RetrogeneDB ID: retro_oniv_1

Retrocopy location

• Organism: Indian wild rice (Oryza nivara)
• Coordinates: 9:14164500..14166087(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ONIVA09G12740
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ONIVA01G50380
• Aliases: None
• Description: None

Sequence

>retro_oniv_1
ATGGGTCGGCGGCTGTTGCTGCTCTTCCTAATGCTGGCACAGGCACCCAATTCCAATGGGGATTCCAAGATAAAGAACGT
GGTGGTGTTGGCGCTGGAGAACCGGTCGTTCGACCACATGCTGGGGTGGATGCAGCGGCTGCTGGGCCTCCCCATCGACG
GCCTCACCGGCGCAGAGTGCAACCCGGCTCCAGGACCAGGTCCAGCCGACTCCCTCCTCCACTGCGTCTCCCCCGACGCC
GACCTCGTCGTCCCCGACGACCCCGCCCACGCCTTCGAGGACGTCCTCGAGCAGCTGCTGGGGTTCCGACCCAATGACTC
TGCTGGCGCCGCCGCCTCCCCCTCAGACATGTCGGGCTTCGTCCGCAGCGCCGTCTCCGTGAGCGCGCTCCTGACCGACG
CCGTCATGCGGGGGTTCACCCCGTCGCGGCTCCCGGCCTTCTCCGCGCTGGCCTCCTCCTTCGCGGTGTTCGACCGCTGG
TTCTCCTCCATCCCGGGGCCCACGCAGCCCAACCGGCTGTTCCTCTACTCCGCCACCTCCCACGGCGCCGTCGCCCACGA
CAAGTGGAACCTCCTCCGCGGCTACCCGCAGCGCACCATCTTCGACTCCCTCGCCGCCGACGCCCTCGACTACCGGGTCT
ACTTCAAGACCATCCCCACCACCCTCTTCTACCGCCGCCTCCGCACCGTCGCCAACGCCGCCCGCGGCACCTTCCGCCGC
TACGACGCCGCCTTCCACGACCACGCCCGCAGGGGCCTCCTCCCGGCGCTCTCCGTCATCGAGCCACGCTACTTCGACCT
CACCGGCACGCCCGCCGACGACGACCACCCGGCGCACGACGTCGCCAACGGCCAGAGGCTGGTCAAGGACGTCTACGAGG
CGCTGCGGGCGGGCCCGCAGTGGAACCACACGCTGCTCATCATCACCTACGACGAGCACGGCGGCTTCTACGACCACGTC
CCGCCGCCCAATGTCGGCGTCCCCAGCCCCGACGCCATCCGTGGCCCGCTGCCCTTCTTCTTCAGGTTCGACCGCCTCGG
CGTCAGGGTGCCCACCATCATGGTGTCGCCGTGGATCAGGAAAGGGACGGTGGTGGGGAGGCCGCCGGGAGGGCCAACGC
CCACGTCCGAGTACGAGCACTCCTCCATCCCGGCCACCATCAAGAAGATATTCAACCTCAGCTCCGACTTCCTCACCAGG
AGGGATGCGTGGGCGGGCACCTTCGAGCACCTCTTCACGGACCTGGACGAGCCAAGGACGGATTGCCCGGAGACATTGCC
GGAGATCCCGCCGCCATCTTCCTCGTCGTCGTCGACCAAGAAAGAAGACGGAGGATGGCTGTCGGACTTCCAGCGCGAGC
TGGTGCAGCTGGCGGCCTTCCTCAACGGCGACTATATGCTGTCAAGCTTCGCACAGGAGTACGAGTCGAGAATGACGATG
ACGGTGAAGCAGGCGGATGCGTATGTGAGGCGAGCCGTCAAACGTTTCCTGGAGGCCAGCAAGCGGGCCAAACGCTTAGG
TGCAAACGACTCCGCCATTGTAACCATGAGACCATCCCTCACTACTGCAACCACCTGCTGCCCTTAG

Alignment

ORF - retro_oniv_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.9 %
• Parental protein coverage: 78.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASGPARMDGFVQQARSLGDNMTAAVMNGFSPDSVAVYRELVGEFAVFDRWFASVPSSTQPNRLFVHSATS
          A..P..M.GFV..A.S.....T.AVM.GF.P........L...FAVFDRWF.S.P..TQPNRLF..SATS
Retrocopy AASPSDMSGFVRSAVSVSALLTDAVMRGFTPSRLPAFSALASSFAVFDRWFSSIPGPTQPNRLFLYSATS

Parental  GGATSNNPELLAKGYPQRTIFDNVHDAGLSFGVYYQDVPAVLFYRNLRKLKYLTK--FHPFHGAFRDHAA
          .GA.......L..GYPQRTIFD......L...VY....P..LFYR.LR.........F.....AF.DHA.
Retrocopy HGAVAHDKWNLLRGYPQRTIFDSLAADALDYRVYFKTIPTTLFYRRLRTVANAARGTFRRYDAAFHDHAR

Parental  RGSLPNYAVVEQHYMDSKSHPANDDHPSHDVFQGQMLVKEVYETLRASPQWNQTLMVVTYDEHGGFYDHV
          RG.LP...V.E..Y.D....PA.DDHP.HDV..GQ.LVK.VYE.LRA.PQWN.TL...TYDEHGGFYDHV
Retrocopy RGLLPALSVIEPRYFDLTGTPADDDHPAHDVANGQRLVKDVYEALRAGPQWNHTLLIITYDEHGGFYDHV

Parental  PTPVTGVPSPDGIVGPPPYNFAFDRLGVRVPAIVISPWINKGTVVHGPNGSPTATSEYEHSSIPATVKKL
          P.P..GVPSPD.I.GP.P..F.FDRLGVRVP.I..SPWI.KGTVV..P.G.PT.TSEYEHSSIPAT.KK.
Retrocopy PPPNVGVPSPDAIRGPLPFFFRFDRLGVRVPTIMVSPWIRKGTVVGRPPGGPTPTSEYEHSSIPATIKKI

Parental  FDLPQDFLTKRDAWAGTFESVVQGRTEPRTDCPE---QLPMPMRIRLTEANEEAK-LSEFQQELVQLASV
          F.L..DFLT.RDAWAGTFE.......EPRTDCPE.....P.P.........E....LS.FQ.ELVQLA..
Retrocopy FNLSSDFLTRRDAWAGTFEHLFTDLDEPRTDCPETLPEIPPPSSSSSSTKKEDGGWLSDFQRELVQLAAF

Parental  LNGDHQLSSLQDTIRDRMN--VREGIAYMRGAVKRFFEAGMSAKRMGVDDEQIVKMRPSLTTRTS
          LNGD..LSS.......RM...V....AY.R.AVKRF.EA...AKR.G..D..IV.MRPSLTT.T.
Retrocopy LNGDYMLSSFAQEYESRMTMTVKQADAYVRRAVKRFLEASKRAKRLGANDSAIVTMRPSLTTATT

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza nivara was not studied using ChIP-Seq data.

EST

Oryza nivara was not studied using EST data.

TSS

Oryza nivara was not studied using FANTOM5 data.

Lab

retro_oniv_1 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza nivara 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA000088	1 retrocopy	retro_oind_49,
Brachypodium distachyon	BRADI2G61140	1 retrocopy	retro_bdis_16,
Leersia perrieri	LPERR01G38640	1 retrocopy	retro_lper_20,
Oryza barthii	OBART01G44250	2 retrocopies	retro_obar_19, retro_obar_5,
Oryza glumaepatula	OGLUM01G48550	1 retrocopy	retro_oglu_24,
Oryza nivara	ONIVA01G50380	1 retrocopy	retro_oniv_1 ,
Oryza glaberrima	ORGLA01G0381200	1 retrocopy	retro_ogla_34,
Oryza rufipogon	ORUFI01G47680	2 retrocopies	retro_oruf_3, retro_oruf_32,