RetrogeneDB ID: retro_opun_3

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 7:31451..33197(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC07G00040
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC01G02400
• Aliases: None
• Description: None

Sequence

>retro_opun_3
ATGGAGGAGGCGGCGGCGGCGACGACGAGTGACGGGACGACGGACCATGGCGGGAAACCGGCGGTGAGGAGCAAGAGCGG
GACGTGGAGGGCGTGCCCGTTCATCCTGGGGAACGAGTGCTGCGAGCGCCTGGCCTACTACGGCATGAGCGCCAACCTCG
TCAACTACATGGTCGACCGCCTCCGCCAGGGCAACGCCGCCGCCGCCGCCAGCGTCAACAACTGGTCCGGCACATGCTAC
GTCATGCCCCTCGTCGGCGCCTTCCTCGCCGACGCCTACCTCGGTCGCTACCGCACCATCGCCGCATTCATGGCGCTCTA
CATCATCGGCCTCGCGTTCCTCACCATGACCGCCTCAGTGCCAGGCATCAAGCCGCCATACTGCACCTCCGCCTCCTCCT
CCTCGTGCGGTCCCTCCCCCGGCCAGAGCGCCGCCTTCTTCGTCGCGCTCTACCTCATCGCCCTGGGCACCGGCGGGATC
AAGCCCTGCGTCTCCTCCTTCGGCGCCGACCAGTTCGACGACGCCGACCCACGCGAGCACCGGAGCAAGGCCTCCTTCTT
CAACTGGTTCTACATGTCCATCAACGTCGGCGCCCTGGTGGCGTCATCGGTGCTCGTCTGGGTGCAGATGAACGTCGGCT
GGGGATGGGGCTTCGGCATCCCGGCTGTCGCCATGGCCGTCGCCGTCGCCAGCTTCCTCATGGGGAGCAGCCTCTACAGG
CACCAGAAGCCCGGGGGGAGCCCGCTCACCAGGATGCTGCAGGTGGTCGTGGCCGCCGCCAGGAACTCAAGGGTGGCGCT
GCCCGCCGACGCCGCGCTCCTCTACGAGGGCGACAAGACCGGCGGGAGGAGGCGGCTGGCTCACACGGAGCAGTTCAGGT
GGCTGGACAGGGCTGCGGTCGTGACACACACACTGACGGGCAACGACGAGTCCACGTCCAGCAGCAGTTGCCGGCTGTGC
CCCGTGACGCAGGTGGAGGAGCTCAAGGCGGTGGTGCGGCTGCTGCCGGTGTGGGCGAGCGGGATCGTGATGTCGGCGGT
GTACGGGCAGATGAGCACCATGTTCGTGCTTCAGGGGAACACGCTGGACCCTCGCATGGGCGGCAACTTCAAGATCCCCT
CGGCCTCGCTCTCCATCTTCGACACCCTCGCCGTCCTCGCCTGGGTCCCCGTCTACGACCGCCTCATCGTCCCCGCCGCC
CGCCGCTTCACCGGCCACCCGCGCGGCTTCACACAGCTCCAGCGCATGGGCATCGGCCTCGTCATCTCCGTCTTCTCCAT
GGTGGCCGCCGGGGTGCTGGAGGTGGTGCGCCTCCGCGTCGCCGCCGCCCACGGAATGCTCGACTCCACCGCCTACCTGC
CCATCTCCATCTTCTGGCAGGTGCCTCAGTACTTCATCATCGGCGCCGCCGAGGTGTTCGCCTTCATCGGCCAGATCGAC
TTCTTCTACGACCAGGCGCCCGACGACATGCGCAGCATGTGCACCGCGCTGTCGCTCACCTCCTCGGCGCTCGGCAACTA
CCTCAGCACGCTGCTCGTCGTCATCGTCACCGCCGCATCCACCAGGGGCGGCGGCCTCGGATGGATCCCAGACAACCTCA
ACCGCGGCCACCTCGACTACTTCTTCTGGCTGCTCGCCGCGCTCAGTGCTGTCAACTTCGTCGTCTACCTCTGGATCGCC
AACTGGTACAGGTGCAAGACAATCACCACCACTGAAACCGAAACTCAAGCAGCCGCCCAGACTTGA

Alignment

ORF - retro_opun_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.19 %
• Parental protein coverage: 96.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EVAEDIYTQDGTVDVKGNPATKKNTGNWRACPYILANECCERLAYYGMSTNLVNYMKTRLGQESAIAANN
          E.A....T.DGT.D..G.PA.....G.WRACP.IL.NECCERLAYYGMS.NLVNYM..RL.Q..A.AA..
Retrocopy EEAAAATTSDGTTDHGGKPAVRSKSGTWRACPFILGNECCERLAYYGMSANLVNYMVDRLRQGNAAAAAS

Parental  VTNWSGTCYITPLLGAFLADAYMGRFWTIASFMIIYILGLALLTMASSVKGLVP--ACDAGGGACHPTEA
          V.NWSGTCY..PL.GAFLADAY.GR..TIA.FM..YI.GLA.LTM..SV.G..P.....A....C.P...
Retrocopy VNNWSGTCYVMPLVGAFLADAYLGRYRTIAAFMALYIIGLAFLTMTASVPGIKPPYCTSASSSSCGPSPG

Parental  QTGVVFLALYLIALGTGGIKPCVSSFGADQFDENDEREKRSKSSFFNWFYFSINIGALVASSVLVYVQTH
          Q....F.ALYLIALGTGGIKPCVSSFGADQFD..D.RE.RSK.SFFNWFY.SIN.GALVASSVLV.VQ..
Retrocopy QSAAFFVALYLIALGTGGIKPCVSSFGADQFDDADPREHRSKASFFNWFYMSINVGALVASSVLVWVQMN

Parental  VGWGWGFGIPAVVMAVAVVSFFVGTPLYRHQRPGGSPLTRIAQVLVASARKWGVDVPADKSRLHETLDKE
          VGWGWGFGIPAV.MAVAV.SF..G..LYRHQ.PGGSPLTR..QV.VA.AR...V..PAD...L.E..DK.
Retrocopy VGWGWGFGIPAVAMAVAVASFLMGSSLYRHQKPGGSPLTRMLQVVVAAARNSRVALPADAALLYEG-DKT

Parental  SGIEGSRKLEHTEQFACLDRAAVETPEDKAAGRTSAWRLCTVTQV---EELKSVVRLLPIWASGIVFATV
          .G....R.L.HTEQF..LDRAAV.T..............C....V...EELK.VVRLLP.WASGIV...V
Retrocopy GG---RRRLAHTEQFRWLDRAAVVTHTLTGNDESTSSSSCRLCPVTQVEELKAVVRLLPVWASGIVMSAV

Parental  YGQMSTMFVLQGNTLDASMGPHFSIPAASLSIFDTLSVIVWVPVYDRLIVPAVRAVTGRPRGFTQLQRMG
          YGQMSTMFVLQGNTLD..MG..F.IP.ASLSIFDTL.V..WVPVYDRLIVPA.R..TG.PRGFTQLQRMG
Retrocopy YGQMSTMFVLQGNTLDPRMGGNFKIPSASLSIFDTLAVLAWVPVYDRLIVPAARRFTGHPRGFTQLQRMG

Parental  IGLVISVFSMLAAGVLDVIRLRAIARHGLYGEKDIVPISIFWQVPQYFIIGAAEVFTFVGQLEFFYDQAP
          IGLVISVFSM.AAGVL.V.RLR..A.HG........PISIFWQVPQYFIIGAAEVF.F.GQ..FFYDQAP
Retrocopy IGLVISVFSMVAAGVLEVVRLRVAAAHGMLDSTAYLPISIFWQVPQYFIIGAAEVFAFIGQIDFFYDQAP

Parental  DAMRSMCSALSLTTVALGNYLSTLLVTIVTHVTTRNGAVGWIPDNLNRGHLDYFFWLLAVLSTINFAVYL
          D.MRSMC.ALSLT..ALGNYLSTLLV.IVT...TR.G..GWIPDNLNRGHLDYFFWLLA.LS..NF.VYL
Retrocopy DDMRSMCTALSLTSSALGNYLSTLLVVIVTAASTRGGGLGWIPDNLNRGHLDYFFWLLAALSAVNFVVYL

Parental  VIAGWYTYK
          .IA.WY..K
Retrocopy WIANWYRCK

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_3 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza punctata	OPUNC01G02400	1 retrocopy	retro_opun_3 ,
Sorghum bicolor	Sb03g006420	1 retrocopy	retro_sbic_24,
Setaria italica	Si000816m.g	1 retrocopy	retro_sita_38,