RetrogeneDB ID: retro_opun_13

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 9:25724577..25725909(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC09G17960
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC02G13140
• Aliases: None
• Description: None

Sequence

>retro_opun_13
ATGGCGCTTCGACCACCGCGGCCGTGTCCGGCCGACGGGCAGCAGCAGCTCGACGACGACGGCGCTGGCAACACCAGAAT
TTCCCCGGAGCAGAAGTTCGGCTTGCTGGACTTGCAGGAGGAGGACGACGAGCTCATCTTCATCGACGACGACGACGAGG
AGGGACACCAGCTGCGCAAGCAGTATGAGTCGCTGAAGCGGGAGTTCTGCCTACTGGAGAAGCAGCGGGACGACGCGCTG
CTCCAGATTCGCGGGCTGAGAGAGAGGGTGCTCTTCGGCGAGGAGCTCGTCAGGCGGCTAAAGGTCACCCCCCTCGTCGC
CGCCCAGCTCGACGAGGTCGTCGACGAGCACCACGCCGTCGTGACGTTGAGCGACGGATGCGAGATGAAGGTGTGCGTGG
GCATCGTCGGCTCGCTTGACCGCAACCTCCTCAAGCCCTCGGCGAACGTCACGCTGAACCGTCGATCGCTCGCGCTCGTC
GGCGTGCTTCCCTCCGATGTCGCCGGCTGCTCGGCCGCGCGGTTCCTCGTGGCGGACGCCGACAAGCCGGGCGTCACCTA
CGACGACATCGGCGGGTGCGAGGCGCAGAAGCAGGAGGTCCGGGAGGCCGTGGAGCTGCCGCTGACGCACCCGGAGCTCT
TCGCCGCCGTCGGCGTCGACCCGCCGCGCGGCGTGCTCCTGCACGGCCCGCCGGGCACCGGGAAGACCATGCTGGCCAAG
GCCGTCGCGCGCGAGACCTCGGCGGCTTTCTTCCGCGTGAACGCCGCCGAGCTCGCGCGGTACAACGGGCCGAGGATGGT
GCGCGACCTGTTCCGGCTCGCCAGGGACAGGGCGCCGGCCATCGTCTTCATCGACGAGGTGGACGCGATCGCGGAGGCGC
GGCGCGGCGGCGGCGGCGGCGCCAGACGCCACGTGCAACGCGTGCTGATGGAGCTGCTCACCCAGATGGACGGCTTCGAC
GAGTCCACCAACGTGCGGGTGATCATGGCGACGAACCGCGCCGACGACCTGGACCCGGCGCTGCTCCGGCCGGGGCGGCT
GGACCGCAAGGTCGAGTTCACGGCGCCCAAGAGCCGGGAGGAGAAGCGGCTGGTGCTGCAGACGTGCACGGCCGGGATGA
GCCTGGACGGCGACGTCGACCTCGACGCCCTGGCGGCGCGGCGCGACAAGCTCAGCGCCGCCGAGATCGCCGCCGTGTGC
CGCGAGGCCGGCATGCAGGCCGTGCGCGACAGGCGGGGCACGGTGACGGCGGACGACTTCGACAAGGGATACCTCGCCGT
CGTCGGCAAGAAGCCCGGCGACGTCGCCAGCGAGTTCCACTTCTACAACTGA

Alignment

ORF - retro_opun_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.2 %
• Parental protein coverage: 91.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EDDDDLYGRLKSLQRHMEFVEIQEEYVKDEQKNLKRELLRAQEEVKRIQSVPLVIGQFMEMVDGNNGIVG
          E....L.....SL.R.....E.Q..........L....L...E.V.R....PLV..Q..E.VD.....V.
Retrocopy EEGHQLRKQYESLKREFCLLEKQRDDALLQIRGLRERVLFGEELVRRLKVTPLVAAQLDEVVDEHHAVVT

Parental  STTGSNYYV--RILSTINRELLKPSASVALHRHSNALVDVLPPEA---DSSISLLGSSEKPNVTYTDIGG
          ...G....V...I.....R.LLKPSA.V.L.R.S.ALV.VLP...........L.....KP.VTY.DIGG
Retrocopy LSDGCEMKVCVGIVGSLDRNLLKPSANVTLNRRSLALVGVLPSDVAGCSAARFLVADADKPGVTYDDIGG

Parental  CDIQKQEIREAVELPLTHHELYKQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTAAFIRVVGSEFVQKY
          C..QKQE.REAVELPLTH.EL....G.DPPRGVLL.GPPGTGKTMLAKAVA..T.AAF.RV...E.....
Retrocopy CEAQKQEVREAVELPLTHPELFAAVGVDPPRGVLLHGPPGTGKTMLAKAVARETSAAFFRVNAAELARY-

Parental  LGEGPRMVRDVFRLAKENAPAIIFIDEVDAIATARFDAQTGADREVQRILMELLNQMDGFDQTVNVKVIM
          ...GPRMVRD.FRLA...APAI.FIDEVDAIA.AR.....GA.R.VQR.LMELL.QMDGFD...NV.VIM
Retrocopy --NGPRMVRDLFRLARDRAPAIVFIDEVDAIAEARRGGGGGARRHVQRVLMELLTQMDGFDESTNVRVIM

Parental  ATNRADTLDPALLRPGRLDRKIEFPLP-DRRQKRLVFQVCTAKMNLSDEVDLEDYVSRPDKISAADIAAI
          ATNRAD.LDPALLRPGRLDRK.EF..P..R..KRLV.Q.CTA.M.L...VDL.....R.DK.SAA.IAA.
Retrocopy ATNRADDLDPALLRPGRLDRKVEFTAPKSREEKRLVLQTCTAGMSLDGDVDLDALAARRDKLSAAEIAAV

Parental  CQEAGMHAVRKNRYVILPKDFEKGYRTNV-KKP---ETDFDFY
          C.EAGM.AVR..R......DF.KGY...V.KKP......F.FY
Retrocopy CREAGMQAVRDRRGTVTADDFDKGYLAVVGKKPGDVASEFHFY

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_13 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA008091	1 retrocopy	retro_oind_47,
Aegilops tauschii	F775_28952	1 retrocopy	retro_atau_13,
Leersia perrieri	LPERR02G11870	1 retrocopy	retro_lper_5,
Oryza barthii	OBART02G14640	1 retrocopy	retro_obar_11,
Oryza punctata	OPUNC02G13140	1 retrocopy	retro_opun_13 ,
Oryza glaberrima	ORGLA02G0127200	1 retrocopy	retro_ogla_44,
Oryza sativa japonica	OS02G0325100	1 retrocopy	retro_osat_48,
Triticum aestivum	Traes_2AL_80D15B4FB	2 retrocopies	retro_taes_103, retro_taes_107,