RetrogeneDB ID: retro_osat_42

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 6:13143887..13145894(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OS06G0331900
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OS04G0567200
• Aliases: None
• Description: None

Sequence

>retro_osat_42
ATGGTGGCCGCCGGCGAGGCAGGTCAGCACCACGAGTCCGGCGGCGCGGAGTGGAGGGTGACGGTGGCGGAGGCGCCGGA
GGCGGAGGTGGAGCATGAGAACGCGAAAGGCGCGCGGCGGGGGTGCTGCTGCGCCCCGGCGGCGGCGGCGTGGGTGCTGT
GGTGGCTGGCCGCGCCGTGGAAGTGGGTGGCCAGGTTCGGGAGGACGGCGTGGAAGGTCGGCGCCGACGACCCGAGGAGG
GTGGTGCACGGGTTCAAGGTGGCGCTGGCGCTTACCTTGTGCTCCGCCTTCTACTACGTCCGCCCGCTCTACGTCTTCAC
CGGCCAGACCGCCATGTGGGCCGTCCTCACCGTCGTCGTCGTCTTCGAGTACACCGTCGGCGGCTGCATGTACAAGGGGC
TGAACAGGGCGATGGCGACGGTGGCCGGCGGCGCGCTGGCGCTCGGCGTGCACTGGGTCGCCGACAAGTCTGGCGACGAC
GCGGAGCCGTTCGTCCTCACCGCCTCGCTCTTCGTGCTGGCCGCGGCGGCGTCCTTCTCCCGCTTCATCCCCACGCTCAA
GGCGCGGTTCGACTACGGCGTCACCATCTTCATCCTCACCTACAGCCTCGTCGCCGTGTCGGGGTACCGCGTCGACACGC
TGGTCACCATGGCGCAGCAGCGCCTCATCACCATCGCCATCGGAGCGTTCATCTGCTTCGCCGTCTGCACGCTCGTCTTC
CCGGTCTGGGCCGGGCAGGAGCTGCACGTCCTCGTCGCGCGCAACATGGACAAGCTCGCCGCCGCCATCGAGGCCTGCGT
CGACGACTACTTCTCCTCCGCCGAGCACGCTGGCGGTGGCGGCGACGCCGCCACGGCGCTGTCGGAGAAGGCGCGCGGGT
ACAGGGCTGTGCTTAACGCCAAGGCGTCGGAGGACTCGCTGGCGAACCTGGCGAGGTGGGAGCCCGGCCATGGCAAGTTC
GGCTTCCGCCACCCGTACGGCCAGTACCAGAATGTCGGCGCCGCCATGCGCTGCTGCGCCTACTGCATCGACGCCCTCGC
GGCCTGCGTCGGCGCGGGCGGGCAGGCGCCGGCGCACGTCAAGAGGCACCTCGCCGGCGCCTGCGTCGCCCTGAGCCAGC
ACTGCGCCGCCGTGCTCCGCGAGGCGTCGGGCTCCGTCACGTCCATGACGCGGTCCGGCCGCCTCGCCCTCGTCGTCGGG
GACATGAACGCCGCCGCCCAAGACCTGAGGAACGAGCTGAGATGCCTCGCCGAGATACTGGACGACGACGAAGAAGAAGA
AGCCGCGTCATCAGAGGCAGAGCAGCACGAGCACAACACCGCGCCGCCGCCGCCGCCGCCGCTCATCGAGGCGCTGCCGC
TCTTCACCGCCGCCTCTCTCCTGCTTGAGATATCCACTAGAGCGGAGGGGGTCGTCGCCGCCGTGGACGCCCTGGGCACC
ACGGCGAAGTTCAAGAAAGCCGACCACGCCGAACCACCAGCAACCACAACGCTCGACGCCGAGGCGGCCATGCCCGTACC
CAACTCCAACGCCATCGCCGCAGACGAGGCGCACGGCAATGCCACCGCCGGCGAGCATGACAAGAAGGAGACGGCGGAGC
AGACGACGACGACGAGCGCGAGCACCGTGGGGCAGCAGCAAGAGGCGCGGGACCAGGTGGGACAGCTGGTGAAGCTGCTG
ATGCGGAGGCGGAGCACCAAGAAGTGGGCGCGCGGCGAGCCCAAGGTGGGCCCGTGCCCGAGGCCGCCGCTGGACTTCCC
GCCGGTCCACGCGCCCAGCCCGAGGAGCCGGTCCACGGAGCTCGCCGGCCACCCGCCGGTGGTGCCCAGCCCGAGGCACC
GGTCCATGGACCTGGCGAGCCACGGGCTCGCGCTGCCGAGCTCGAGACACCGGTCCATGGACCTCGCAAGCCATGGGCCC
GTGCTGCCGAGCCCAAGGAACAGGTCCATGGACTTCACGGCCCACGCGCCGAGCCCGAGAAACCGATCCATTCTTGGGAT
GGCTTGA

Alignment

ORF - retro_osat_42 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.03 %
• Parental protein coverage: 71.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WKIGADDPRRAVHGVKVGLALALVSVFYYTRPLYDGVGGAAMWAVMTVVVVFEFTVGGCVYKGFNRATAT
          WK.GADDPRR.VHG.KV.LAL.L.S.FYY.RPLY...G..AMWAV.TVVVVFE.TVGGC.YKG.NRA.AT
Retrocopy WKVGADDPRRVVHGFKVALALTLCSAFYYVRPLYVFTGQTAMWAVLTVVVVFEYTVGGCMYKGLNRAMAT

Parental  VSAGAVALGVHWIASKSGDKLEPVVRSGSVFLLAAAATFSRFIPTVKARFDYGVTIFILTYSLVAVSGYR
          V..GA.ALGVHW.A.KSGD..EP.V...S.F.LAAAA.FSRFIPT.KARFDYGVTIFILTYSLVAVSGYR
Retrocopy VAGGALALGVHWVADKSGDDAEPFVLTASLFVLAAAASFSRFIPTLKARFDYGVTIFILTYSLVAVSGYR

Parental  VDALVAMAQQRVSTIAIGIFICLAVCLLICPVWAGQELHRLTARNMDKLAGAVEACVEGYFVAGEEEAAG
          VD.LV.MAQQR..TIAIG.FIC.AVC.L..PVWAGQELH.L.ARNMDKLA.A.EACV..YF...E....G
Retrocopy VDTLVTMAQQRLITIAIGAFICFAVCTLVFPVWAGQELHVLVARNMDKLAAAIEACVDDYFSSAEHAGGG

Parental  PEYKRRPAAAAAAEGYKCVLNSKASEDAQANLARWEPAHGRFGFRHPYAQYKAVGAAMRHCAYCVEALSG
          .......A....A.GY..VLN.KASED..ANLARWEP.HG.FGFRHPY.QY..VGAAMR.CAYC..AL..
Retrocopy GD--AATALSEKARGYRAVLNAKASEDSLANLARWEPGHGKFGFRHPYGQYQNVGAAMRCCAYCIDALAA

Parental  CIRSAEAQSPEGVNRHLAGASTRVATRCAAVLREASSSVAAMTTPSRGLDFAVADMNTAVQELQSEVREL
          C...A..Q.P..V.RHLAGA.......CAAVLREAS.SV..MT...R.L...V.DMN.A.Q.L..E.R.L
Retrocopy CV-GAGGQAPAHVKRHLAGACVALSQHCAAVLREASGSVTSMTRSGR-LALVVGDMNAAAQDLRNELRCL

Parental  PSKLAAAAGEPAAAQQ
          ...L.....E.AA...
Retrocopy AEILDDDEEEEAASSE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryza sativa japonica was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza sativa japonica was not studied using ChIP-Seq data.

EST

Oryza sativa japonica was not studied using EST data.

TSS

Oryza sativa japonica was not studied using FANTOM5 data.

Lab

retro_osat_42 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza sativa japonica 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 ,