

Oryza sativa indica was not studied using EST data.

TSS

Oryza sativa indica was not studied using FANTOM5 data.

Lab

retro_oind_87 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza sativa indica 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00006p00059970	1 retrocopy	retro_atri_7,
Arabidopsis thaliana	AT5G08670	1 retrocopy	retro_atha_12,
Oryza sativa indica	BGIOSGA017602	2 retrocopies	retro_oind_104, retro_oind_87 ,
Brassica rapa	Bra006013	2 retrocopies	retro_brap_51, retro_brap_57,
Chlamydomonas reinhardtii	CHLREDRAFT_78348	1 retrocopy	retro_crei_1,
Aegilops tauschii	F775_32946	1 retrocopy	retro_atau_18,
Hordeum vulgare	MLOC_70791	1 retrocopy	retro_hvul_13,
Oryza glaberrima	ORGLA01G0220100	1 retrocopy	retro_ogla_47,
Triticum aestivum	TRAES3BF058700080CFD_g	2 retrocopies	retro_taes_170, retro_taes_31,