RetrogeneDB ID: retro_opun_32

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 2:39473899..39475021(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC02G35690
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC01G09850
• Aliases: None
• Description: None

Sequence

>retro_opun_32
ATGAACTGCTTCTCCTGGAACCACAGCCTGCGGTGCTGGCATCGCAGCAATGACGGCGGCAGCCCGTGCAGCCCCTGCAG
CCAGGCCGCGCAGAGTTCCATGGGCATGCGCCGCCGATCGGAGCAGCAGCAGGCGGAGGCGGCGGGGGTGGGGGCGGGCG
GTGCGAAGAAGTTCACGCTGGCGCAGCTGTCGGCGGCCACGGACGGGTTCCACGAGTCCAACCTTGTCGGCGAGGGCGGG
TTCGGCAGGGTGTACAGGGGCCGCCTCCTCGTCGACCAAGGGGTCGGACCCGTCGCCGTGAAGCAACTCTGCCACGGCGG
CGCGCAGGGAACCCGCGAGTTCCTGGTGGAATGCATGATGCTCATGATGCTGCACCACCCCAACCTCGTCTCCCTCGTCG
GCTACTGCGCCGACGCCGGCGAGCGCCTCCTCGTCTACGAGTTCCTGCCACGCGGCAGCCTCGACGCGCACCTCTTCGGC
GGTGGCGACTGTGGCAGGAGGCAGGAGCCCCCGCTGGGCTGGGGCGCGCGGGTCAGGATCGCGCTCGGCGCGGCCAGGGG
GCTGCGCTACCTGCACGAGGTGGTGACGCCGCCGGTGATCTACCGCGACCTCAAGGCGTCCAACATCCTGCTCGACGACG
ACCTCAACCCCAAGCTGTCAGACTTTGGCCTCGCCAAGCTGGGCCCCATCGGCGACGACACCCACGTGTCCACGCGCGTC
ATGGGCACCTACGGCTACTGCGCGCCCGACTACGCCATGAGCGGCAAGCTCAACGTTAAGTCCGACGTGTACAGCTTCGG
CGTCGTGCTCCTCGAGCTCATCACGGGACGCAGGGCCTTCGACGCCGCCCGCTCCGCCCCGGAGGAGCAGCGCCTCCTCC
TCTGGGCGCGCCCCTACCTTAACCTCGCCGGCGACCGCAGGAGGTGCTTCGCCCTGGCCGACCCGGCGTTGCAGGGCCGC
TACCCCCGCCGCGCCTTCTACCAGCTCGCCGTCGTCACCTCGCTCTGCCTCCGAGACAACCCCAACCTCCGCCCCTCCAT
GACAGACGTCACCCAAGCCCTCGACCACGTCGCCTCCCAGTCACAGCCATGGGAAGACAAGCAAAGAGCCATGCCTGATT
AA

Alignment

ORF - retro_opun_32 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.98 %
• Parental protein coverage: 65.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GHGEATIFTLRELADATNNFRTEYLLGRGGFGSVY--KAFLNDGM-VVAIKQLDLNGLQGNREFLVEVLM
          G.G.A..FTL..L..AT..F....L.G.GGFG.VY........G...VA.KQL...G.QG.REFLVE..M
Retrocopy GAGGAKKFTLAQLSAATDGFHESNLVGEGGFGRVYRGRLLVDQGVGPVAVKQLCHGGAQGTREFLVECMM

Parental  LSLLHHPNLVKLFGYCVDGDQRLLIYEYMPLGSLEDHLH---DLRPGQEP-LDWTTRMKIAADAAAGLEY
          L..LHHPNLV.L.GYC.D...RLL.YE..P.GSL..HL....D....QEP.L.W..R..IA..AA.GL.Y
Retrocopy LMMLHHPNLVSLVGYCADAGERLLVYEFLPRGSLDAHLFGGGDCGRRQEPPLGWGARVRIALGAARGLRY

Parental  LHDEAIPAVIYRDIKPSNILLGEGYNAKLSDFGLAKLGPVGDKTHVTTRVMGTHGYCAPEYLSTGKLTIK
          LH....P.VIYRD.K.SNILL....N.KLSDFGLAKLGP.GD.THV.TRVMGT.GYCAP.Y...GKL..K
Retrocopy LHEVVTPPVIYRDLKASNILLDDDLNPKLSDFGLAKLGPIGDDTHVSTRVMGTYGYCAPDYAMSGKLNVK

Parental  SDIYSFGVVFLELITGRRALDSNR-PPEEQDLVAWARP---LFKDQRKFPKMADPSLHGHFPKRGLYQAL
          SD.YSFGVV.LELITGRRA.D..R..PEEQ.L..WARP...L..D.R.....ADP.L.G..P.R..YQ..
Retrocopy SDVYSFGVVLLELITGRRAFDAARSAPEEQRLLLWARPYLNLAGDRRRCFALADPALQGRYPRRAFYQLA

Parental  AIAAMCLQEKAKNRPSIREVAVALSYLASQT
          .....CL......RPS...V..AL...ASQ.
Retrocopy VVTSLCLRDNPNLRPSMTDVTQALDHVASQS

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_32 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza punctata	OPUNC01G09850	1 retrocopy	retro_opun_32 ,