RetrogeneDB ID: retro_ogla_73

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 8:14596239..14597973(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA06G0255900
• Aliases: None
• Description: None

Sequence

>retro_ogla_73
CTTTTGTTTGCTTTTCATGTAGCTTACTTCATGGATGCGTTGCGGCCGGTGAAGAAGGGCGACCGGTTCTTGGTGCGCGG
CCACATGCACGCCGTGGAGTTCAAGGTGATGGACACGGAGCCGAACAACGAGCCCGTGATCGTGGCGGGCGACACGGAGA
TCTTTTGCGACGAGGGCGACCCGGTGAAGCGCGAGGACGAGGAGCGGCTCGACGGACCGGGCTACGACGACGTCGGCGGC
GTCCGCAAGCAGCTGGCGCAGATCAGGGAGCTCGTCGAGCTGCCCCTGCGCCACCCCAAGCTGTTCCAGACGCTCGGCGT
GCGCCCGCCCAAGGGCATCCTCCTCTACGGGCCCCCCGGCACCGGCAAGACGCTGCTGGCACGCGCCATCGCCGCCGAGT
CCGGCGCCCACTTCGTCGTCGTCAACGGGCCGGAGATCATGTCCGGGATGCCCGGCGAGAGCGAGGCCAACCTGCGCGCC
GTGTTCGCCGAGGCGGACGCCGCGGCGCCGTCCATCGTGTTCATGGACGAGATCGACTCCATCGCGCCCAGCCGCGAGAA
GGCGCACGGCGAGGTGGAGCGCCGCGTCGTGTCGTAGCTGCTCACGCTCATGGACGGCCTCCGCCCGCGGGCCCAGGTGA
TCGTCATCGGCGCCACCAACCGCCCCAACAGCCTCGACCCGGCGCTCCGCCGCTTCGGCCGCTTCGACCGCGAGCTCGAC
ATCGGCGTCCCCGACGAGCTCGGCCGCCTCGAGATCCTCCGCATCCACACCAAGAACATGCCGCTCTCCGACGACGTCGA
CCTCGAGCGCGTCGGCAAGGACACCCACGGGTTCGTCGGCTCCGACCTCGCCTCGCTCTGCTCCGAGGCCGCCATGCAGT
GCATCCGGGAGAAGCTGGACATCATCGACATTGAGAACGACACCATCGACGTGGAGATCCTCAACTCGCTGACCGTCACC
ATGGACCACCTCAAGTTCGCCATGGAGGTCACCAAGCCCTCCGCCCTGCGCGAGACCGGGATCGTCGAGGTGCCCAAGGT
GTCTTGGGACGACATCGGCGGCCTGGGCGAGGTCAAGCGCGAGCTCCAGGAGACGGTGCAGTACCCGGTGGAGCACCCGG
AGATGTTCGACCTGTTTGGCATGTCGCCGTCGCGCGGCGTGCTCTTCTACGGCCCGCCGGGGTGCGGCAAGACGATGATG
GCCAAGGCCATCGCCAAGGAGTGCAAGGCCAACTTCATCAGCATCAAGGGGCCCGAGCTGCTCACCATGTGGTTCGGCGA
GAGCGAGGGCAACGTCCGCAACCTGTTCGACAAGGCGCGGCAGTCGGCGCCGTGCATCCTCTTCTTCGACGAGCTCGACT
CCATCGCCGTCAAGCGCGGGAACAGCGTCGGCGACGCCGGCGGCACGCCGGACCGCGTGCTCAACCAGCTGCTCACCGAG
ATGGACGGCATCAACGCCAAGAAGACGGTGTTCGTCATCGGCGCCACCAACCGGCCGGACATCATCGACCCGGCGATGCT
CCGGCCGGGCCGCCTCGACCAGCTCATCTACATCCCGCTCCCGGACGCCTCGTCGCGGCTGGAGATCTTCAGGGCGAACC
TCCACAAGGCGCCCATGTCCCGCCACGTCGACCTGCCGGCAATGGCCGCCTCCACCGACGGGTTCAGCGGCGCCGACATC
AAGGAGATCTGCCAGCGCGCGTGCAAGCTCGCGGTGCGCGAGGTGGTCCAGAAG

Alignment

ORF - retro_ogla_73 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.43 %
• Parental protein coverage: 71.16 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LFDAFLKPYFLEAYRPVRKGDLFLVRGGMRSVEFKVIETDPT-EYCIVAPDTEIFCD-GEPIKREDEERL
          L..AF...YF..A.RPV.KGD.FLVRG.M..VEFKV..T.P..E..IVA.DTEIFCD.G.P.KREDEERL
Retrocopy LLFAFHVAYFMDALRPVKKGDRFLVRGHMHAVEFKVMDTEPNNEPVIVAGDTEIFCDEGDPVKREDEERL

Parental  DEVGYDDVGGVRKQMAQIRELVELPLRHPQLFKSIGVKPPKGILLYGPPGSGKTLIARAVANETGAFFFL
          D..GYDDVGGVRKQ.AQIRELVELPLRHP.LF...GV.PPKGILLYGPPG.GKTL.ARA.A.E.GA.F..
Retrocopy DGPGYDDVGGVRKQLAQIRELVELPLRHPKLFQTLGVRPPKGILLYGPPGTGKTLLARAIAAESGAHFVV

Parental  INGPEIMSKLAGESESNLRKAFEEAEKNAPSIIFIDEIDSIAPKREKTNGEVERRIVSQLLTLMDGLKAR
          .NGPEIMS...GESE.NLR..F.EA...APSI.F.DEIDSIAP.REK..GEVERR.VS.LLTLMDGL..R
Retrocopy VNGPEIMSGMPGESEANLRAVFAEADAAAPSIVFMDEIDSIAPSREKAHGEVERRVVS*LLTLMDGLRPR

Parental  SHVIVMGATNRPNSIDPALRRFGRFDREIDIGVPDEVGRLEVLRIHTKNMKLAEDVDLELIAKDTHGYVG
          ..VIV.GATNRPNS.DPALRRFGRFDRE.DIGVPDE.GRLE.LRIHTKNM.L..DVDLE...KDTHG.VG
Retrocopy AQVIVIGATNRPNSLDPALRRFGRFDRELDIGVPDELGRLEILRIHTKNMPLSDDVDLERVGKDTHGFVG

Parental  ADLAALCTEAALQCIREKMDIIDLEDETIDAEILNSMAVTNDHFKTALGTSNPSALRET-VVEVPNVSWE
          .DLA.LC.EAA.QCIREK.DIID.E..TID.EILNS..VT.DH.K.A.....PSALRET..VEVP.VSW.
Retrocopy SDLASLCSEAAMQCIREKLDIIDIENDTIDVEILNSLTVTMDHLKFAMEVTKPSALRETGIVEVPKVSWD

Parental  DIGGLENVKRELQETVQYPVEHPEKFEKFGMSPSKGVLFYGPPGCGKTLLAKAIANECQANFISVKGPEL
          DIGGL..VKRELQETVQYPVEHPE.F..FGMSPS.GVLFYGPPGCGKT..AKAIA.EC.ANFIS.KGPEL
Retrocopy DIGGLGEVKRELQETVQYPVEHPEMFDLFGMSPSRGVLFYGPPGCGKTMMAKAIAKECKANFISIKGPEL

Parental  LTMWFGESEANVREIFDKARQSAPCVLFFDELDSIATQRGSSVGDAGGAADRVLNQLLTEMDGMNAKKTV
          LTMWFGESE.NVR..FDKARQSAPC.LFFDELDSIA..RG.SVGDAGG..DRVLNQLLTEMDG.NAKKTV
Retrocopy LTMWFGESEGNVRNLFDKARQSAPCILFFDELDSIAVKRGNSVGDAGGTPDRVLNQLLTEMDGINAKKTV

Parental  FIIGATNRPDIIDPALLRPGRLDQLIYIPLPDEQSRLQIFKACLRKSPVAKDVDLNALAKYTQGFSGADI
          F.IGATNRPDIIDPA.LRPGRLDQLIYIPLPD..SRL.IF.A.L.K.P....VDL.A.A..T.GFSGADI
Retrocopy FVIGATNRPDIIDPAMLRPGRLDQLIYIPLPDASSRLEIFRANLHKAPMSRHVDLPAMAASTDGFSGADI

Parental  TEICQRACKYAIRENIEK
          .EICQRACK.A.RE...K
Retrocopy KEICQRACKLAVREVVQK

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_73 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G74922	1 retrocopy	retro_bdis_9,
Zea mays	GRMZM2G063060	1 retrocopy	retro_zmay_7,
Leersia perrieri	LPERR03G03650	1 retrocopy	retro_lper_1,
Hordeum vulgare	MLOC_74069	2 retrocopies	retro_hvul_38, retro_hvul_40,
Hordeum vulgare	MLOC_76416	1 retrocopy	retro_hvul_59,
Oryza glaberrima	ORGLA06G0255900	1 retrocopy	retro_ogla_73 ,
Populus trichocarpa	POPTR_0006s12740	1 retrocopy	retro_ptri_3,
Sorghum bicolor	Sb01g046840	1 retrocopy	retro_sbic_42,