RetrogeneDB ID: retro_opun_9

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 1:22321808..22322897(-)
• Located in intron of: OPUNC01G19330

Retrocopy information

• Ensembl ID: OPUNC01G19340
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC01G35260
• Aliases: None
• Description: None

Sequence

>retro_opun_9
ATGGGCGCCTCCTGCTCCTCCCCCTTCCCCCCTCCACCTGCAGAATCCAACGCCCCCTCCGCCTCCGCGATGCACCACCA
CCAGCACCCGCCTCACCCCGCGGGCGGAGGAGGACCCGTCATGCCGTACGCCGACGCCGACCGCACCCTCCGCGCGCTCG
CCGGCGCGGCGGAGGGGTTCGGCCGCCGCGCCATCGGTGGACTCCACGGCCCGCTCTACCGCGTCACCTCCCTGGAGGAC
GACGGCCACGGCACCCTCCGCCAGGCGTGCCGGACCCACGGCCCGCTCTGGATCGTCTTCGACGTCTCCGGCGACATCCA
CCTCCGCACCTACCTCCGCGTCTCCTCCCACAAGACCATCGACGGCCGCGGCCAGCGCGTCCGCCTCGTCGGCAAGGGGC
TCCAGCTCAAGGAGTGCCACCACGTGATCGTCTGCAACCTCGAGATCGAGGGCGGCCGCGGCCACGACGTGGACGCCGTG
CAGATCAAGCCGGCCTCCACCCACATCTGGATCGACCGATGCAGCCTCGCCGACTGCGACGACGGCCTCGTCGACATCAC
CCGCGGGAGCACAGACATCACCGTCTCCAGGTGCCGCTTCTCCCGCCACGACAAGACCATGCTGGTCGGCGCCGATCCCA
CCCACACCGGCGACCGCTGCATCCGCGTCACCATCCACCACTGCTTCTTCGACGGCACGCGGCAGCGCCACCCGCGGCTA
CGCTTCGGCAGGGCGCACCTGTACAACAACTACACGAGGGATTGGGGCATCTACGCCGCCGGCGCCGGCGTGGAGGCGCA
GATCGCGTCGCAGTGCAATATCTACGAAGCCGGGGAGAAGAAGACGGTGTTCAAGTACGTACCGGAGAAGGCGGCGGACC
GGGAGGAGGCGGAGGCAGGGTGGATCAGGTCGGAGGGCGACGCGTTCCTCAACGGCGCGCGGCCGTGCTTGGTGGACGGC
GGCGCGGCGGTGTTCAGGCCGGAGGAGTACTACGAGAGGTGGACCATGGAGGCGGCGTCGCCGGCGCTCAAGGAGGTGGT
GCAGCTGTGCGCCGGTTGGCAGCCCGTGCCGAGGCCGCCGGGCGAGTGA

Alignment

ORF - retro_opun_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.99 %
• Parental protein coverage: 74.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPYATADSSLRAMAGQAEGFGRHAIGGLHGDVYHVTTLEDDGDGSLREGCRRREPLWIVFDVSGTIHLST
          MPYA.AD..LRA.AG.AEGFGR.AIGGLHG..Y.VT.LEDDG.G.LR..CR...PLWIVFDVSG.IHL.T
Retrocopy MPYADADRTLRALAGAAEGFGRRAIGGLHGPLYRVTSLEDDGHGTLRQACRTHGPLWIVFDVSGDIHLRT

Parental  GLRVSSYKTIDGRGQRVVLSGKGLQLRECEHVIVCNLEVEGCRGRDADAVAVKPGSRHVWIDRCGLRGCG
          .LRVSS.KTIDGRGQRV.L.GKGLQL.EC.HVIVCNLE.EG.RG.D.DAV..KP.S.H.WIDRC.L..C.
Retrocopy YLRVSSHKTIDGRGQRVRLVGKGLQLKECHHVIVCNLEIEGGRGHDVDAVQIKPASTHIWIDRCSLADCD

Parental  DGLVDVTRGSTDVTVSRCRFSAHDKAVLIGGSAGHVEDRAIRVTIHHCLFDGTRQRHPRVRFGRVHLYNN
          DGLVD.TRGSTD.TVSRCRFS.HDK..L.G....H..DR.IRVTIHHC.FDGTRQRHPR.RFGR.HLYNN
Retrocopy DGLVDITRGSTDITVSRCRFSRHDKTMLVGADPTHTGDRCIRVTIHHCFFDGTRQRHPRLRFGRAHLYNN

Parental  YTRGWGIYAVCASVESQIVSQCNIYEAGEKKKVFKYMTEQAADRDRSSTGLIRSEGDLFLNGA
          YTR.WGIYA..A.VE.QI.SQCNIYEAGEKK.VFKY..E.AADR.....G.IRSEGD.FLNGA
Retrocopy YTRDWGIYAAGAGVEAQIASQCNIYEAGEKKTVFKYVPEKAADREEAEAGWIRSEGDAFLNGA

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza punctata was not studied using ChIP-Seq data.

EST

Oryza punctata was not studied using EST data.

TSS

Oryza punctata was not studied using FANTOM5 data.

Lab

retro_opun_9 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza punctata 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA004758	1 retrocopy	retro_oind_37,
Leersia perrieri	LPERR01G31380	1 retrocopy	retro_lper_4,
Oryza meridionalis	OMERI01G33590	1 retrocopy	retro_omer_1,
Oryza nivara	ONIVA01G41460	1 retrocopy	retro_oniv_25,
Oryza punctata	OPUNC01G35260	1 retrocopy	retro_opun_9 ,
Oryza punctata	OPUNC06G17690	1 retrocopy	retro_opun_11,
Oryza glaberrima	ORGLA01G0303100	1 retrocopy	retro_ogla_4,
Oryza sativa japonica	OS01G0837100	1 retrocopy	retro_osat_37,