RetrogeneDB ID: retro_opun_23

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 5:19523739..19526976(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC05G13190
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC08G10350
• Aliases: None
• Description: None

Sequence

>retro_opun_23
ATGGCGGCGAGCGATGATGGCCAGCTCAAGACGTGGGTCTCCGACCGCCTCATGGCGCTCCTCGGATACTCCCAGGGCGT
TGTGGCGCGGTTCGTCGTCCGCCTCGCGCGGGAGTGCGCCTCCGCGGGTGACCTCGCGGCGCGGCTCATCGACCTCGGCG
GGTTCCCGCCTTCCCCCGACACCGCGGCGTTCGCCGAGGACGTGTACGGGAGGGTTCCCCGCAGTTGCGGCGGCGGTGAC
GCTGGGGTCAGTGAGTACCAGAGGCAGATGCAGGAGGCGGCGGCTCTGGCCAAGAAGCAGAGCACCTTCAAGCTGCTCAA
CGACGGGGACGAGGACGGCGAGATCGGCGTTTCGGCCCCGTCCTCCAGCAGCGGCAGGAAGCGTTTCAGGAGGAAGGCCG
CGAGCGAAGACGATGAGGCGATCGTAACGCACGATGCCGGACGGAACCGGAACGTGCGACGGCGGCGTAGCCCGGATGAG
GAGGAGGAGGAGGAGGACGGCGACGCCAGCGAGGAAGAAGAGATGGAGCGGGATCAGATTGAGAAGGCGCAGCTCGAGCG
GAACATGAGGGAGCGCGACGCGGCGAACACGAGGAGGCTGATGGATCGGAAGCCGACCAAGCGAGAGCTGGACGAGCTCG
CGCGCCGGTCGGAAGCCATGGACAAGAACGACGCCTCGGAGCTCAGGAGGCTCTCCCGGCGCGCGTACCTGAAGAAGCGA
AAGGAGAAGAAGGTTGACGAGATGCGCGACGAGATCGTCGACCACGAGTTCCTCTTCCCCTGTGTCGAGCTGACGGCCGC
CGAGGAGAGGGACATGAGGCACAAGAAGGAAGTCTACGGCCTCGTGCACGACCGCGACAAGAGCGACGACGGCGCCGGCG
ACCACTACTACAGAATGCCGGACGCCTACGACGCCGCCGCGAACGTCGATCAGGATAAGAGGTTCTCGGTGGTGCGGCGG
CGGTACGAGGAGCCAGCCGAGGCGACGAGAGGCGGCAAGACGGCGAACGCCTCCTCCGAGCAGGAGGCCTGGGAGGAGCA
GCAGATATGGAAGTCGAGGCTGCAGTTCGGATCCATGGATCGCGGCCGGCGGGGCGACGAGTACGAGCTCCTGTTCGACG
ACGGCGTCGAGTTCGTCAGGTCGACGGTGATGGCGGGCACCATGCCTGACGACGACGACGCGGCGGCCGCCGAGCATCAT
GCCGATGCCATGGATGCCAAGGCCACGTTGCAAGACGAGAGGAAGACTCTCCCGGTGTACAAGCTCAAGGACGACCTGCT
CAAGGCCATTGACGAGTATCAGGTCCTGATCGTCGTCGGCGAGACCGGCTCCGGCAAGACGACGCAGATACCGCAGTACC
TCCACGAGGCCGGGTACACGGCGAAGGGGAAGAAGAAGGTGGCGTGCACGCAGCCGCGCCGCGTGGCGGCGATGAGCGTG
GCGGCGAGGGTGGCCGACGAGATGGGCGTCAAGCTCGGGCACGAGGTCGGCTATTCCATCCGGTTCGAGGACTGCACGTC
GGAGAAGACGGTGATCAAGTACATGACCGACGGGATGCTCCTCCGCGAGTTCCTCGGCGAGCCCGACCTGGGCAGCTACA
GCGTCGTCGTCGTCGACGAGGCCCACGAGCGGACGCTCTCCACCGACATCCTCTTCGGCCTCGTCAAGGACATCGCCCGC
TTCCGCCCTGACATGAAGCTGCTCATCTCCAGCGCGACGCTCAATGCCAACAAGTTCAGCGACTTCTTCGACGCGGCGCC
CATCTTCCGGATCCCCGGGCGGCGGTTCGAGGTGGACATCCACTACACCATGGCACCGGAGGCGGACTACATCGACGCCG
CCGTCGTGACGGTGCTGCAGCTGCACGTCACGGAGCCCTCCGGCGGCGGTGACATCCTGCTGTTCCTGACGGGGCAAGAG
GAGATCGACACGGTCGAGGAGATCCTGAGGCAGCGGCTGCGGGTGCTCGGCGGCAAGGTGGCGGAGCTGGTGATCTGCCC
CATCTACGCCAACCTCCCCGCCGAGCTGCAGGCCAAGATCTTCGAGCCGGCGCCGGCAGGCGCGCGCAAGGTGGTGCTCG
CCACCAACATCGCCGAGACGTCGCTGACCATCGACGGGATCAAGTACGTGGTCGACCCGGGGTTCTGCAAGGTGAAGTCG
TACAACCCGCGCACGGGAATGGAGTCGCTGCTCGTGGCGCCGGTGTCCAGGGCGTCAGCGGAGCAGCGCGCCGGCCGGTC
GGGGCGCACCGGGCCGGGCAAGTGCTTCCGGCTCTACACGGAGTACAACTTCGTCAACGACCTCGACGACGACACGGTGC
CGGAGATCCAGCGGAGCAACCTCGCCAACGTCGTGCTGGCGCTCAAGGCTCTCGGGATCAACGACCTCGTCGGCTTCGAC
TTCATGGACCCGCCGCCGGCGGAGTCGCTGCTCAAGGCGCTGGAGGAGCTCTTCGCCCTCGGCGCGCTCAACAGCCGCGG
CGAGCTCACCAAGACCGGGAGGAGGATGGCGGAGTTCCCCCTCGACCCCATGCTCTCCAAGGCCGTCGTCGCGTCCGAGA
GGTTCGGGTGCTCCGAGGAGGTGATCACCATCGCGGCCATGCTGTCCGCCGGGAACGCCGTGTTCTACCGCCCCAAGGAC
AAGCAGGTCCACGCCGACGCCGCGCGGCGGGCGTTCCACGCCGGCGACGTCGGCGACCACATCGCGCTGCTCAACGTGTA
CAACGCGTGGGCGGAGTCCGGCTACTCGCCGCAGTGGTGCCGCGAGAGCTTCGTGCAGCACCGCATCATGCGGCGCGCGC
GGGACGTGCGGGACCAGCTTGGGGCGCTGCTTGAGCGGGTGGAGATCGCGCCGTGCTCCGCAGGCGGCGACCTCGACGTG
GTCCGGAAGGCGGTCACGGCGGGCTACTTCCGCCACGCGGCGCGGCTGCAGAGGGACGGGTCGTACCGCGCCGTGAAGAG
CCGGCAGACGGTGTTCGTCCACCCGAGCTGCGGGGTGGCGCAGTCGCCGCCGCGGTGGGCGGTGTACCACGAGCTGGTGC
TCACGACCAAGGAGTACATGCGGCAGGTGACGGAGCTCAAGCCGGAGTGGCTGTTGGAGATCGCGCCGCACTGCTACGAG
CGCAAGGACGTAGACGAGCGTGAGCCCAAGAAGACGGCCGGCGCTACACCAACGAAGCAGACAACGAATCTGAATGTTTC
TTCGACGTGTAAAGAGTACCACCATTGGAGCTTATAA

Alignment

ORF - retro_opun_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.89 %
• Parental protein coverage: 80.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DDETTIKQDSGRNV---KRRTEEVDDEDDDNDTDEEQERIKDQQERAQLEKNMRERDAANTRKLMERQLS
          DDE.....D.GRN.....RR......E..D.D..EE.E...DQ.E.AQLE.NMRERDAANTR.LM.R...
Retrocopy DDEAIVTHDAGRNRNVRRRRSPDEEEEEEDGDASEEEEMERDQIEKAQLERNMRERDAANTRRLMDRKPT

Parental  KEEQEEITRRSQAMDKNDTSDLRKFSRQAYLQKRRDKKIDEIRDEILDHEYIFQDVKLTEAEEKEFRYKK
          K.E..E..RRS.AMDKND.S.LR..SR.AYL.KR..KK.DE.RDEI.DHE..F..V.LT.AEE...R.KK
Retrocopy KRELDELARRSEAMDKNDASELRRLSRRAYLKKRKEKKVDEMRDEIVDHEFLFPCVELTAAEERDMRHKK

Parental  KIYDLVKEHVESADDVAE--YKMPEAYDMGDSVNQEKRFSVAMQRYKDPEARDKMNPFAEQEAWEE----
          ..Y.LV.....S.D......Y.MP.AYD....V.Q.KRFSV...RY..P.........A......E....
Retrocopy EVYGLVHDRDKSDDGAGDHYYRMPDAYDAAANVDQDKRFSVVRRRYEEPAEATRGGKTANASSEQEAWEE

Parental  HQIGKSKLQFGSKDRKRYSDDYQYVFEDGIDFVKSSVIEGTQHEEDSDQEDIDEKDML--KRELQDERKT
          .QI.KS.LQFGS.DR.R..D.Y...F.DG..FV.S.V..GT....D.........D....K..LQDERKT
Retrocopy QQIWKSRLQFGSMDRGRRGDEYELLFDDGVEFVRSTVMAGTMPDDDDAAAAEHHADAMDAKATLQDERKT

Parental  LPIYKFRDELLKAVEEYQVIVIVGETGSGKTTQIPQYLHEAGYTAKG--KVACTQPRRVAAMSVAARVSQ
          LP.YK..D.LLKA..EYQV...VGETGSGKTTQIPQYLHEAGYTAKG..KVACTQPRRVAAMSVAARV..
Retrocopy LPVYKLKDDLLKAIDEYQVLIVVGETGSGKTTQIPQYLHEAGYTAKGKKKVACTQPRRVAAMSVAARVAD

Parental  EMGVKLGHEVGYSIRFEDCTSEKTLIKYMTDGMLLREFLGEPDLASYSVVMVDEAHERTLSTDILFGLVK
          EMGVKLGHEVGYSIRFEDCTSEKT.IKYMTDGMLLREFLGEPDL.SYSVV.VDEAHERTLSTDILFGLVK
Retrocopy EMGVKLGHEVGYSIRFEDCTSEKTVIKYMTDGMLLREFLGEPDLGSYSVVVVDEAHERTLSTDILFGLVK

Parental  DISRFRPDLKLLISSATLDAEKFSDYFDSAPIFKIPGRRYPVEVHYTKAPEADYIDAAIVTVLQIHVTQP
          DI.RFRPD.KLLISSATL.A.KFSD.FD.APIF.IPGRR..V..HYT.APEADYIDAA.VTVLQ.HVT.P
Retrocopy DIARFRPDMKLLISSATLNANKFSDFFDAAPIFRIPGRRFEVDIHYTMAPEADYIDAAVVTVLQLHVTEP

Parental  P--GDILVFLTGQEEIETIDEILKHRTRGLGTKIAELIICPIYANLPTELQAKIFEPTPEGARKVVLATN
          ...GDIL.FLTGQEEI.T..EIL..R.R.LG.K.AEL.ICPIYANLP.ELQAKIFEP.P.GARKVVLATN
Retrocopy SGGGDILLFLTGQEEIDTVEEILRQRLRVLGGKVAELVICPIYANLPAELQAKIFEPAPAGARKVVLATN

Parental  IAETSLTIDGIKYVIDPGFCKIKSYNPRTGMESLLINPISKASANQRAGRSGRTGPGKCFRLYTSYNYMH
          IAETSLTIDGIKYV.DPGFCK.KSYNPRTGMESLL..P.S.ASA.QRAGRSGRTGPGKCFRLYT.YN...
Retrocopy IAETSLTIDGIKYVVDPGFCKVKSYNPRTGMESLLVAPVSRASAEQRAGRSGRTGPGKCFRLYTEYNFVN

Parental  DLEDNTVPEIQRTNLANVVLTLKSLGIHDLVNFDFMDPPPSEALLKALEQLFALSALNSRGELTKTGRRM
          DL.D.TVPEIQR.NLANVVL.LK.LGI.DLV.FDFMDPPP.E.LLKALE.LFAL.ALNSRGELTKTGRRM
Retrocopy DLDDDTVPEIQRSNLANVVLALKALGINDLVGFDFMDPPPAESLLKALEELFALGALNSRGELTKTGRRM

Parental  AEFPLDPMLSKMIVASEKYKCSDEVISIASMLSVGNSIFYRPKDKQVHADNARLNFHTGNVGDHIALLNV
          AEFPLDPMLSK..VASE...CS.EVI.IA.MLS.GN..FYRPKDKQVHAD.AR..FH.G.VGDHIALLNV
Retrocopy AEFPLDPMLSKAVVASERFGCSEEVITIAAMLSAGNAVFYRPKDKQVHADAARRAFHAGDVGDHIALLNV

Parental  YNSWKETDYSTQWCYENYIQVRSMKRARDIRDQLEGLLERVEIEISSNASDLDAIKKAITSGFFHHSSRL
          YN.W.E..YS.QWC.E...Q.R.M.RARD.RDQL..LLERVEI...S...DLD...KA.T.G.F.H..RL
Retrocopy YNAWAESGYSPQWCRESFVQHRIMRRARDVRDQLGALLERVEIAPCSAGGDLDVVRKAVTAGYFRHAARL

Parental  QKNGSYRTVKNPQTV
          Q..GSYR.VK..QTV
Retrocopy QRDGSYRAVKSRQTV

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza punctata was not studied using ChIP-Seq data.

EST

Oryza punctata was not studied using EST data.

TSS

Oryza punctata was not studied using FANTOM5 data.

Lab

retro_opun_23 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza punctata 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,