RetrogeneDB ID: retro_opun_27

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 3:17756520..17758746(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC03G19650
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC03G14590
• Aliases: None
• Description: None

Sequence

>retro_opun_27
ATGGCGGGAGAGAGCCGCGGCAGCATCGCCTTCTTCGCCACCTACCGCCCGCCGGTGCCGCTCGACGTCTTCTCCTGCCC
GGTTGCACCGCCATCGTCCTCCCCGCGACACGAGCTGCACCTCACCGATGGCGTCTCCTACAACCACAGCTGCCGCCCCA
TCCCGCCCGCCTCGCTCAAGGCGCTCCTCCAGCGCCCCAAGCTGGCCTCCGACTCCGAGGCCACCGCCGCCGACGTCGAC
GCCGGCCGCGTCACCGGCCTTGTGTTCGTCTCCGAGAGGGACAGCAGCCTGGAGACGCTGCACGTAGCCCTCTGCTTCGA
TGGCAGCAGCAAGCAGGTGAAGGTGTTCAGCCTGGCCGACATCTTCGGCGCCGGCGCCGGCTTCAGCGGCGTCCGCATGG
AGGACAGCGGCTGCTTCGGCGGCGGCTACAAGGAGCGCGGCCGCGCCGTGGACCACACGCTGGTGTACGTTTCCACCAAG
GAACCGGTGACGGCTCGCCGGAGCCCCTGGACGGTGGTGTACGCCACCAACCTGAGAACCGGCGAGACGAGCCGCCTCAC
CCCGAGGGGGACCTTCGACTTGAGCCCCGCCGTGTCGCCGTCGGGGAAGAGGGTGGCGGTGGCCTCGTGGCAAGGCAAGC
CCGGCCTGTGGGGCGGCGAGATCGAGGACCTGAGGACGGACATCTACGTCATGAACGTGCACAAGCCGCCGCTGGGGCGG
ACGGGCCCAGTGATCAAGAACGGTGGGTGGCCGACGTGGGGCAGCGACGACGTCATCTTCTTCCACCGTCGGGTCGGCAC
CACCTGGGGCGTGTTCCGCTTCACCATGAGCACTAGGGAGGAAGTGCGTGTGACACCCAAGGTGTTCGACGCCGTGACTC
CGGCAGCCATCAGCGAGACGAAGGTGGCGGTGGCCACCATCCGCAAGAAGTCCCAGTTCAGCGACGTCCGCGTCGAGGAG
CAGTACCGGCACATCGAGATCTTCGACGTGACCTCGCCGGAGCAGCCGGTGAAGGTCACCCAGATGACCAGGCCCAAGAC
CGACCACTTCAACCCCTTCGTCCTCGACGGCGGCAGCCGCATCGGCTACCACCGCTGCAAGAGCGAGCAGCTTCACCAGA
ACGGCGGCAGCAGTGTACCGAACAACTTCCACAAGCTGCAGTCGCCGCACAAGGACGTGGGCTTGTTCAGGGTGTCCGGC
GTGTGCCCGACCATCTCCAAGGACGGCTCCAAGCTCGCGTTCGTGGACAACGAGTTCAAGGCCGTGTGGCTCGCCGACAG
CCATGGCCTGCGCGTGGTGTACGAGAAGAAGGGGCCCAACAGCGTGTTCTCCACGGCGTGGAACCAGAACCCGGCGCTCG
ACACGCTCTACGTCTGCGTCGGCCCCTCGTTCAGCGCCGACAAGCCGCTCCAGATCTACGCCATCCACGACGTGTCCACG
CTCGGCGGCCGCCAGCAGCGCCGCCTCACCAGCGGCTCCAACAACGCCTTCCCCTCAAGCAGCCCCGACGGCGGCAGGCT
CGTGTTCCGCTCCACCCGCGACGGCGGCGACAGGCGGTACAAGAACCTCTACATCATGGAGGACGCCACCGTTGGCGAGT
TCGGCACCGGCAAGGTGACGCGCCTCACCAACGGCTCGTGGACGGACACCCACTGCAGCTGGTCGCCGCGGGAAGGGAGC
GACTGGATCGTCTTCTCCTCCACCCGCGACAAGCCCGCCGCCGCGCCGGCCGACGACAACGGCCTCGACCCGGGCTACTT
CGCCGTCTTCCTCGTCCGCGCCTCCGACCCCACGGTGGTGGTCAGGGTGATCACGAGCGCCGACAGCATCGCCGGCCACG
TCAACCACCCGGTGTTCAGCCCCGACGGCCGCAGCATCGCCGTCACCGCCGACCTCGCCGCGGTGTCCGCCGACCCAATC
TCGCTGCCGCTGTTCCTGCACTCCGTCCGGCCCTACGGCGACATCTTCACCGTGGACATCGACCCCGACGACATCAGCAA
GAACAAGGACGTCAGGGCGTTCCACCGCGTCACGCACAGCCGCTACGAGAACTCCACGCCGGCGTGGACCATGTTCGCCA
CCGACGACCCCAACGCGCAGTGGAGCACGCTCGTGACCACCAAGGAGGCGGCGGTTTACCGGCCGGCCTGCCCGTACGCC
TACCCCGACGGCGGCGAGAGCTGGCACATGACCGGCCACCTCCTCCTCCCCAAGAGATGCTGCTAG

Alignment

ORF - retro_opun_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.8 %
• Parental protein coverage: 99.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GESRGSIAFFASYRPPVALDIFCCP-APPSS-PQEELHLTDGDSYNYNCQPIPPAALKTIVERLGV-SRG
          GESRGSIAFFA.YRPPV.LD.F.CP.APPSS.P..ELHLTDG.SYN..C.PIPPA.LK....R....S..
Retrocopy GESRGSIAFFATYRPPVPLDVFSCPVAPPSSSPRHELHLTDGVSYNHSCRPIPPASLKALLQRPKLASDS

Parental  DAVEDDIDSGRITGLVFVSEREHNLETLHIALRFTDDG-EVQVFSLADAYGADGLFSGARMEDSGCIAGG
          .A...D.D.GR.TGLVFVSER...LETLH.AL.F......V.VFSLAD..GA...FSG.RMEDSGC..GG
Retrocopy EATAADVDAGRVTGLVFVSERDSSLETLHVALCFDGSSKQVKVFSLADIFGAGAGFSGVRMEDSGCFGGG

Parental  YEVDGRTVDHYLVYVSTKEPVQERRSPWNVSYKTNLRTGETERLTPPGTFDISPSVSPSGKKVAVASYQG
          Y...GR.VDH.LVYVSTKEPV..RRSPW.V.Y.TNLRTGET.RLTP.GTFD.SP.VSPSGK.VAVAS.QG
Retrocopy YKERGRAVDHTLVYVSTKEPVTARRSPWTVVYATNLRTGETSRLTPRGTFDLSPAVSPSGKRVAVASWQG

Parental  KK--WDGEIKNLNTNIYVMSLENPSNDRER-VIENGGWPSWGSEDVIFFHRKDGDGENSCWGVFRYTLST
          K...W.GEI..L.T.IYVM....P...R...VI.NGGWP.WGS.DVIFFHR..G......WGVFR.T.ST
Retrocopy KPGLWGGEIEDLRTDIYVMNVHKPPLGRTGPVIKNGGWPTWGSDDVIFFHRRVG----TTWGVFRFTMST

Parental  GETVRVTPVAFDAVTPAAIDETRVAVAAIRQKSEFNDVRVEAQYRHIEVFDMSSPERPLQITRNTRPKAD
          .E.VRVTP..FDAVTPAAI.ET.VAVA.IR.KS.F.DVRVE.QYRHIE.FD..SPE.P...T..TRPK.D
Retrocopy REEVRVTPKVFDAVTPAAISETKVAVATIRKKSQFSDVRVEEQYRHIEIFDVTSPEQPVKVTQMTRPKTD

Parental  HFNPFVMDGGKFIGYHRCKSELLQH--GDDLPRKFHKLQSPHEDVGVFRVSGVFPTFSKDGSQLAFVDNE
          HFNPFV.DGG..IGYHRCKSE.L....G...P..FHKLQSPH.DVG.FRVSGV.PT.SKDGS.LAFVDNE
Retrocopy HFNPFVLDGGSRIGYHRCKSEQLHQNGGSSVPNNFHKLQSPHKDVGLFRVSGVCPTISKDGSKLAFVDNE

Parental  FKSVWLADSQGMRVVFKTDGPDSVFSPWWNSKK--DILYVCMGPSFKASETLEIHSIHNVST-GDRKSRQ
          FK.VWLADS.G.RVV....GP.SVFS..WN.....D.LYVC.GPSF.A...L.I..IH.VST.G.R..R.
Retrocopy FKAVWLADSHGLRVVYEKKGPNSVFSTAWNQNPALDTLYVCVGPSFSADKPLQIYAIHDVSTLGGRQQRR

Parental  LTFGGFNNAFPSTNPDGTKFVFRSTRDGGAKYSKNLYIMEDADAGEDEGGGQSSVTRMTAGEWIDTHCQW
          LT.G..NNAFPS..PDG...VFRSTRDGG....KNLYIMEDA..GE....G...VTR.T.G.W.DTHC.W
Retrocopy LTSGS-NNAFPSSSPDGGRLVFRSTRDGGDRRYKNLYIMEDATVGEF---GTGKVTRLTNGSWTDTHCSW

Parental  SPN--GKWIVFSSNRDRPADAPERDHGLDPGYFAVYLMDVASRSVV-RVIRSGYDVAGHVNHPVFSPDGR
          SP.....WIVFSS.RD.PA.AP..D.GLDPGYFAV.L.......VV.RVI.S....AGHVNHPVFSPDGR
Retrocopy SPREGSDWIVFSSTRDKPAAAPADDNGLDPGYFAVFLVRASDPTVVVRVITSADSIAGHVNHPVFSPDGR

Parental  SIAVTSDLAAVTADPMSLPLFLHSVRPYGDIFTVDIDPDDMAKNRDVERFVRITHSRYENSTPAWTVFST
          SIAVT.DLAAV.ADP.SLPLFLHSVRPYGDIFTVDIDPDD..KN.DV..F.R.THSRYENSTPAWT.F.T
Retrocopy SIAVTADLAAVSADPISLPLFLHSVRPYGDIFTVDIDPDDISKNKDVRAFHRVTHSRYENSTPAWTMFAT

Parental  HDPHAQWNLLVVEDE---HVPTCPYAHPDGGESWHMTGQICIPKRHC
          .DP.AQW..LV...E.....P.CPYA.PDGGESWHMTG....PKR.C
Retrocopy DDPNAQWSTLVTTKEAAVYRPACPYAYPDGGESWHMTGHLLLPKRCC

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_27 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza punctata	OPUNC03G14590	1 retrocopy	retro_opun_27 ,
Sorghum bicolor	Sb01g037140	1 retrocopy	retro_sbic_20,