RetrogeneDB ID: retro_oruf_19

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 3:23255263..23256610(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI03G28220
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI03G37950
• Aliases: None
• Description: None

Sequence

>retro_oruf_19
ATGGCGAGCTGGGCATTGGCAATGGCGAGCTCGCCGATGGCCATGGACGCGGACAAGCTCAGCTACGAGATCTTCTCCCT
GCTGGAGAGCAAGTTCCTCTTCGGCGCCGGCGGCGGCGGGTGCCTGTCGTCGGGGCCGTGCACGCCGGCGAGGCCGTTTC
TTGGCGGCGGCGGCGGCATGGACGGGCGGGTGCGGGTGCTGGCCATCGACGGGTGCGGCTCGTCGGGCGCCGGGGACGCG
CTGCTCGCCGCGGCGGCGCTCGCGCGGCTGGAGGCCGGGCTGCGGAAGCGAACCGGGGACTCCGACGCCCGCGTCGCGGA
TTTCTTCGACGTCGCGGCGGGCGCCGGCGCCGGTGGGGTGCTCGCGGCGATGCTGTTCTTGAGGGGCCCCGACGGGAGGC
CGAGGTACACGGCGGAGGAGGCGCTTGAGTTCGTGGCTGCTAGCGTCGGGAGGGACTGGGCCGGCCGGCGCGGGCGGTGG
GCGCGGCTGTTCCGCGGCGGCGCGCGGGGGGCGGAGAGGTCGTTCCGGCGGGTGTTCGGCGACGCCACGCTCAAGGACAC
CGTCGCGCCGCTGCTCGTCCCGTGCTACGACCTCGCCACCGCCGCGCCTTTCATGTTCTCGCGCGCCGACGCCGTCGAGA
GCGACAGCTACGACTTCGCCCTCCGCGACGTCTGCGCGGCCACCTGCGCCGCCGGGAGCACGGCCGCCGCCGTCAGGTCG
GTGGACGGGCGCACCGCCATCGCCGCGGCTTCCGGCGGCGTGGCGGCCATGGGCAACCCGGCCGCGGCGGCCATCACGCA
CGTGCTCCACAACAAGCAGGAGTTCCCCCTCGCCACCACCGTCGACGACATCCTCGTCCTCTCCATCGGCACCGGCGCCT
CCACCTCCGCCACCGCGACGCCGATGCCCACGCGCTCCCCGTCGCCGCGCGAGATGGCGCGCGTCACCGCCGAGGGCGTG
GCGGACATGGTCGACGAGTCCGTCGCCATGGCGTTCGGCCACACGAGCGGGAGCAGCAGCAACTACGTGCGCATCCAGGC
CAGCAAGGCGGCGACCGCGCTCCACGGCGCCGCCGCCGCGGGCGCGATGCTGTCGCAGCGGAACGTGGAGTCCGTGCTGT
TCCGCGGGCGGAGGATGTCGGAGAGGACGAACGCCGAGAAGGTGGACGCCGCGGCGGCGGAGGTGGTGAAGGAGCACGAG
CGGCGGCGGCGCAGCCCGCTGCCGAACGTGGTGATCAAGCAGGTGGGCACGCCGCGGGTATCGTCGGCGACCACGGCGTC
GTCGGGGACGGCGAGGACGGCGGCGTCGACGTTGGCGTCGCCGGCGTCGTACGGCTCCCGCCAATAG

Alignment

ORF - retro_oruf_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.14 %
• Parental protein coverage: 76.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAAAAAGQLDVDKLTYEIFSILESKFLFGYDDPKLVFSGGDEPQGAVKGTPARGPAVVERGKVCVLSIDG
          A.A......D.DKL.YEIFS.LESKFLFG........SG...P.....G....G.....R..V......G
Retrocopy AMASSPMAMDADKLSYEIFSLLESKFLFGAGGGGCLSSGPCTPARPFLG---GGGGMDGRVRVLAIDGCG

Parental  GGRAADGLLAGAALVSLEASLRRRTGDETARLADFFDVAAGSGAGGVLAAMLVARGGDGRPMFSAEDALA
          ...A.D.LLA.AAL..LEA.LR.RTGD..AR.ADFFDVAAG.GAGGVLAAML..RG.DGRP...AE.AL.
Retrocopy SSGAGDALLAAAALARLEAGLRKRTGDSDARVADFFDVAAGAGAGGVLAAMLFLRGPDGRPRYTAEEALE

Parental  FLMRSLRRGWSGGGGGGAAGGIRALFRRPGAAFRKVFGDLTLRDTVRPVLVPCYDLASAGPFLFSRADAV
          F...S..R.W.G..G..A....R...R.....FR.VFGD.TL.DTV.P.LVPCYDLA.A.PF.FSRADAV
Retrocopy FVAASVGRDWAGRRGRWAR-LFRGGARGAERSFRRVFGDATLKDTVAPLLVPCYDLATAAPFMFSRADAV

Parental  ETAAYDFRLRDVCAATCAGSDGSASAVEVRSSDGATRIAAVGGGL-ALGNPTAAAITHVLNNKREFPLAA
          E...YDF.LRDVCAATCA.......A..VRS.DG.T.IAA..GG..A.GNP.AAAITHVL.NK.EFPLA.
Retrocopy ESDSYDFALRDVCAATCA---AGSTAAAVRSVDGRTAIAAASGGVAAMGNPAAAAITHVLHNKQEFPLAT

Parental  GVEDLLVISIGSGECDN---RPTGGAAASTSEIVRIAAEGVADMVDQAVAMAFGH--NRTNNYIRIQAMG
          .V.D.LV.SIG.G........P......S..E..R..AEGVADMVD..VAMAFGH......NY.RIQA..
Retrocopy TVDDILVLSIGTGASTSATATPMPTRSPSPREMARVTAEGVADMVDESVAMAFGHTSGSSSNYVRIQASK

Parental  SPRASRGGMRCG
          ...A..G....G
Retrocopy AATALHGAAAAG

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza rufipogon was not studied using ChIP-Seq data.

EST

Oryza rufipogon was not studied using EST data.

TSS

Oryza rufipogon was not studied using FANTOM5 data.

Lab

retro_oruf_19 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza rufipogon 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 ,