RetrogeneDB ID: retro_omer_5

Retrocopy location

• Organism: Oryza meridionalis
• Coordinates: 5:16990456..16993612(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OMERI05G13440
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OMERI08G09070
• Aliases: None
• Description: None

Sequence

>retro_omer_5
ATGGCGGCGAGCGATGATGGCCGCCAGCTCAGGACGTGGGTCTCCGACCGCCTCATGGCGCTCCTCGGATACTCCCAGGG
CGTCGTGGCGCGGCTCGTCGTCCGCCTCGCGCGGGAGTGCGCCTCCGCGGGTGACCTCGCGGCGCGGCTCGTCGACCTCG
GCGGGTTCCCGCCTTCCCCCGACACCGCCGCGTTCGCCGAGGACGTGTACGGGAGGGTGCCCCGCAGCGGCGGCGGTGGT
GGCGACGACGGGGTCAGCGAGTACCAGAGGCAGATGCAGGAGGCTGCGGCGATGGCCAAGAAGCAGAGCACCTTCAAGCT
GCTCGACGACGACGGCGAGATCGGCGTTTCCACGTCGCCCTCCGGCAGCGGAAGGAAGCGTTTCAAGAGGAAGGCCGTGG
GCGAAGACGATGACGATGCCGGACGGAACGCGCGACGGCGGCGTAGCCCGGACGACGAGGAGGAGGACGGCGACGCCGGC
GAGGAAGAAGAGATGGAGCGGGATCAGATCGAGAGGGCGCAGCTCGAGCGGAACATCAGGGAGCGCGACGCGGCGAGCAC
GAGGAGGCTGATGGATCGGAAGCCGACCAAGCGGGAGCAGGACGAGCTCGCGCGCCGGTCGGAAGCCATGGACAAGAACG
ACACCTCGGGGCTCAGGAGGCTCTCCCGGCGCGCGTACCTGCGGATGCGGAAGGAGAAGAAGGTCGAGGAGATGCGCGAC
GAGATCGTCGACCACGAGTTCCTCTTCCCCGGCGTCCAGCTGACGGCCGCCGAGGAGAGGGACATGAGGCACAAGAAGCA
AGTCTACGGCCTCGTGCACGATCGCGACGACGGCGCCGGCGCCGGCGACGACTACTACAGAATGCCGGACGCCTACGACG
CCGCCGCGAACGTCGATCAGGAGAAGAGGTTCTCGGTGGCGCGGCGGCGGTACGAGGAGCCGGCCGAGGCGGCGAGGGAC
GGCAAGACGGCGAACGCCTACACCGAGCAGGAGGCCTGGGAGGAGCAGCAGATACGGAAGTCGAGGCTGCAGTTCGGATC
CATGGATCGCGGCCGGCGCGGCGACGAGTACGAGCTCCTGCTCGACGACGGCGTCGAGTTCGTCAGGTCGACGGTGATGG
CGGGCACCGTGCCTGCAGACGACGACGACGCGGCGGCGGCGGCGGCGGCGGGCGACGAGTACCAGGCCGAGGCCATGGAT
ACCAAGGCCACGTTGCAAGACGAGAGGAAGACTCTCCCGGTGTACAAGCTCAAGGACGACCTGCTCAAGGCCATCGCCGA
GCACCAGGTCCTGATCGTCGTCGGCGAGACCGGCTCCGGCAAGACGACGCAGATACCGCAGTACCTCCACGAGGCCGGGT
ACACGGCGGAGGGGAGGAAGAAGGTGGCGTGCACGCAGCCGCGGCGCGTGGCGGCGATGAGCGTGGCGGCGAGGGTGGCG
GAGGAGATGGGCGTCAAGCTCGGCGACGAGGTCGGCTACTCCATCCGGTTCGAGGACTGCACGTCGGAGAAGACGGTGAT
CAAGTACATGACCGACGGGATGCTCCTCCGCGAGTTCCTCGGCGAGCCCGACCTGGGCAGCTACAGCGTCGTCGTCGTCG
ACGAGGCCCACGAGCGGACGCTCGCCACCGACATCCTCTTCGGCCTCGTCAAGGACATCGCCCGCCTCCGCCCTGACATG
AAGCTGCTCATCTCCAGCGCGACGCTCAACGCCGACAAGTTCAGCGACTTCTTCGACGCGGCGCCCATCTTCCGGATCCC
CGGGCGGCGGTTCGAGGTGGGCATCCACTACACCGTGGCGCCGGAGGCGGACTACATCGACGCCGCCGTCGTCACGGTGC
TGCAGCTGCACGTCACGGAGCCCCCCGGCGGTGGCGACATCCTGCTGTTCCTGACCGGGCAGGAGGAGATCGAGACGGTG
GAGGAGATCCTGAGGCAGCGGCTGCGGGTGCTCGGCGGCATGGTGGCGGAGCTGGTGATCTGCCCCATCTACGCCAACCT
CCCCGCCGAGCTGCAGGCCAAGATCTTCGAGCCGGCGCCGCCGGGCGCGCGCAAGGTGGTGCTCGCCACCAACATCGCCG
AGACGTCGCTGACCATCGACGGGATCAAGTACGTGGTCGACCCGGGGTTCTGCAAGGTGAAGTCGTACAACCCGCGCACG
GGGATGGAGTCGCTGCTGGTGGCGCCGGTGTCGAGGGCGTCGGCGGAGCAGCGCGCCGGCCGGTCGGGGCGCACCGGGCC
GGGCAAGTGCTTCCGGCTCTACACGGAGTACAACTTCGTCAGCGACCTCGACGACGACGCGGTGCCGGAGATCCAGCGGA
GCAACCTCGCCAGCGTCGTGCTGGCGCTCAAGGCGCTCGGGATCAACGACCTCGTCGGCTTCGACTTCATGGACCCGCCG
CCGGCGGAGTCGCTGCTCAAGGCGCTGGAGGAGCTCTTCGCCCTCGGCGCGCTCAACAGCCGCGGCGAGCTCACCAAGAC
CGGGAGGAGGATGGCGGAGTTCCCCCTGGACCCCATGCTCTCCAAGGCCATCGTCGCGTCGGAGAGGTACGGGTGCTCCG
AGGAGGTGATCACCATCGCGGCCATGCTGTCCGCCGGGAACGCCGTCTTCTACCGCCCCAGGGACAAGCGGGTCCACACC
GACGCCGCGCGGCGCGGGTTCCATGCCGGGAACGCCAGCGACCACGTCGCGCTGCTCAACGTGTACAACGCGTGGGCGGA
GTCCGGCTACTCGCCGCAGTGGTGCCGCGAGAGCTTCGTGCAGCACCGCACCATGCGGCGCGCGCGGGACGTGCGGGACC
AGCTGGGGGCGCTGCTTGAGCGGGTGGAGATCGCGCCGTGCTCCTCCGCCGACCTCGACGCGGTCAGGAAGGCGGTCACG
GCGGGGTACTTCCGCCACGCCGCGCGGCTGCAGAGGGACGGGTCGTACCGCGCCGTGAAGAGCCGGCAGACGGTGTTCGT
CCACCCGAGCTCCGGGGTGGCGCAGGCGCCGCCGCGGTGGGCGTTGTACCACGAGCTGGTGCTCACGACCAAGGAGTACA
TGAGGCAGGTGACGGAGCTCAAGCCGGAGTGGCTGGTGGAGATCGCGCCGCACTACTACGAGCGCAAGGACGTCGACGAG
CCTGAGCCCAAGAAGATGGCGGTGGCGGCGGCGTAG

Alignment

ORF - retro_omer_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.95 %
• Parental protein coverage: 55.87 %
• 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...VGETGSGKTTQIPQYLHEAGYTA.G..KVACTQPRRVA
Retrocopy KATLQDERKTLPVYKLKDDLLKAIAEHQVLIVVGETGSGKTTQIPQYLHEAGYTAEGRKKVACTQPRRVA

Parental  AMSVAARVSQEMGVKLGHEVGYSIRFEDCTSEKTLIKYMTDGMLLREFLGEPDLASYSVVMVDEAHERTL
          AMSVAARV..EMGVKLG.EVGYSIRFEDCTSEKT.IKYMTDGMLLREFLGEPDL.SYSVV.VDEAHERTL
Retrocopy AMSVAARVAEEMGVKLGDEVGYSIRFEDCTSEKTVIKYMTDGMLLREFLGEPDLGSYSVVVVDEAHERTL

Parental  STDILFGLVKDISRFRPDLKLLISSATLDAEKFSDYFDSAPIFKIPGRRYPVEVHYTKAPEADYIDAAIV
          .TDILFGLVKDI.R.RPD.KLLISSATL.A.KFSD.FD.APIF.IPGRR..V..HYT.APEADYIDAA.V
Retrocopy ATDILFGLVKDIARLRPDMKLLISSATLNADKFSDFFDAAPIFRIPGRRFEVGIHYTVAPEADYIDAAVV

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

Parental  GARKVVLATNIAETSLTIDGIKYVVDPGFCKIKSYNPRTGMESLLINPISKASANQRAGRSGRTGPGKCF
          GARKVVLATNIAETSLTIDGIKYVVDPGFCK.KSYNPRTGMESLL..P.S.ASA.QRAGRSGRTGPGKCF
Retrocopy GARKVVLATNIAETSLTIDGIKYVVDPGFCKVKSYNPRTGMESLLVAPVSRASAEQRAGRSGRTGPGKCF

Parental  RLYTSYNYMHDLEDNTVPEIQRTNLANVVLTLKSLGIHDLVNFDFMDPPPSEALLKALEQLFALSALNSR
          RLYT.YN...DL.D..VPEIQR.NLA.VVL.LK.LGI.DLV.FDFMDPPP.E.LLKALE.LFAL.ALNSR
Retrocopy RLYTEYNFVSDLDDDAVPEIQRSNLASVVLALKALGINDLVGFDFMDPPPAESLLKALEELFALGALNSR

Parental  GELTKTGRRMAEFPLDPMLSKMIVASEKYKCSDEVISIASMLSVGNSIFYRPKDKQVHADNARLNFHTGN
          GELTKTGRRMAEFPLDPMLSK.IVASE.Y.CS.EVI.IA.MLS.GN..FYRP.DK.VH.D.AR..FH.GN
Retrocopy GELTKTGRRMAEFPLDPMLSKAIVASERYGCSEEVITIAAMLSAGNAVFYRPRDKRVHTDAARRGFHAGN

Parental  VGDHIALLNVYNTWKETDYSTQWCYENYIQVRSMKRARDIRDQLEGLLERVEIEISSNASDLDAIKKAIT
          ..DH.ALLNVYN.W.E..YS.QWC.E...Q.R.M.RARD.RDQL..LLERVEI...S.A.DLDA..KA.T
Retrocopy ASDHVALLNVYNAWAESGYSPQWCRESFVQHRTMRRARDVRDQLGALLERVEIAPCSSA-DLDAVRKAVT

Parental  SGFFHHSSRLQKNGSYRTVKNPQTV
          .G.F.H..RLQ..GSYR.VK..QTV
Retrocopy AGYFRHAARLQRDGSYRAVKSRQTV

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_5 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 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,