RetrogeneDB ID: retro_ogla_26

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 5:14409908..14413136(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORGLA05G0129700
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA08G0098600
• Aliases: None
• Description: None

Sequence

>retro_ogla_26
ATGGCGGCGAGCGATGATGGCCAGCTCAGGACGTGGGTCTCCGACCGCCTCATGGCGCTCCTCGGATACTCCCAGGGCCT
CGTGGCGCGGCTCGTCGTCCGCCTCGCGCGGGAGTGCGCCTCCGCGGGTGACCTCGCGGCGCGGCTCGTCGACCTCGCCG
GGTTCCCGCCTTCCCCCGACACCGCCGCGTTCGCCGAGGACGTGTACGGGAGGGTGCCCCGCAGTTGCGGCGGCGGCGGC
GACGACGCCGGGGTCAGCGAGTACCAGAGGCAGATGCAGGAGGCTGCGGCGATGGCCAAGAAGCAGAGCACCATCAAGCT
GGTCGACGACGACGGCGAGATCGGCGTTTCCGCGTCGCCCTCCAGCGGCGGCAGGAAGCGTTTCAGGAGGAAGGCCGTGG
GCGAAAACGATGACGATGCCGGACGGAACGCGCGACGGCGGCGTAGCCCGGACGACGAGGAGGAGGACGGCGACGCCGGC
GAGGAAGAAGAGATGGAGCGGGATCAGATCGAGAGGGCGCAGCTCGAGCGGAACATCAGGGAGCGCGACGCGGCGAGCAC
GAGGAGGCTGACGGATCGGAAGACGACCAAGCGGGAGCAGGGCGAGCTCGCGCGCCGGTCGGACGCCATGGACAAGAACG
ACACCTCGGGGCTCAGGAGGCTCTCCCGGCGCGCGTACCTGCAGAGGCGGAAGGAGAAGAAGGTCGAGGAGATGCGCGAC
GAGATCGTCGACCACGAGTTCCTCTTCCCCGGCGTCCAGCTGACGGCCGCCGAGGAGAGGGACATGAGGCACAAGAAGCA
AGTCTACGGCCTCGTGCACGATCGCGACGACGGCGCCGGCGACGACTACTACAGAATGCCGGACGCCTACGACGCCGCCG
CGAACGTCGATCAGGAGAAGAGGTTCTCGGTGGCGCGGCGGCGGTACGAGGAGCCAGCTGAGGCGGCGAGGGACGGCAAG
ACGGCGAACGCCTTGTCCGAGCAGGAGGCCTGGGAGGAGCAGCAGATACGGAAGTCGAGGCTGCAGTTCGGATCCATGGA
TCGCGGCCAGCGCGGCGACGAGTACGAGCTCCTGTTCGACGACGGCGTCGAGTTCGTCAGGTCGACGGTGATGGCGGGCA
CCGCGCCTGCAGACGACGACGACACGGCGGCGGCGGCGGCGGCCGACGAGTACCATGCCGAGGCCATGGATGCCAAGGCC
ACGTTGCAAGACGAGAGGAAGACTCTCCCGGTGTACAAGCTCAAGGACGACCTGCTCAAGGCCATCGACGAGCACCAGGT
CCTGATCGTCGTCGGCGAGACCGGCTCCGGCAAGACGACGCAGATACCGCAGTACCTCCACGAGGTCGGGTACACGGCGG
GGGGGAGGAAGAAGGTGGCGTGCACGCAGCCGCGGCGCGTGGCGGCGATGAGCGTGGCGGCGAGGGTGGCGGAGGAGATG
GGCGTCAAGCTCGGGCACGAGGTCGGCTACTCCATCCGGTTCGAGGACTGCACGTCGGAGAAGACGGTGATCAAGTACAT
GACCGACGGGATGCTCCTCCGCGAGTTCCTCGGCGAGCCCGACCTGGGCAGCTACAGCGTCGTCGTCGTCGACGAGGCCC
ACGAGCGGACGCTCGCCACCGACATCCTCTTCGGCCTCGTCAAGGACATCGCCCGCCTCCGCCCTGACATGAAGCTGCTC
ATCTCCAGCGCGACGCTCAACGCCGACAAGTTCAGCGACTTCTTCGACGCGGCGCCCGTCTTCCGGATCCCCGGGCGGCG
GTTCGAGGTGGGCATCCACTACACCGTGGCGCCGGAGGCGGACTACATCGACGCCGCCGTCGTGACGGTGCTGCAGCTGC
ACGTCACGGAGCCCCCCGGCGGCGGCGACATCCTGCTGTTCCTCACGGGGCAGGAGGAGATCGAGACGGTGGAGGAGATC
CTGAGGCATCGGCTGCGGGTGCTCGGCGGCAAGGTGGCGGAGCTGGTGATCTGCCCCATCTACGCCAACCTCCCCGCCGA
GCTGCAGGCCAAGATCTTCGAGCCGGCGCCGGCGGGCGCGCGCAAGGTGGTGCTCGCCACCAACATCGCCGAGACGTCGC
TGACCATCGACGGGATCAAGTACGTGGTCGACCCGGGGTTCTGCAAGGTGAAGTCGTACAACCCGCGCACCGGGATGGAG
TCGCTGGTGGTGGCGCCGTTGTCGAGGGCGTCGGCGGAGCAGCGCGCCGGCCGGTCGGGGCGCACCGGGCCGGGCGAGTG
CTTCCGGCTCTACACGGAGTACAACTTCGTCAGCGACCTCGACGACGACGCGGTGCCGGAGATCCAGCGGAGCAACCTCG
CCAGCGTCGTGCTGGCGCTCAAGGCGCTCGGGATCAACGACCTCGTCGGCTTCGACTTCATGGACCCGCCGCCGGCGGAG
TCGCTGCTCAGGGCGCTGGAGGAGCTCTTCGCCCTCGGCGCGCTCAACAGCCGCGGCGAGCTCACCAAGACCGGGAGGAG
GATGGCGGAGTTCCCCCTGGACCCCATGCTCTCCAAGGCCATCGTCGCGTCGGAGAGGTACGGGTGCTCCGAGGAGGTGA
TCACCATCGCGGCCATGCTGTCCACCGGGAACGCCGTCTTCTACCGCCCCAGGGACAAGCGGGTCCACGCCGACGCCGCG
CGGCGGGCGTTCCACGCCGGCAACGCCGGCGACCACGTCGCGCTGCTCAACGTGTACAACGCGTGGGCGGAGTCCGGCTA
CTCGCCGCAGTGGTGCCGCGAGAGCTTCGTGCAGCACCGCACCATGCGGCGCGCGCGGGACGTGCGGGACCAGCTGGGGG
CGCTGCTCGAGCGGGTGGAGATCGCGCCGTGCTCCTCCGCCGGCGGCGGCGACCTCGACGCGGTCAGGAAGGCGGTCACG
GCGGGCTACTTCCGCCACGCTGCGCGGCTGCAGAGGGACGGGTCGTACCGCGCCGTGAAGAGCCGGCAGACGGTGTTCGT
CCACCCGAGCTCCGGGGTGGCGCAGGCGCCGCCGCGGTGGGCGTTGTACCACGAGCTGGTGCTCACGACCAAGGAGTACA
TGAGGCAGGTGACGGAGCTCAAGCCGGAGTGGCTGGTGGAGATCGCGCCGCACTACTACGAGCGCAAGGACGTCGACGAG
CCTGAGCCCAAGAAGAAGACGGCGGCGGCTACGCCGCAAGAGCAGACGACGGCCGGCTCTACACCAACGAAGCAGACTCC
GAATCTGAATAGTTTCTTCGACGTGTAA

Alignment

ORF - retro_ogla_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.74 %
• Parental protein coverage: 60.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KRELQDERKTLPIYKFRDELLKAVEEYQVIVIVGETGSGKTTQIPQYLHEAGYTAKG--KVACTQPRRVA
          K..LQDERKTLP.YK..D.LLKA..E.QV...VGETGSGKTTQIPQYLHE.GYTA.G..KVACTQPRRVA
Retrocopy KATLQDERKTLPVYKLKDDLLKAIDEHQVLIVVGETGSGKTTQIPQYLHEVGYTAGGRKKVACTQPRRVA

Parental  AMSVAARVSQEMGVKLGHEVGYSIRFEDCTSEKTLIKYMTDGMLLREFLGEPDLASYSVVMVDEAHERTL
          AMSVAARV..EMGVKLGHEVGYSIRFEDCTSEKT.IKYMTDGMLLREFLGEPDL.SYSVV.VDEAHERTL
Retrocopy AMSVAARVAEEMGVKLGHEVGYSIRFEDCTSEKTVIKYMTDGMLLREFLGEPDLGSYSVVVVDEAHERTL

Parental  STDILFGLVKDISRFRPDLKLLISSATLDAEKFSDYFDSAPIFKIPGRRYPVEVHYTKAPEADYIDAAIV
          .TDILFGLVKDI.R.RPD.KLLISSATL.A.KFSD.FD.AP.F.IPGRR..V..HYT.APEADYIDAA.V
Retrocopy ATDILFGLVKDIARLRPDMKLLISSATLNADKFSDFFDAAPVFRIPGRRFEVGIHYTVAPEADYIDAAVV

Parental  TVLQIHVTQPPG--DILVFLTGQEEIETIDEILKHRTRGLGTKIAELLICPIYANLPTELQAKIFEPTPE
          TVLQ.HVT.PPG..DIL.FLTGQEEIET..EIL.HR.R.LG.K.AEL.ICPIYANLP.ELQAKIFEP.P.
Retrocopy TVLQLHVTEPPGGGDILLFLTGQEEIETVEEILRHRLRVLGGKVAELVICPIYANLPAELQAKIFEPAPA

Parental  GARKVVLATNIAETSLTIDGIKYVVDPGFCKIKSYNPRTGMESLLINPISKASANQRAGRSGRTGPGKCF
          GARKVVLATNIAETSLTIDGIKYVVDPGFCK.KSYNPRTGMESL...P.S.ASA.QRAGRSGRTGPG.CF
Retrocopy GARKVVLATNIAETSLTIDGIKYVVDPGFCKVKSYNPRTGMESLVVAPLSRASAEQRAGRSGRTGPGECF

Parental  RLYTSYNYMHDLEDNTVPEIQRTNLANVVLTLKSLGIHDLVNFDFMDPPPSEALLKALEQLFALSALNSR
          RLYT.YN...DL.D..VPEIQR.NLA.VVL.LK.LGI.DLV.FDFMDPPP.E.LL.ALE.LFAL.ALNSR
Retrocopy RLYTEYNFVSDLDDDAVPEIQRSNLASVVLALKALGINDLVGFDFMDPPPAESLLRALEELFALGALNSR

Parental  GELTKTGRRMAEFPLDPMLSKMIVASEKYKCSDEVISIASMLSVGNSIFYRPKDKQVHADNARLNFHTGN
          GELTKTGRRMAEFPLDPMLSK.IVASE.Y.CS.EVI.IA.MLS.GN..FYRP.DK.VHAD.AR..FH.GN
Retrocopy GELTKTGRRMAEFPLDPMLSKAIVASERYGCSEEVITIAAMLSTGNAVFYRPRDKRVHADAARRAFHAGN

Parental  VGDHIALLNVYNSWKETDYSTQWCYENYIQVRSMKRARDIRDQLEGLLERVEIEISSNA--SDLDAIKKA
          .GDH.ALLNVYN.W.E..YS.QWC.E...Q.R.M.RARD.RDQL..LLERVEI...S.A...DLDA..KA
Retrocopy AGDHVALLNVYNAWAESGYSPQWCRESFVQHRTMRRARDVRDQLGALLERVEIAPCSSAGGGDLDAVRKA

Parental  ITSGFFHHSSRLQKNGSYRTVKNPQTVFIHPSSGLAQVLPRWVIYHELVLTTKEYMRQVTELKPDWLVEI
          .T.G.F.H..RLQ..GSYR.VK..QTVF.HPSSG.AQ..PRW..YHELVLTTKEYMRQVTELKP.WLVEI
Retrocopy VTAGYFRHAARLQRDGSYRAVKSRQTVFVHPSSGVAQAPPRWALYHELVLTTKEYMRQVTELKPEWLVEI

Parental  APHYYQLKDVDDTGTKK
          APHYY..KDVD....KK
Retrocopy APHYYERKDVDEPEPKK

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_26 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 16 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA027162	1 retrocopy	retro_oind_65,
Brassica oleracea	Bo5g087070	1 retrocopy	retro_bole_7,
Brassica rapa	Bra010168	1 retrocopy	retro_brap_26,
Brachypodium distachyon	BRADI1G61220	1 retrocopy	retro_bdis_4,
Glycine max	GLYMA06G21821	1 retrocopy	retro_gmax_7,
Leersia perrieri	LPERR08G09260	1 retrocopy	retro_lper_14,
Hordeum vulgare	MLOC_5589	1 retrocopy	retro_hvul_14,
Oryza meridionalis	OMERI08G09070	1 retrocopy	retro_omer_5,
Oryza nivara	ONIVA08G11780	1 retrocopy	retro_oniv_26,
Oryza punctata	OPUNC08G10350	1 retrocopy	retro_opun_23,
Oryza glaberrima	ORGLA08G0098600	1 retrocopy	retro_ogla_26 ,
Oryza rufipogon	ORUFI08G12410	1 retrocopy	retro_oruf_44,
Solanum tuberosum	PGSC0003DMG402024649	1 retrocopy	retro_stub_33,
Prunus persica	PRUPE_ppa000714mg	1 retrocopy	retro_pper_32,
Sorghum bicolor	Sb04g022460	1 retrocopy	retro_sbic_37,
Setaria italica	Si021302m.g	1 retrocopy	retro_sita_41,