RetrogeneDB ID: retro_opun_16

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 6:358114..358837(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC06G00520
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC09G08360
• Aliases: None
• Description: None

Sequence

>retro_opun_16
ATGACGACGGGGGGGATGGAGGCCGTGCTGTTCGACATCGACGGCACCATGTGCGTCTCCGACCCATTCCACCACAGGGC
CTTCTCCGAGCTCCTCCAGACACTCGGCTACAACTCCGGCGTCCCCATCACGCCGGAGTTCGGCATGGCCCACATGGCCG
GCCGGAGCAACGATCAGATCGGCCGCTTCCTCTTCCCGGACTGGCCCCAGCACCGCCTCGACGCCTTCTTCGCCAACAAG
GAGGCCCTCTTCGCGCGCTACGCCGCCGAGGGCCTCCGGGAGGTCGCCGGACTCACCGACCTCTGCCGGTGGGCCGCCGC
CCGAGGCCTCAAGCTCGCCGCCGTCACCAACGCGCCGCGGGCCAACGCCGAGCTCATGATCTCCATCCTCGGCCTCTCCG
ACTTCTTCCAGCTCATCGTCGCCGCCGCCGACGACTGCGACCACCCCAAGCCCTCGCCGGAGCCCTACCTCCGGGCGCTC
AGCCTGCTCGGCGCGTCCCCCGATCACACGCTCGTCTTCGAGGACTCGGTGGTCGGCGTGAAGGCCGGCGTCGCCGCCGG
GGTGCCGGTGATCGCCGTCGCGGAGGAGGCCCGGGAGGCCAAGCTCGTCGGCGCTGGAGCGTCCCTCGTCATCAGGGACT
ACAAAGACGACAAGCTCTGGGCAGCATTAGACAAGCTCGACACAGCATCAGCTCAAGCCAATGGACAACTGGAGCATAGT
TGA

Alignment

ORF - retro_opun_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.74 %
• Parental protein coverage: 89.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IEAVLFDIDGTLCDSDPLHHVAFQEMLLEIGYNNGVPIDEEFFINNIAGRSDVEAAQNLFPDWPPEKGLK
          .EAVLFDIDGT.C.SDP.HH.AF.E.L...GYN.GVPI..EF.....AGRS.......LFPDWP......
Retrocopy MEAVLFDIDGTMCVSDPFHHRAFSELLQTLGYNSGVPITPEFGMAHMAGRSNDQIGRFLFPDWPQHRLDA

Parental  FLEDKEAKYRSLAKERLEPVKGLAKVVQWVKDHGYKRAAVTNAPRINSELMISLLGLTDFFQAIIVGG-E
          F...KEA.....A.E.L..V.GL.....W....G.K.AAVTNAPR.N.ELMIS.LGL.DFFQ.I......
Retrocopy FFANKEALFARYAAEGLREVAGLTDLCRWAAARGLKLAAVTNAPRANAELMISILGLSDFFQLIVAAADD

Parental  CEKPKPAPFPYLKALKELQVSADHTFIFEDSASGTRAGVAAGIPVVAVATRNPEKSLLDAGATLIIKDYE
          C..PKP.P.PYL.AL..L..S.DHT..FEDS..G..AGVAAG.PV.AVA....E..L..AGA.L.I.DY.
Retrocopy CDHPKPSPEPYLRALSLLGASPDHTLVFEDSVVGVKAGVAAGVPVIAVAEEAREAKLVGAGASLVIRDYK

Parental  DPKLWSALEEIDREEAK
          D.KLW.AL...D...A.
Retrocopy DDKLWAALDKLDTASAQ

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_16 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	BGIOSGA029783	1 retrocopy	retro_oind_12,
Oryza barthii	OBART09G09890	1 retrocopy	retro_obar_14,
Oryza glumaepatula	OGLUM09G10170	1 retrocopy	retro_oglu_30,
Oryza meridionalis	OMERI09G07660	1 retrocopy	retro_omer_18,
Oryza punctata	OPUNC09G08360	1 retrocopy	retro_opun_16 ,
Oryza glaberrima	ORGLA09G0073400	1 retrocopy	retro_ogla_33,
Oryza rufipogon	ORUFI09G10540	1 retrocopy	retro_oruf_11,
Oryza sativa japonica	OS09G0407700	1 retrocopy	retro_osat_26,