RetrogeneDB ID: retro_oniv_28

Retrocopy location

• Organism: Indian wild rice (Oryza nivara)
• Coordinates: 3:24022888..24024214(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ONIVA03G28340
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ONIVA03G37650
• Aliases: None
• Description: None

Sequence

>retro_oniv_28
ATGGCGAGCTCGCCGATGGCCATGGACGCGGACAAGCTCAGCTACGAGATCTTCTCCCTGCTGGAGAGCAAGTTCCTCTT
CGGCGGCGGCGGCGGCGGGTGCCTGTCGTCGGGGCCGTGCACGCCGGCGAGGCCGTTTCTTGGCGGCGGTGGCGGCATGG
ACGGGCGGGTGCGGGTGCTGGCCATCGACGGGTGCGGCTCGTCGGGCGCCGGGGACGCGCTGCTCGCCGCGGCGGCGCTC
GCGCGGCTGGAGGCCGGGCTGCGGAAGCGAACCGGGGACTCCGACGCCCGCGTCGCGGATTTCTTCGACGTCGCGGCGGG
CGCCGGCGCCGGTGGGGTGCTCGCGGCGATGCTGTTCTTGAGGGGCCCCGACGGGAGGCCGAGGTACACGGCGGAGGAGG
CGCTTGAGTTCGTGGCTGCTAGCGTCGGGAGGGACTGGGCCGGCCGGCGCGGGCGGTGGGCGCGGCTGTTCCGCGGCGGC
GCGCGGGGGGCGGAGAGGTCGTTCCGGCGGGTGTTCGGCGACGCCACGCTCAAGGACACCGTCGCGCCGCTGCTCGTCCC
GTGCTACGACCTCGCCACCGCCGCGCCTTTCATGTTCTCGCGCGCCGACGCCGTCGAGAGCGACAGCTACGACTTCGCCC
TCCGCGACGTCTGCGCGGCCACCTGCGCCGCCGGGAGCACGGCCGCCGCCGTCAGGTCGGTGGACGGGCGCACCGCCATC
GCCGCGGCTTCCGGCGGCGTGGCGGCCATGGGCAACCCGGCCGCGGCGGCCATCACGCACGTGCTCCACAACAAGCAGGA
GTTCCCCCTCGCCACCACCGTCGACGACATCCTCGTCCTCTCCATCGGCACCGGCGCCTCCACCTCCGCCACCGCGACGC
CGATGCCCACGCGCTCCCCGTCGCCGCGCGAGATGGCGCGCGTCACCGCCGAGGGCGTGGCGGACATGGTCGACGAGTCC
GTCGCCATGGCGTTCGGCCACACGAGCGGGAGCAGCAGCAACTACGTGCGCATCCAGGCCAGCAAGGCGGCGACCGCGCT
CCACGGCGCCGCCGCCGCGGGCGCGATGCTGTCGCAGCGGAACGTGGAGTCCGTGCTGTTCCGCGGGCGGAGGATGTCGG
AGAGGACGAACGCCGAGAAGGTGGACGCCGCGGCGGCGGAGGTGGTGAAGGAGCACGAGCGGCGGCGGCGCAGCCCGCTG
CCGAACGTGGTGATCAAGCAGGTGGGCACGCCGCGGGTATCGTCGGCGACCACGGCGTCGTCGGGGACGGCGAGGACGGC
GGCGTCGACGTTGGCGTCGCCGGCGTCGTACGGCTCCCGCCAATAG

Alignment

ORF - retro_oniv_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.17 %
• Parental protein coverage: 76.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAAAGQLDVDKLTYEIFSILESKFLFGYDDPKLVFSGGDEPQGAVKGTLARGPAVVERGKVCVLSIDGGG
          A......D.DKL.YEIFS.LESKFLFG........SG...P.......L..G.....R..V......G..
Retrocopy ASSPMAMDADKLSYEIFSLLESKFLFGGGGGGCLSSG---PCTPARPFLGGGGGMDGRVRVLAIDGCGSS

Parental  RAADGLLAGAALVSLEASLRRRTGDETARLADFFDVAAGSGAGGVLAAMLVARGGDGRPMFSAEDALAFL
          .A.D.LLA.AAL..LEA.LR.RTGD..AR.ADFFDVAAG.GAGGVLAAML..RG.DGRP...AE.AL.F.
Retrocopy GAGDALLAAAALARLEAGLRKRTGDSDARVADFFDVAAGAGAGGVLAAMLFLRGPDGRPRYTAEEALEFV

Parental  MRSLRRGWSGGGGGGAAGGIRALFRRPGAAFRKVFGDLTLRDTVRPVLVPCYDLASAGPFLFSRADAVET
          ..S..R.W.G..G..A....R...R.....FR.VFGD.TL.DTV.P.LVPCYDLA.A.PF.FSRADAVE.
Retrocopy AASVGRDWAGRRGRWAR-LFRGGARGAERSFRRVFGDATLKDTVAPLLVPCYDLATAAPFMFSRADAVES

Parental  AAYDFRLRDVCAATCAGSDGSASAVEVRSSDGATRIAAVGGGL-ALGNPTAAAITHVLNNKREFPLAAGV
          ..YDF.LRDVCAATCA.......A..VRS.DG.T.IAA..GG..A.GNP.AAAITHVL.NK.EFPLA..V
Retrocopy DSYDFALRDVCAATCA---AGSTAAAVRSVDGRTAIAAASGGVAAMGNPAAAAITHVLHNKQEFPLATTV

Parental  EDLLVISIGSGECDN---RPTGGAAASTSEIVRIAAEGVADMVDQAVAMAFGH--NRTNNYIRIQAMGSP
          .D.LV.SIG.G........P......S..E..R..AEGVADMVD..VAMAFGH......NY.RIQA....
Retrocopy DDILVLSIGTGASTSATATPMPTRSPSPREMARVTAEGVADMVDESVAMAFGHTSGSSSNYVRIQASKAA

Parental  RASRGGMRCG
          .A..G....G
Retrocopy TALHGAAAAG

Legend:

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

Expression

RNA-Seq

Oryza nivara was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza nivara was not studied using ChIP-Seq data.

EST

Oryza nivara was not studied using EST data.

TSS

Oryza nivara was not studied using FANTOM5 data.

Lab

retro_oniv_28 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza nivara 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA009703	1 retrocopy	retro_oind_23,
Oryza glumaepatula	OGLUM03G36170	1 retrocopy	retro_oglu_8,
Oryza nivara	ONIVA03G37650	1 retrocopy	retro_oniv_28 ,
Oryza rufipogon	ORUFI03G37950	1 retrocopy	retro_oruf_19,