RetrogeneDB ID: retro_opun_6

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 6:13808651..13810649(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC06G12600
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC04G19720
• Aliases: None
• Description: None

Sequence

>retro_opun_6
ATGGTGGCCGCCGGCGAGGCAGATCAGCACCACGAGTTCGGCGGCGCGGAGTGGAGAGTGACGGTGGCAGAGGCGTCGGA
GGCGGAACTGGAGCACGAGAACGCAAAAGGCGCGCGGCGTGCGTGCTGCTGCTCTCCGGCGGCGGCGGCGGCGGCGGCGG
CGTGGGTGTTGTCGTGGTTAGCCGCGCCGTGGAAGTGGGCGGCCCGGTTCGGAAGGACGGCGTGGAAGGTCGGCGCCGAC
GACCCGAGGAGGGTGGTGCACGGGTTCAAGGTGGCGCTGGCGCTCACCTTGTGCTCCGCCTTCTACTACGTTCGCCCGCT
CTACGTCTTCACCGGCCAGACTGCCATGTGGGCCGTCCTCACCGTCGTTGTCGTCTTCGAGTACACCGTCGGTGGTTGCA
TGTACAAGGGACTGAACAGGGCAATGGCGACTGTGACCGGTGGCGCGCTGGCGCTCGGCGTGCATTGGGTGGCCGACAAG
TCCGGCGATGACCTGGAGCCCTTCATCCTCACCGCTTCCCTCTTCGTGTTGGCCGCGGCGGCGTCGTTCTCCCGGTTCAT
TCCGACGCTGAAGGCGCGGTTCGACTACGGCGTCACCATCTTCATCCTGACCTACAGCCTCGTCGCCGTGTCGGGGTACC
GCGTCGACACGCTGGTGGCCATGGCGGAGCAGCGGCTCATCACTATCGCCATCGGGGCGTTCATCTGCTTCGCCGTCTGC
ACGCTCGTGTTCCCGGTCTGGGCGGGGCAGGAGCTGCACGTCCTCGTCGCGCGCAACATGGACAAGCTCGCCACCGCCGT
CGAGGCCTGCGTCCATGAATACTTCTCCGCCGAGCACGCCGGCGGCGACGCCGCCACGGCGCTGTCGGAGAAGGTGCGCG
GGTACAGGGCTGTGCTCAACGCCAAGGCATCGGAGGACTCGCTGGCGAACTTGGCGAGGTGGGAGCCCGGCCATGGCAAG
TTCGGCTTCCGACACCCGTACAGCCAGTACCAGAAGGTCGGCGCCGCAATGCGCTGCTGCGCCTACTGCGTGGACGCCCT
CGCGGCCTGCGTGGGCGCGGGCGGGCAGGCGCCGGCGCACGTCAAGAGGCACCTCGCAGCCGCCTGCGTCGTCCTGAGCC
AGCACTGCGCCGCCGTGCTCCGCGAGGCGTCGGGCTCCGTCACGTCAATGACGCGCTCCGGCCGCCTCGCACTCGTCGTC
GCCGTCATGAACGCCGCCGCCCAGGACCTGAGGGACGAGCTGAGATGCCTCGCCGAGATACTGGACGAAGAAGAAGATGC
CGCGTCATCAGAGGCAGAGCACGAGCACAACACCGCAACGCCGCCGCCGCCACCGCTCATCGAGGCGCTGCCGCTCTTCA
CCGCCGCCTCCCTCCTGCTGGAGATATCCACTAGAGCGGAGGGGGTCGTCGCCGCCGTGGACGCCCTGGCCACCACGGCG
AAGTTCAAGAAAGCCGACCACGACGGGCCAGCACCCACAACGCTCGGCACCGAGGCGGCCATGCCCGTACCGATCTCAAA
CCCCATCGCCGCAGACGAAGCACACACCAAGGCCACCGCCGGCGAGCATGACAAGAAGGAGACGGCGGAGCAGACGACGA
CGACGACGAGCGCGAGCACCGGGCAGCAGCAAGAGCCGCGCGACCAGGTGGGGCAGCTAGTGAAGCTGCTGATGCGGAGG
CGAAGCACCAAGAAGTGGGCACGCGGCGAGCCCAAGGTGCGCCCGTGCCCGAGGCCACCGCTGGACTTCCCGCCGGTCCA
CGCGCCCAGCCCGAGGAGCCGGTCCACGGAGCTGGCCGGCCACCCGCCGGTGGTGCCCAGCCCGAGGCACCGGTCCATGG
ACCTGGCGAACCACGGTCTGGCGCTTCCAAGCCCAAGGCACCGGTCCATAGACCTCACGAGCCATGGACCCGTGCTGCCG
AGCCCAAGGAACAGGTCCATGGACTTCGCGACCCACACGCCGAGTCCGAGAAACCGATCCATTCTTGGGATGGCTTGA

Alignment

ORF - retro_opun_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.16 %
• Parental protein coverage: 77.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAVAWAWLVSCVAALVSRASGLAGRVWKIGADDPRRAVHGVKVGLALALVSVFYYTRPLYDGVGGAAMWA
          AA.A.AW..S..AA....A.......WK.GADDPRR.VHG.KV.LAL.L.S.FYY.RPLY...G..AMWA
Retrocopy AAAAAAWVLSWLAAPWKWAARFGRTAWKVGADDPRRVVHGFKVALALTLCSAFYYVRPLYVFTGQTAMWA

Parental  VMTVVVVFEYTVGGCAYKGFNRATATVSAGAVALGVHWIASKSGDKLEPVVRSGSVFLLAAAATFSRFIP
          V.TVVVVFEYTVGGC.YKG.NRA.ATV..GA.ALGVHW.A.KSGD.LEP.....S.F.LAAAA.FSRFIP
Retrocopy VLTVVVVFEYTVGGCMYKGLNRAMATVTGGALALGVHWVADKSGDDLEPFILTASLFVLAAAASFSRFIP

Parental  TVKARFDYGVTIFILTYSLVAVSGYRVDALVAMAQQRVSTIAIGIFICLAVCVLICPVWAGQELHRLTAR
          T.KARFDYGVTIFILTYSLVAVSGYRVD.LVAMA.QR..TIAIG.FIC.AVC.L..PVWAGQELH.L.AR
Retrocopy TLKARFDYGVTIFILTYSLVAVSGYRVDTLVAMAEQRLITIAIGAFICFAVCTLVFPVWAGQELHVLVAR

Parental  NMDKLAGAVEACVEGYFVAEEEAAPDKRRTPAAAEGYKCVLNSKASEDAQANLARWEPAHGRFGFRHPYA
          NMDKLA.AVEACV..YF.AE...............GY..VLN.KASED..ANLARWEP.HG.FGFRHPY.
Retrocopy NMDKLATAVEACVHEYFSAEHAGGDAATALSEKVRGYRAVLNAKASEDSLANLARWEPGHGKFGFRHPYS

Parental  QYKAVGAAMRHCAYCVEALNGCIRSTEAQSPEGVKRHLAGASTRVATRCAAVLREASSSVTAMTTASRVL
          QY..VGAAMR.CAYCV.AL..C......Q.P..VKRHLA.A.......CAAVLREAS.SVT.MT...R.L
Retrocopy QYQKVGAAMRCCAYCVDALAACV-GAGGQAPAHVKRHLAAACVVLSQHCAAVLREASGSVTSMTRSGR-L

Parental  DLAVADMNTAVQELQSEVRALPSKLAAAGEPAAAQ
          .L.VA.MN.A.Q.L..E.R.L...L......A...
Retrocopy ALVVAVMNAAAQDLRDELRCLAEILDEEEDAASSE

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_6 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA014531	1 retrocopy	retro_oind_18,
Oryza glumaepatula	OGLUM04G22000	1 retrocopy	retro_oglu_11,
Oryza meridionalis	OMERI04G18490	1 retrocopy	retro_omer_4,
Oryza nivara	ONIVA04G20520	1 retrocopy	retro_oniv_18,
Oryza punctata	OPUNC04G19720	1 retrocopy	retro_opun_6 ,
Oryza glaberrima	ORGLA04G0190200	1 retrocopy	retro_ogla_38,
Oryza sativa japonica	OS04G0567200	1 retrocopy	retro_osat_42,