RetrogeneDB ID: retro_ogla_38

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: Oglab06_unplaced163:29327..31355(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORGLA06G0272500
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA04G0190200
• Aliases: None
• Description: None

Sequence

>retro_ogla_38
ATGGTGGCCGCCAGCGAGGCAGGTCAGCACCACGAGTCCGGCGGCGCGGAGTGGAGGGTGACGGTGGCGGAGGCGCCGGA
GGCGGAGGTGGAGCATGAGAACGCGAAAGGCGCGCGGCGGGGGTGCTGCTGCGCCCCGGCGGCGGCGGCGGCGTGGGTGC
TGTGGTGGCTGGCCGCGCCGTGGAAGTGGGTGGCCAGGTTCGGGAGGACGGCGTGGAAGGTCGGCGCCGACGACCCGAGG
AGGGTGGTGCACGGGTTCAAGGTGGCGCTGGCGCTTACCTTGTGCTCCGCCTTCTACTACGTCCGCCCGCTCTACGTCTT
CACCGGCCAGACCGCCATGTGGGCCGTCCTCACCGTCGTCGTCGTCTTCGAGTACACCGTCGGCGGCTGCATGTACAAGG
GGCTGAACAGGGCGATGGCGACGGTGGCCGGCGGCGCGCTGGCGCTCGGCGTCCACTGGGTCGCCGACAAGTCCGGCGAC
GACGCGGAGCCGTTCGTCCTCACCGCCTCGCTCTTCGTGCTGGCCGCGGCGGCGTCCTTCTCCCGCTTCATCCCCACGCT
CAAGGCGCGGTTCGACTACGGCGTCACCATCTTCATCCTCACCTACAGCCTCGTCGCCGTGTCGGGGTACCGCGTCGACA
CGCTGGTCACCATGGCGCAGCAGCGCCTCATCACCATCGCCATCGGAGCGTTCATCTGCTTCGCCGTCTGCACGCTCGTC
TTGCCGGTCTGGGCCGGGCAGGAGCTGCACGTCCTCGTCGCGCGCAACATGGACAAGCTCGCCGCCGCCATCGAGGCCTG
CGTCGATGACTACTTCTCCTCCGCCGAGCACGCTGGCGGTGGCGGCGACGCCGCCACGGCGCTGTCGGAGAAGGCGCGCG
GGTACAGGGCTGCGCTTAACGCCAAGGCGTCGGAGGACTCGCTGGCGAACCTGGCGAGGTGGGAGCCCGGCCATGGCAAG
TTCGGCTTCCGCCACCCGTACGGCCAGTACCAGAATGTCGGCGCCGCCATGCGCTGCTGCGCCTACTGCATCGACGCCCT
CGCGGCCTGCGTCGGCGCGGGCGGGCAAGCGCCGGCGCACGTCAAGAGGCACCTCGCCGGCGCCTGCGTCGCCCTGAGCC
AGCACTGCGCCGCCGTGCTCCGCGAGGCGTCGGGCTCCGTCACGTCCATGACGCGGTCCGGCCGCCTCGCCCTCGTCGTC
GGGGACATGAACGCCGCCGCCCAAGACCTGAGGAACGAGCTGAGATGCCTCGCCGAGATACTGGACGACGACGAAGAAGA
AGAAGCCGCGTCATCAGAGGCAGAGCAGCACGAGCACAACACCGCGCCGCCGCCGCCGCCGCCGCTCATCGAGGCGCTGC
CGCTCATCGAGGCGCTGCCGCTCTTCACCGCCGCCTCTCTCCTGCTTGAGATATCCACTAGAGCGGAGGGGGTCGTCGCC
GCCGTGGACGCCCTGGCCACCACGGCGAAGTTCAAGAAAGCCGACCACGCCGAACCACCAGCAACCACAACGCTCGACGC
CGAGGCGGCCATGCCCGTACCCATCTCCAACGCCATCGCCGCAGACGAGGCGCACGGCAATGCCACCGCCGGCGAGCATG
ACAAGAAGGAGACGGCGGAGCAGACGACGACGACGAGCGCGAGCACCGTGGGGCAGCAGCAAGAGGCGCGGGACCAGGTG
GGGCAGCTGGTGAAGCTGCTGATGCGGAGGCGGAGCACCAAGAAGTGGGCGCGCGGCGAGCCCAAGGTGGGCCCGTGCCC
GAGGCCGCCGCTGGACTTCCCGCCGGTCCACGCGCCCAGCCCGAGGAGCCGGTCCACGGAGCTCGCCGGCCACCCGCCGG
TGGTGCCCAGCCCGAGGCACCGGTCCATGGACCTGGCGAGCCACGGGCTCGCGCTGCCGAGCTCGAGACACCGGTCCATG
GACCTCGCAAGCCATGGGCCCGTGCTGCCGAGCCCAAGGAACAGGTCCATGGACTTCACGGCCCACGCGCCGAGCCCGAG
AAACCGATCCATTCTTGGGATGGCTTGA

Alignment

ORF - retro_ogla_38 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.81 %
• Parental protein coverage: 77.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GRCRRAAVAWAWQLVSCVAALGSRASGLAGRVWKIGADDPRRAVHGVKVGLALALVSVFYYTRPLYDGVG
          G.C...A.A.AW......AA............WK.GADDPRR.VHG.KV.LAL.L.S.FYY.RPLY...G
Retrocopy GCCCAPAAAAAW-VLWWLAAPWKWVARFGRTAWKVGADDPRRVVHGFKVALALTLCSAFYYVRPLYVFTG

Parental  GAAMWAVMTVVVVFEFTVGGCVYKGFNRATATVSAGAVALGVHWIASKSGDKLEPVVRSGSVFLLAAAAT
          ..AMWAV.TVVVVFE.TVGGC.YKG.NRA.ATV..GA.ALGVHW.A.KSGD..EP.V...S.F.LAAAA.
Retrocopy QTAMWAVLTVVVVFEYTVGGCMYKGLNRAMATVAGGALALGVHWVADKSGDDAEPFVLTASLFVLAAAAS

Parental  FSRFIPTVKARFDYGVTIFILTYSLVAVSGYRVDALVAMAQQRVSTIAIGIFICLAVCVLICPVWAGQEL
          FSRFIPT.KARFDYGVTIFILTYSLVAVSGYRVD.LV.MAQQR..TIAIG.FIC.AVC.L..PVWAGQEL
Retrocopy FSRFIPTLKARFDYGVTIFILTYSLVAVSGYRVDTLVTMAQQRLITIAIGAFICFAVCTLVLPVWAGQEL

Parental  HRLTARNMDKLAGAVEACVEGYFVAGEEEAAGPEYKRRPAAAAAAEGYKCVLNSKASEDAQANLARWEPA
          H.L.ARNMDKLA.A.EACV..YF...E....G.......A....A.GY...LN.KASED..ANLARWEP.
Retrocopy HVLVARNMDKLAAAIEACVDDYFSSAEHAGGGGD--AATALSEKARGYRAALNAKASEDSLANLARWEPG

Parental  HGRFGFRHPYAQYKAVGAAMRHCAYCVEALSGCIRSAEAQSPEGVKRHLAGASTRVATRCAAVLREASSS
          HG.FGFRHPY.QY..VGAAMR.CAYC..AL..C...A..Q.P..VKRHLAGA.......CAAVLREAS.S
Retrocopy HGKFGFRHPYGQYQNVGAAMRCCAYCIDALAACV-GAGGQAPAHVKRHLAGACVALSQHCAAVLREASGS

Parental  VAAMTTPSRGLDFAVADMNTAVQELQSEVRELPSKLAAAAGEPAAAQQ
          V..MT...R.L...V.DMN.A.Q.L..E.R.L...L.....E.AA...
Retrocopy VTSMTRSGR-LALVVGDMNAAAQDLRNELRCLAEILDDDEEEEAASSE

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza glaberrima was not studied using ChIP-Seq data.

EST

Oryza glaberrima was not studied using EST data.

TSS

Oryza glaberrima was not studied using FANTOM5 data.

Lab

retro_ogla_38 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza glaberrima 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,