RetrogeneDB ID: retro_oruf_15

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 3:20493787..20494771(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI03G25290
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI06G23740
• Aliases: None
• Description: None

Sequence

>retro_oruf_15
ATGGACCAGGAGATAATGAAGAAGCACAGCGCGTGGCTTAAGCTGCTCCTCGGGCCCAAGATCGCGTCGGGGTCCAACAG
CCGCATCCACCGCGGCATGTACGGGGAGCAACCAGTGGCCGTGAAGATCATGCACGCGCCAGTGGGCGACGACGACGACG
ACGTGCAGGTCCGGCGTGAGATGGAGGCGCAGTTCGACGCCGAGGTGTCCCTCCTGTCGCGGCTGCGCCACCCCAACGTC
GTGCGGCTCGTCGGCGTGTGCCGGGAGCCGGAGGTGTACTGGATCATCACCGAGCTCATGCGACGCGGCACGCTCAGCGC
GTACCTGCACGGGCGGGAGCCCTACTCGCTGCCGCCGGAGACCATCGTCCGCCTCGCGCTTGACGTCGCCCGTGGCATGG
AGTACCTCCACGCGCGTGGCGTCGTCCACCGCGACCTCAAGCCGGAGAACCTGCTGCTCGACGGCGGCGGGCGCGTCAAG
GTCGCCGACCTGGGCACGTCCTGCCTCGAGGCCACCTGCCGCGGCGACAAGTGCTCCTCCAAGGCGGGCACGTTCCGGTG
GATGGCGCCGGAGATGATCCATGACAAGCGCTGCAACCGCAAGGTGGACGTGTACAGCTTCGGCCTCGTGCTGTGGGAGC
TCACCACTTGCCTCGTGCCGTTCCAGAACTTGAGCCCCGTGCAGGTCGCTTTCTCCGTCTGCGACAGGGACGCCAGGCCG
CCGCTCTCGCCGTCGTGCCCGCCGGCCATCAACAGCCTCATCAAGAGGTGCTGGTCCACCGAACCAGCGAGGCGTCCCGA
GTTCAAACAGATCGTGTCCGTGCTGGAGAGCTACGACCGCTGCCTCCGGCAAGGCCTGCCAATGGTGGCGCTGCCGGAGC
CGTCGTCATCGCCGCTGGCCTCGTTGCTCGGCGCCTTCAAGATCCGATCCTGCACGAGCACAACGCGTTCCTCCATAACC
GATCATAGAAGAGTTCATCCTTAG

Alignment

ORF - retro_oruf_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.06 %
• Parental protein coverage: 68.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFIGNKFASGANSRIYRGIYKQRAVAVKMVRIP----ERDEARRAVLEDQFNSEVAFLSRLYHPNIVQFI
          L..G.K.ASG.NSRI.RG.Y....VAVK....P......D...R...E.QF..EV..LSRL.HPN.V...
Retrocopy LLLGPKIASGSNSRIHRGMYGEQPVAVKIMHAPVGDDDDDVQVRREMEAQFDAEVSLLSRLRHPNVVRLV

Parental  AACKKPPVYCIITEYMSQGTLRMYLNKKDPYSLSSETILKLALDISRGMEYLHAQGVIHRDLKSQNLLLN
          ..C..P.VY.IITE.M..GTL..YL....PYSL..ETI..LALD..RGMEYLHA.GV.HRDLK..NLLL.
Retrocopy GVCREPEVYWIITELMRRGTLSAYLHGREPYSLPPETIVRLALDVARGMEYLHARGVVHRDLKPENLLLD

Parental  DEMRVKVADFGTSCLETACQATK--GNKGTYRWMAPEMTKEKPYTRKVDVYSFGIVLWELTTCLLPFQGM
          ...RVKVAD.GTSCLE..C...K.....GT.RWMAPEM...K...RKVDVYSFG.VLWELTTCL.PFQ..
Retrocopy GGGRVKVADLGTSCLEATCRGDKCSSKAGTFRWMAPEMIHDKRCNRKVDVYSFGLVLWELTTCLVPFQNL

Parental  TPVQAAYAASEKNLRPPLSTSCSPVLNNLIKRCWSANPARRPEFSYIVSVLEKYDHCVKEGMPIMAHQE
          .PVQ.A........RPPLS.SC.P..N.LIKRCWS..PARRPEF..IVSVLE.YD.C...G.P..A..E
Retrocopy SPVQVAFSVCDRDARPPLSPSCPPAINSLIKRCWSTEPARRPEFKQIVSVLESYDRCLRQGLPMVALPE

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_15 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA023324	1 retrocopy	retro_oind_40,
Oryza glumaepatula	OGLUM06G23210	1 retrocopy	retro_oglu_33,
Oryza meridionalis	OMERI06G22050	1 retrocopy	retro_omer_20,
Oryza nivara	ONIVA06G26030	1 retrocopy	retro_oniv_29,
Oryza glaberrima	ORGLA06G0183600	1 retrocopy	retro_ogla_6,
Oryza rufipogon	ORUFI06G23740	1 retrocopy	retro_oruf_15 ,
Oryza sativa japonica	OS06G0636600	1 retrocopy	retro_osat_5,