RetrogeneDB ID: retro_opun_33

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 1:27193702..27195982(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC01G23690
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC04G21280
• Aliases: None
• Description: None

Sequence

>retro_opun_33
ATGGGCTCGGGCGAGCTCGTCGACGTCGAGCGCGGCCTCCGCGGGATGGTCGGTGAGGAGGAGGTAGACGACGACGCCTC
GCCGATCGAGGAGGTCCGGCTGACGGTTCCGGTCACTGATGACCCGTCCCTTCCGGTGTGGACGTTCCGGATGTGGACAC
TCGGGCTGCTCTCGTGCGTGCTCATGAGCTTCCTGAACCAGTTCTTCTCCTACCGCACAGAGCCGCTCATCGTCACCCAG
ATCACCGTGCAGGTGGCCTCGCTACCGCTGGGCCACCTCCTCGCCCGCGTGCTGCCGCGCCGCAAGTTCAAGGCCCCCGC
CCTGCTCGGCGGCGGGGAGTGGAGCCTGAACCCGGGGCCCTTCAACATGAAGGAGCACGTGCTCGTCTCCATCTTCGCCA
ACGCCGGCTGCGCCTTCGGCAGCGGGTCCGCCTACGCCGTCATGATCGTCGACATCATCCGCGCCTTCTACCGGCGGTCC
ATTTCCTTCTTCCCCGCATGGCTCCTCATCACCACCACGCAGGTGCTCGGCTACGGGTGGGCGGGGCTGATGCGCAAGTA
CGTGGTGGAGCCGGCGCAAATGTGGTGGCCCGGCACGCTCGTGCAGGTGTCGCTGTTCCAGGCGCTGCACGGGAAGGAGG
AGCAGGAGGAGAAGACGGAGGGCGGCAGCGGCGGCGGCGGAATGTCTCAGGCTAAGTTCTTCCTGATTGCGCTCGCCTGC
AGCTTCGTGTGGTACGCCGTGCCGGGCTACCTATTCCCGACGCTGACCTCCGTCTCGTGGGTCTGCTGGATCTTCTCCAA
GTCCGTCACCGCGCAGCAGCTGGGCTCCGGCATGAAGGGCCTGGGCCTCGGCGTCTTCACCCTCGATTGGACGGCCGTAT
CAGCCTTCCTGTACAGCCCGCTGATCTCGCCGTTCTTTGCCACCGCCAACATCTTGGCCGGCTACGTGCTCCTGATGTAC
GTGATTGTGCCGGTGTCGTACTGGGGCCTCGACCTGTACAACGCCCGGAGGTTCCCCATCTTCTCGTCGCACCTGTTCAC
GGCCAGCGGCAGGACATACGACATCACGGCCATCGTGAACGACCGCTTCGAGATCGACATGGACGCGTACCAGCAGATGG
GGCGGATCAACATGAGCACGTTCTTCGCGCTGTCCTACGGGCTCGGCTTCGCGACGATCGCGGCCACCGTCACGCACGTG
GCGCTGTTCCACGGGAAGGAGATCTACCGCCGGTTCCGCGCGTCGCAGAGGGACAAGCCCGACGTGCACACGAGGCTGAT
GAAGAGCTACCGCGACGTGCCGAACTGGTGGTTCTACGCGATGCTCGCGCTCTCCGTGGCCGTCTCGCTCGTGCTCTGCA
CCGTCCTCAGGACGGCGGTGCAGCTCCCGTGGTGGGGACTCCTCTTCGCCTGCGCCATGGCCTTCGTGTTCACGCTGCCG
ATCAGCATCATCACGGCCACGACCAACCAGACGCCGGGGCTCAACATCATCACCGAGTACGTCATCGGGCTCATGCTTCC
GGGCAAGCCCATCGCTAATGTCTGCTTCAAGGCGTACGGCTACATGAGCATGTCGCAGGCCGTGTCCTTCCTGTCCGACT
TCAAGCTCGGCCACTACATGAAGATACCCCCCAAGTCCATGTTCCTCGTGCAGTTCGTCGGCACGGTGGTCGCCGCCACG
GTCAACCTCGTGGTGGCGTACTGGCTGCTGGGTTCCATCCCCAACATCTGCCAGGACGCGCTCCTCCCGGCAGACAGCCC
GTGGACGTGCCCGAACGACCGCGTCTTCTTCGACGCGTCCGTCATCTGGGGCCTCGTCGGACCGCGCCGCATCTTTGGTC
CCCTCGGCAACTACGGCGCGCTCAACTGGTTCTTCCTCGCTGGCGCCGTGGGACCCGTCATCGTGTACTTGCTCCACAGG
GCGTTCCCCAGCAAAACCTGGATACCGATGATCAACCTGCCGGTGCTCATCGGAGCGACCTCCTACATGCCGCCGGCGAC
GGCTCTGAACTACAACTCGTGGCTGATCATCGGGATCGTCTTCAACTTCTTCGTGTTCCGGTACAGGAAGCTGTGGTGGA
AGAGGTACAATTACATCCTCTCGGCTGCGCTCGACGCCGGCGTCGCGTTCATGGCGGTGCTGCTCTACTTCTCGCTGTCG
ATGGAGAACCGGAGCATCAGCTGGTGGGGGACGGCCGGCGAGCACTGCCCGCTGGCCTCATGCCCTACCGCCAAAGGGAT
AAACTTGGGCCCTGATAGCGTCTGCCCTGTTGTATTATAA

Alignment

ORF - retro_opun_33 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.41 %
• Parental protein coverage: 71.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTRAKFFLIALICSAAWYVVPGYLFPTVGAVSWLCWAFPRSVTMQQIGSGMSGLGVGAFTLDWATVVSFL
          M..AKFFLIAL.CS..WY.VPGYLFPT...VSW.CW.F..SVT.QQ.GSGM.GLG.G.FTLDW..V..FL
Retrocopy MSQAKFFLIALACSFVWYAVPGYLFPTLTSVSWVCWIFSKSVTAQQLGSGMKGLGLGVFTLDWTAVSAFL

Parental  GSPLVYPFFAIVNVWVGFVLLVYVMLPIAYWVLNLYQASTFPFFSASLFDHAGQEYRIREIVNDRFELDT
          .SPL..PFFA..N...G.VLL.YV..P..YW.L.LY.A..FP.FS..LF...G..Y.I..IVNDRFE.D.
Retrocopy YSPLISPFFATANILAGYVLLMYVIVPVSYWGLDLYNARRFPIFSSHLFTASGRTYDITAIVNDRFEIDM

Parental  DAYARQGKIHLSLFFATSYGLGFATIAATLSHVTLFYGTEMYRRFRQAAREKPDVHTRLMRRYDDIPNWW
          DAY...G.I..S.FFA.SYGLGFATIAAT..HV.LF.G.E.YRRFR...R.KPDVHTRLM..Y.D.PNWW
Retrocopy DAYQQMGRINMSTFFALSYGLGFATIAATVTHVALFHGKEIYRRFRASQRDKPDVHTRLMKSYRDVPNWW

Parental  FYGMLALAMAGALVLCIVFKDEVQLPWWALLCAMAVAFFFTLPISVITATTNTTPGLNIITEYVMGLIMP
          FY.MLAL..A..LVLC.V....VQLPWW.LL.A.A.AF.FTLPIS.ITATTN.TPGLNIITEYV.GL..P
Retrocopy FYAMLALSVAVSLVLCTVLRTAVQLPWWGLLFACAMAFVFTLPISIITATTNQTPGLNIITEYVIGLMLP

Parental  GKPIANVCFKVYGYISMNQAVSFLTDFKLGHYMKIPPRSMFLVQFIGTIVAGTVNMSVAWWLLSTVPHIC
          GKPIANVCFK.YGY.SM.QAVSFL.DFKLGHYMKIPP.SMFLVQF.GT.VA.TVN..VA.WLL...P.IC
Retrocopy GKPIANVCFKAYGYMSMSQAVSFLSDFKLGHYMKIPPKSMFLVQFVGTVVAATVNLVVAYWLLGSIPNIC

Parental  DKKHLPDGSPWTCPGSRVFFDASVIWGLVGPRRIFGPLGYYGALNWFFLGGLAGPAVVWLLAWALPRHAS
          ....LP..SPWTCP..RVFFDASVIWGLVGPRRIFGPLG.YGALNWFFL.G..GP..V.LL..A.P....
Retrocopy QDALLPADSPWTCPNDRVFFDASVIWGLVGPRRIFGPLGNYGALNWFFLAGAVGPVIVYLLHRAFP-SKT

Parental  WIRLIHLPVLLGATANMPPASTLNYTAWCSVGAVFNYLVFRRRKAWWQRYNYVLSAAMDAGVAIMGVLIF
          WI..I.LPVL.GAT..MPPA..LNY..W...G.VFN..VFR.RK.WW.RYNY.LSAA.DAGVA.M.VL..
Retrocopy WIPMINLPVLIGATSYMPPATALNYNSWLIIGIVFNFFVFRYRKLWWKRYNYILSAALDAGVAFMAVLLY

Parental  FCLSSRGITPDWWGTSAINIDHCDLSTCPTAKGV
          F.LS.......WWGT......HC.L..CPTAKG.
Retrocopy FSLSMENRSISWWGTAG---EHCPLASCPTAKGI

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_33 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza punctata	OPUNC04G21280	1 retrocopy	retro_opun_33 ,