RetrogeneDB ID: retro_omer_4

Retrocopy location

• Organism: Oryza meridionalis
• Coordinates: 6:14849079..14851089(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OMERI06G15020
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OMERI04G18490
• Aliases: None
• Description: None

Sequence

>retro_omer_4
ATGGTGGCCGCCGGCGAGGCAGGTCAGCACCACGAGTCCGGCGGCGCGGAGTGGAGGGTGACGGTGGCGGAGGCGCCGGA
GGCGGAGGTGGAGCACGAGAACGCGAAATGCGCGCGGCGGGCGTGCTGCTGCGCTCCGGCGGCGGCGGCGGCCGCGGCGT
GGGTGCTGTGGTGGTTGGCCGCGCCGTGGAAGTGGGTGGCGCGGTTCGGGAGGACGGCGTGGAAGGTCGGCGCCGACGAC
CCGAGGAGGGTGGTGCACGGGTTCAAGGTGGCGCTGGCGCTCACCCTCTGCTCCGCCTTCTACTACGTCCGCCCGCTCTA
CGTCTTCACCGGCCAGACCGCCATGTGGGCCGTCCTCACCGTCGTCGTCGTCTTCGAGTACACCGTCGGCGGCTGCATGT
ACAAGGGGCTGAACAGGGCGATGGCGACGGTGGCCGGCGGCGCGCTGGCGCTCGGCGTGCACTGGGTCGCCGACAAGTCC
GGCGACGACGCGGAGCCCTTCGTCCTCACCGCCTCGCTCTTCGTGCTGGCCGCGGCGGCGTCCTTCTCCCGCTTCATCCC
CACGCTGAGGGCGCGGTTCGACTACGGTGTCACCATCTTCATCCTCACCTACAGCCTCGTCGCCGTGTCCGGGTACCGCG
TCGACACGCTGGTGACCATGGCGCAGCAGCGGCTCATCACCATCGCCATCGGGGCGTTCATCTGCTTCGCCGTCTGCACG
CTCGTGTTCCCGGTCTGGGCCGGGCAGGAGCTGCACGTCCTCGTCGCACGGAACATGGACAAGCTCGCCGCCGCCGTCGA
GGCCTGCGTCGACGACTACTTCTCCTCCGCCGAGCACGCTGGCGGTGGCGGCGACGCCGCCACGGCGCTGTCGGAGAAGG
CGCGCGGGTGCAGGGCCGTGCTCAACGCCAAGGCGTCGGAGGACTCGCTGGCGAACCTGGCGAGGTGGGAGCCCGGCCAT
GGAAAGTTCGGCTTCCGCCACCCGTACGGCCAGTACCAGAACGTCGGCGCCGCCATGCGCTGCTGCGCCTACTGCGTCGA
CGCCCTCGCGGCCTGCGTCGGCGGGGGCGGGCAGGCGCCGGCGCACGTCAAGAGGCACCTCGCGGGCGCCTGCGTCGCCC
TGAGCCAGCACTGCGCCGCCGTGCTCCGCGAGGCGTCGGGCTCCGTCACGTCCATGACGCGGTCCGGCCGCCTCGCCCTC
GTCGTCGGCGACATGAACACCGCCGCCCAGGGCCTGAGGAACGAGCTGAGATGCCTCGCCGAGATACTGGACGACGACGA
AGAAGAAGAAGCCGCGTCATCAGGGGCAGATCAGCACGAGCACAACACCGCGCCGCCGCCGCCGCCGCTCATCGAGGCGC
TGCCGCTCTTCACTGCCGCCTCCCTCCTGCTTGAGATATCCACTAGAGCGGAGGGGGTCGTCGCCGCCGTGGACGCCCTG
GCCACCACGGCGAAGTTCAAGAAAGCCGACCACGCCGAGCCAGCTGCACCCACAACGCTCGACACCGAGGCGGCCATGCC
CGTACCCATCTCCAACGCCATCGCCGCAGACGAGGCGCACGGCAAGGCCACCGCCGGCGAGCATGACAAGAAGGAGACGG
CGACAACGACGACGACGAGCGCGAGCACCGTGGGGCAGCAGCAAGAGCCGCGGGACCAGGTGGGGCAGCTGGTGAAGCTG
CTGATGCGGAGGCGGAGCACCAAGAAGTGGGCGCGCGGCGAGCCCAAGGTGGGCCCGTGCCCGAGGCCGCCGCTGGACTT
CCCGCCGGTCCACGCGCCCAGCCCGAGGAGCCGGTCCACGGAGCTCGCCGGCCACCCGCCGGTGGTGCCCAGCCCGAGGC
ACCGGTCCATGGACCTGGCGAGCCACGGGCTCGCGCTGCCGAGCCCGAGACACCGGTCCATGGACCTCGCGAGCCATGGG
CCCGTGCTGCCGAGCCCAAGGAACAGGTCCATGGACTTCACGGCCCACGCGCCGAGCCCGAGAAACCGATCCATTCTTGG
GATGGCTTGA

Alignment

ORF - retro_omer_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.82 %
• Parental protein coverage: 76.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAVAWAWQLVSSVAALGSRASGLAGRVWKIGADDPRRAVHGFKVGLALALVSVFYYTRPLYDGVGGAAMW
          AA.A.AW......AA............WK.GADDPRR.VHGFKV.LAL.L.S.FYY.RPLY...G..AMW
Retrocopy AAAAAAW-VLWWLAAPWKWVARFGRTAWKVGADDPRRVVHGFKVALALTLCSAFYYVRPLYVFTGQTAMW

Parental  AVMTVVVVFEFTVGGCVYKGFNRATATVSAGAVALGVHWIASKSGDKLEPVVRSGSVFLLAAAATFSRFI
          AV.TVVVVFE.TVGGC.YKG.NRA.ATV..GA.ALGVHW.A.KSGD..EP.V...S.F.LAAAA.FSRFI
Retrocopy AVLTVVVVFEYTVGGCMYKGLNRAMATVAGGALALGVHWVADKSGDDAEPFVLTASLFVLAAAASFSRFI

Parental  PTVKARFDYGVTIFILTYSLVAVSGYRVDALLAMAQQRVSTIAIGIFICLAVCVLICPVWAGQELHRLTA
          PT..ARFDYGVTIFILTYSLVAVSGYRVD.L..MAQQR..TIAIG.FIC.AVC.L..PVWAGQELH.L.A
Retrocopy PTLRARFDYGVTIFILTYSLVAVSGYRVDTLVTMAQQRLITIAIGAFICFAVCTLVFPVWAGQELHVLVA

Parental  RNMDKLAGAVEACVEGYFVAGEEEAAPEYKRRPAAAAAAEGYKCVLNSKASEDAQANLARWEPAHGRFGF
          RNMDKLA.AVEACV..YF....E.A........A....A.G...VLN.KASED..ANLARWEP.HG.FGF
Retrocopy RNMDKLAAAVEACVDDYF-SSAEHAGGGGDAATALSEKARGCRAVLNAKASEDSLANLARWEPGHGKFGF

Parental  RHPYAQYKAVGAAMRHCAYCVEALSGCIRSAEAQSPEGVKRHLAGASTRVATRCAAVLREASSSVAAMTT
          RHPY.QY..VGAAMR.CAYCV.AL..C......Q.P..VKRHLAGA.......CAAVLREAS.SV..MT.
Retrocopy RHPYGQYQNVGAAMRCCAYCVDALAACV-GGGGQAPAHVKRHLAGACVALSQHCAAVLREASGSVTSMTR

Parental  PSRGVDFAVADMNTAVQELQSEVRELPSKLAAAAGEPAAA
          ..R.....V.DMNTA.Q.L..E.R.L...L.....E.AA.
Retrocopy SGR-LALVVGDMNTAAQGLRNELRCLAEILDDDEEEEAAS

Legend:

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

Expression

RNA-Seq

Oryza meridionalis was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza meridionalis was not studied using ChIP-Seq data.

EST

Oryza meridionalis was not studied using EST data.

TSS

Oryza meridionalis was not studied using FANTOM5 data.

Lab

retro_omer_4 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza meridionalis 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,