RetrogeneDB ID: retro_opun_5

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 8:6762438..6763296(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC08G06740
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC04G21880
• Aliases: None
• Description: None

Sequence

>retro_opun_5
ATGGCCGTGGACCTCATGGGCTTCAGCCCGCGCGGCGGCTGCCCGTCTGTGGAGAAGGAGCAGCTCGCGTTCCAGGAGGC
CGCCGCCGCGGGGCTCCGCAGCCTCGAGCTGCTCGTCTCGTCCCTCTCCGGCGGGGAACGCCGCCCGCAGCCGCTGGAAG
AGATCGCGGACCAGGCGGTGTTCAGGTTCAGGAAGGTGATATCGATTCTTGACCGTACCGGCCACGCCCGCTTCCGCCGT
GGCCCTGTCGTCGGAGCTGCTGCCGCGGAGGCGGCGTCGGCGGCTTCACCGTCTTCGTCTCCTGTTTCGCCTCTTCCGCC
GGTGACGACGCAGCCGGCGGCTGTGAAGAGCCTGACGCTGGACTTCACGAATCCAGCCAAGGTCGCGGCGGCGTCGGTGA
CATCGACGTCGTTCTTCTCGTCGGTGACAGCTGGCGGAGACGGCAGCGTGTCGAAGGGCCGGAGCCTTGTCTCCTCCGGG
AAACCCCCGCTCGCCGGCGGCGTCAAGCGCAAGCACCCGCACCCGCCCTGCGCAGGCGGCGACGGGCACGGCGCCGGCGC
AGCCCACGCGCACGCGCACGGCGGGTGCCACTGTTCCAAGAAGCGGAAGCACCGCGTGCGGCGCACGGTGCGCGTTCCCG
CGGCGAGCGCGCGGGTGGCGGACATCCCCGCCGACGAGTACTCGTGGCGGAAGTACGGGCAGAAGCCGATCAAGGGGTCC
CCCTACCCGCGCGGCTACTACCGATGCAGCTCAGTCAAGGGTTGCCCCGCCCGGAAGCACGTCGAGCGCGCCGCCGACGA
CCCCGCCACCCTCGTCGTCACCTACGAGGGCGACCACCGCCACTCGCCGCCGGCGTGA

Alignment

ORF - retro_opun_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.24 %
• Parental protein coverage: 72.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QPFGEIADQAVSKFRKVISILDRTGHARFRRGPVESSAPAAPVAAAPPPPPPPPAPVAALAPTSSQPQSL
          QP..EIADQAV..FRKVISILDRTGHARFRRGPV...A.AA..A.A..P...P..P............SL
Retrocopy QPLEEIADQAVFRFRKVISILDRTGHARFRRGPVVGAA-AAEAASAASPSSSPVSPLPPVTTQPAAVKSL

Parental  TLDFTKPNLAMSAATSVTSTSFFSSVTA-GEGSVSKGRSLLSSGKPPLSGH-KRK----PCAGGHSE-AT
          TLDFT.P..A..AA.SVTSTSFFSSVTA.G.GSVSKGRSL.SSGKPPL.G..KRK....PCAGG....A.
Retrocopy TLDFTNP--AKVAAASVTSTSFFSSVTAGGDGSVSKGRSLVSSGKPPLAGGVKRKHPHPPCAGGDGHGAG

Parental  ANGSRCH--CSKRRKNR--VKRTIRVPAISSKIADIPPDEYSWRKYGQKPIKGSPYPRGYYKCSTVRGCP
          A.....H..C....K....V.RT.RVPA.S...ADIP.DEYSWRKYGQKPIKGSPYPRGYY.CS.V.GCP
Retrocopy AAHAHAHGGCHCSKKRKHRVRRTVRVPAASARVADIPADEYSWRKYGQKPIKGSPYPRGYYRCSSVKGCP

Parental  ARKHVERATDDPAMLVVTYEGEHRHTP
          ARKHVERA.DDPA.LVVTYEG.HRH.P
Retrocopy ARKHVERAADDPATLVVTYEGDHRHSP

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_5 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Leersia perrieri	LPERR04G20020	1 retrocopy	retro_lper_26,
Oryza punctata	OPUNC04G21880	1 retrocopy	retro_opun_5 ,
Oryza rufipogon	ORUFI04G26070	1 retrocopy	retro_oruf_29,
Oryza sativa japonica	OS04G0605100	1 retrocopy	retro_osat_10,