RetrogeneDB ID: retro_opun_1

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 6:34219383..34220205(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC06G25510
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC03G02420
• Aliases: None
• Description: None

Sequence

>retro_opun_1
ATGGAGGTGGAGCAGCTGCCGGGATTTAGGTTCCACCCGACGGAGGAGGAGCTGCTGGAGTTCTACCTGAAGCAGGTGGT
GCAGGGGAAGAAGCTCAAGTTCGACATCATCCCCACCGTGCAGCTCTACCGCCATGACCCGCGCGAGCTCCCCGGCCTCG
CCCGCATCGGCGAGCGCGAGTGGTACTTCTTCGTCCCGCGCGACCGCAAGCAGGCCGCCGGCGCCGGCGGCGGCAGGCCC
AGCCGCACCACGGAGCGCGGCTTCTGGAAGGCCACCGGCTCCGACCGCGCCGTCCGCTGCGCCGCCGACCCCAAGCGCCT
CATCGGCCGCAAGAAGACGCTCGTCTACTACGAGGGACGCGCCCCACGCGGCACCAAGACCGACTGGGTCATGAACGAGT
ACCGCCTCCCCGACGCCGCCGCCGCCGCCATTCCCATGCAAAAGCAACACGACGACATGGTGCTGTGCAAAGTCTACCGG
AAGGCAGTGTCTCTCAAGGAGCTGGAGCAGAGGGTCGCCATGGAGGAGCTTGCACGGTCGTCGACTACCACGTCGTCCAA
CAACACCGGCTCGCCCCTGCAGGACTCCTCCTCCATCTCCATCTCCTCCTCGTCGGACGCCATGAAGAAAGAGGTGGTGC
TGGTGGATGAGGCGGCGGCGGCGCATGAACTGCTCCGGCCGGCGACGCTGAGCCTGCCGCAGCTGGAGGTGGCGAGGCCG
CAGAGCGGTCTGGAGTGGATGCAGGAGCCATTCCTGACGCAGCTGCGGAGCCCATGGATGGAGAGCTGGTCGCCCTACTA
CGCCAGCGTCCTCAACTTCTGA

Alignment

ORF - retro_opun_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.14 %
• Parental protein coverage: 63.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEVEQDLPGFRFHPTEEELLDFYLSRVVLGKKLHFDIIGTLNIYRHDPWDLPGMAKIGEREREWYFFVPR
          MEVEQ.LPGFRFHPTEEELL.FYL..VV.GKKL.FDII.T...YRHDP..LPG.A.IGERE..WYFFVPR
Retrocopy MEVEQ-LPGFRFHPTEEELLEFYLKQVVQGKKLKFDIIPTVQLYRHDPRELPGLARIGERE--WYFFVPR

Parental  DRK---AGNGGRPNRTTERGFWKATGSDRAIRSSGDPKRVIGLKKTLVFYQGRAPRGTKTDWVMNEYRLP
          DRK......GGRP.RTTERGFWKATGSDRA.R...DPKR.IG.KKTLV.Y.GRAPRGTKTDWVMNEYRLP
Retrocopy DRKQAAGAGGGRPSRTTERGFWKATGSDRAVRCAADPKRLIGRKKTLVYYEGRAPRGTKTDWVMNEYRLP

Parental  DHGAARAATPPPKEDMVLCKIYRKATPLKELEQRASAMEEMQRRSSHGDYRATRASLVHDASAS
          D..AA.........DMVLCK.YRKA..LKELEQR..AMEE..R.S.......T...L....S.S
Retrocopy DAAAAAIPMQKQHDDMVLCKVYRKAVSLKELEQRV-AMEELARSSTTTSSNNTGSPLQDSSSIS

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_1 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Leersia perrieri	LPERR03G02450	1 retrocopy	retro_lper_29,
Oryza meridionalis	OMERI03G02480	1 retrocopy	retro_omer_9,
Oryza punctata	OPUNC03G02420	1 retrocopy	retro_opun_1 ,