RetrogeneDB ID: retro_ogla_39

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 8:15092254..15093850(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORGLA08G0132700
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA02G0273700
• Aliases: None
• Description: None

Sequence

>retro_ogla_39
ATGGCGGCGGCGACGACAATGTGCGCCGCGGTGGCGGTGCTCCTCGTTCTGACGTCGACAATGGCGGCCGCCGCCGGCGA
TGGCGATGGCGATGGCGATGGCGGTGGCTTCGACTACAAGAAGGCGCTGCACAGCGGGCTGCTCTACTTCGAGGCGCAGC
GGTCGGGGCACCTGCCGTACAACCAGCGGGTGCGGTGGCGCGGCCACTCGGGGCTCGCCGACGGGCTGCAGCAAGGGGTG
GACCTCGTCGGCGGCTACTACGACGCCGGCGACAACGTGAAGTTCGGCCTGCCCATGGCGTTCACGATGACGATGCTGTC
GTGGGCCGCGGCGGAGTTCTGGGACGAGATCGCCGCCGCCGGCGAGCGGCGGCACGTGCTGGAGGCCATCAAGTGGGGCA
CCGACTACCTCGTGAAGGCGCACACCGCCGCCGACGAGCTGTGGGCCGAGGTCGGCGACGGCGACACCGACCACTACTGC
TGGCAGCGGCCGGAGGACATGACGACGTCGAGGCAGGCCTACAAGGTGGACCGCGACAACCCCGGCTCCGACGTCGCCGG
CGAGACCGCCGCCGCGCTCGCCGCCGCGTCCATCGTGTTCCGCCGCTCCAACCCCCGCTACTCCCGCCTCCTCCTCCGCC
ACGCCGAGCAGCTGTTCGACTTCGGCGACAGGTACAGGGGCAAGTACGACAGCAGCATCGGCGAGGTGAGGGCGTACTAC
GCGTCGGTGAGCGGCTACGGCGACGAGCTGCTGTGGGCGGCGCTGTGGCTGCACCGCGCCACCGGCCGCCGCGGCTACCT
CGACTACGCCGTCGCCATGGCCGACGAGCTCGGCGGCGTCGGCTGGGCCGTCACCGAGTTCAGCTGGGACGTCAAGTACG
CCGGCCTCCAGATCCTCGCCGCCAAGGTGCTCATGGACGGCGGCGACCACCCGGCGGCGCACGCGGCGACGCTGGAGCAG
TACAGGTCCAAGGCGGAGCAGTACCTCTGCGCCTGCCTCGGCAAGAACGCCGCCGCCGGCGACAACGTCAACCGCACCGC
CGGCGGCATGCTGTTCGTCCGCCGCTGGAACAACATGCAGTACGTCACCAACGCCGCCTTCCTCCTCACCGTCTACTCCC
GCTACCTCCGCGACTCCGGCGGCGACACCATCCGGTGCTCCGGTGGGGCTATGGCAACCGGCGACGAGTTGGCGGCGATG
GCGAGGGCGCAGGCGGACTACGTGCTGGGCGACAACCCGGCGGGGGTGAGCTACATGGTCGGGTACGGGCGGCGGTTCCC
GCGGCGGGTGCACCACCGCGGGGCGTCCATGGTGTCGCACCGCGCGGACGGGCGGTTCGTGGGGTGCGTGCAGGGGTACG
ACCGCTGGTTCCGGCGCGGCGGCGCGAACCCGAACGTGGTCGCCGGAGCCATCGTCGGCGGGCCGGACCACCGCGACAGG
TTCAGGGACAGCCGCGACAACTACATGCAGACGGAGGCGTGCACGTACAACACCGCGCCCATGGTCGGCGTCTTCGCGCA
CCTGCACGCCCAGAAGATGGCGGCGAGGACTGCTAATAATAATGCCGATCGATCGATGATTAAACGAGTGGATTGA

Alignment

ORF - retro_ogla_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.06 %
• Parental protein coverage: 90.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAALLLQLLLLAAAGGAGAAATERKAHNYEDALRKSLLYFEAQRSGRLPHNQRVAWRDHSGLTDGLEQGV
          VA.LL......AAA.G.G..........Y..AL...LLYFEAQRSG.LP.NQRV.WR.HSGL.DGL.QGV
Retrocopy VAVLLVLTSTMAAAAGDGDGDGDGGGFDYKKALHSGLLYFEAQRSGHLPYNQRVRWRGHSGLADGLQQGV

Parental  DLVGGYYDAGDHVKFGLPMAFTVTMLSWSMIEYGDDVEAAGELGHALEAIKWGTDYFIKAHTKPNELWAE
          DLVGGYYDAGD.VKFGLPMAFT.TMLSW...E..D...AAGE..H.LEAIKWGTDY..KAHT...ELWAE
Retrocopy DLVGGYYDAGDNVKFGLPMAFTMTMLSWAAAEFWDEIAAAGERRHVLEAIKWGTDYLVKAHTAADELWAE

Parental  VGDGDTDHYCWQRPEDMTTSRQAYKVDRERPGSDVAGETAAAMAAASIVFRKSNPHYASLLLHHAQQLFE
          VGDGDTDHYCWQRPEDMTTSRQAYKVDR..PGSDVAGETAAA.AAASIVFR.SNP.Y..LLL.HA.QLF.
Retrocopy VGDGDTDHYCWQRPEDMTTSRQAYKVDRDNPGSDVAGETAAALAAASIVFRRSNPRYSRLLLRHAEQLFD

Parental  FADKYRGKYDSSIAEVKSYYASVSGYKDELLWAALWLHRATGKAHYLDYVVDNADCFGGTGWAITEFSWD
          F.D.YRGKYDSSI.EV..YYASVSGY.DELLWAALWLHRATG...YLDY.V..AD..GG.GWA.TEFSWD
Retrocopy FGDRYRGKYDSSIGEVRAYYASVSGYGDELLWAALWLHRATGRRGYLDYAVAMADELGGVGWAVTEFSWD

Parental  VKYAGVQILAARLLL-RGEHEERHRSTLEQYRAKAEHYVCGCLGRNADGGADANVERSPGGMLYVRQWNN
          VKYAG.QILAA..L...G.H...H..TLEQYR.KAE.Y.C.CLG.NA..G...NV.R..GGML.VR.WNN
Retrocopy VKYAGLQILAAKVLMDGGDHPAAHAATLEQYRSKAEQYLCACLGKNAAAG--DNVNRTAGGMLFVRRWNN

Parental  MQYVTNAAFLLAAYADYLGDDADGAVSCAGGETAGAGEVAALARAQVDYVLGTNPRGISYLVGYGAKYPN
          MQYVTNAAFLL..Y..YL.D.......C.GG..A...E.AA.ARAQ.DYVLG.NP.G.SY.VGYG...P.
Retrocopy MQYVTNAAFLLTVYSRYLRDSGGDTIRCSGGAMATGDELAAMARAQADYVLGDNPAGVSYMVGYGRRFPR

Parental  RVHHRAASIVPYKHSKEFIGCTQGFDHWFGRRSSNPNVLVGAIVGGPDRRDRFRDNRENYMQTEACTYNT
          RVHHR.AS.V.......F.GC.QG.D.WF.R...NPNV..GAIVGGPD.RDRFRD.R.NYMQTEACTYNT
Retrocopy RVHHRGASMVSHRADGRFVGCVQGYDRWFRRGGANPNVVAGAIVGGPDHRDRFRDSRDNYMQTEACTYNT

Parental  APMVGMFAKLN
          APMVG.FA.L.
Retrocopy APMVGVFAHLH

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_39 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA009019	1 retrocopy	retro_oind_14,
Oryza barthii	OBART02G31860	1 retrocopy	retro_obar_24,
Oryza glaberrima	ORGLA02G0273700	1 retrocopy	retro_ogla_39 ,
Oryza rufipogon	ORUFI02G33530	1 retrocopy	retro_oruf_46,
Oryza sativa japonica	OS02G0738600	1 retrocopy	retro_osat_30,