RetrogeneDB ID: retro_oniv_7

Retrocopy location

• Organism: Indian wild rice (Oryza nivara)
• Coordinates: 11:19000380..19002510(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ONIVA11G17660
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ONIVA03G32120
• Aliases: None
• Description: None

Sequence

>retro_oniv_7
ATGCCGGCGCCGCTGGTGCCGTATAGGGAGGAAGAGCTCCGGAACCTGAGAGGCGACGACAATCCGGGCCCGTACAAGGA
CCATGACCGTGTCTACCGCTACGACGTCTACAACGACCTCGGCGAGCCAGACAGTGGCAACCCGCGCCCCGTGCTGGGTG
GCTCCGACGAGCAACCTTACCCTCGCCGCTGCCGCACCGGCCGGAGGCGGACCAACACCGACCCCGACTCCGAGAGCCGC
AACGTCGGCTTCCCCCTAACCAACCATTTCTACGTGCCCCGCGACGAGGTGTTCAACGACCGCAAGAAGGCCTACTTCGA
CACCAACAACCTCAAGCTCTATATCATGCAAAAGTACGCCACCTTTCTCTTGCACGCCGACCAGCAGACCCCCTTCGAGT
TCGACAGCTTCGCCGACGTGCTAAGCCTCTACGACGAGGGCTCCATCAACCTGCCCGGATGGCTCAACACTTTCCTCCAA
CCATTGCTCGGCATAATCCCCTTCAAGTTGCTCCAGCAAGTCCTCACCCCCGACAGCGAGTTCATCCTCAAGTTCCCCAT
GCCGGCGGTCATCAGGGAGGACAAGACGGCATGGCAAACAGACGAAGAGTTTGCGCGCGAGATGCTCGCCGGCACCAACC
CGGTCGTCATCCGCCGGCTCGGGGAAACCGAGTTCCCGCCCAAGAGCAAGCTAGACACAAGCAAGTATCACAACCAGAAC
AGCAGGATCACAGCGGCACACGTCGAGAAGTGCCTCGAGGTCGAGGGCCTCACCGTCGAGCAGGCGCTAGCCGACGGCCG
CCTCTTCATCCTCGACCACCACGACCACTTCATGCCGTACCTGCTCGATGCCAACCATCAACCAGACACTTTCGTCTACG
CGACGAGGACACTGCTCTTCCACCGCAACGATGGCACTCTCCAGCCTGCAGCAATCGAGCTCAGCCTACCTCGCTTTGAG
GCCGGCAGCACACTCATCTCGTCCGTCGGCGAGGTCTACACGCCGGCGTCAGACGGCGTGGAGGGCCACATCTGGCAGCT
TGCCAAGGCCTACGTCACCGTCAATGACTACTCGTGGCACCAGCTCGTCAGCCACTGGCTCAACACGCACGCGGTGATGG
AGCCGTTCGCCATTGCCACGCACCGGCAGCTCAGCGTGGCGCACCCTATCCACAAGCTCCTCCACCCGCACTATCGTGAC
AACTTGTTTATCAACGCCCTCGGCCGCCAGAGTCTGATCAACGCCGGTGGTAGCTCCGAGAACACCGTCTTCCTCGGCAA
GTATGGGCTCTCCATGACATCGGAGGTGTACAGGAACTGGAACTTCACCGAGCAGGCGCTCCCGGAGGACCTCATCAAGA
GGGGCATCGCCAAGCGCCGCTCCAATGGCGAGCTGGAGCTGCTGATCAAGGACTACCCGTACGCCGTCGATGGGCTCGCC
ATCTGGTCGGCAATCGAGACTTGGGTCCGCGACTATTGTGCCATCTACTACGCGGACGATGCCGCGGTCCAGGGCGACGC
CGAGCTGCAGTCGTGGTGGAAAGATGTGCGCGAGGAAGGACACGGAGACCTCAAGGACCACAAATGGTGGCCGGAGATGA
AGACGGTGGCCGAGCTTGTCCAGTCATGCGCCACCATCATCTGGATCGCCTCGGCGCTGCACGCGGCCGTCAACTTCGGC
CAGTACATGTACGCCGGCTACGTCCCGAACCGGCCGTCGGTGAGTCGGCGGCCGATGCCGAAGCCGGGCACCGACTTGTA
CAGGGAGCTGGAGCTCCACCCGGAGAAGGAATTCCTTCTCACCATCACTAAGCAGGACCTGTCCATAGCTGGCATTGCCC
TCGTCGAGCTCCTATCTAGCCATTCCGATGACGAGGTCTACCTCGGGCAGCGCGACTCGCCGAACTGGACGTCCGACCTG
GATGCCATGAACGCGTTCGACCGCTTCCGTGAACGGCTCTTGGAGGTGGAGAAGAACATCGTGGCCAAGAACGACAAGGG
CAGTGGATTCAAGAACAGGACAGGGCCGGTCAACATCCCCTACAATTTGCTCTTCCCTTATGCCTCCGGCGACGCGGAGG
CCAACACCGGGGTCACCGGCAAGGGCATCCCCAACAGCGCCTCCATCTGA

Alignment

ORF - retro_oniv_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.03 %
• Parental protein coverage: 54.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LEELRKSFPVQLIKDLLPVGGSYLLKFPKPDIIKENEVAWRTDEEFAREILAGLNPMVIRRL--TEFPPK
          L..L....P..L....L.......LKFP.P..I.E...AW.TDEEFARE.LAG.NP.VIRRL..TEFPPK
Retrocopy LQPLLGIIPFKLLQQVLTPDSEFILKFPMPAVIREDKTAWQTDEEFAREMLAGTNPVVIRRLGETEFPPK

Parental  STLDPSKYGDQTSTITPAHIEKNLE--GLSVQQALDSNRLYILDHHDHFMPFLIDINSLDGIFTYATRTL
          S.LD.SKY..Q.S.IT.AH.EK.LE..GL.V.QAL...RL.ILDHHDHFMP.L.D.N.....F.YATRTL
Retrocopy SKLDTSKYHNQNSRITAAHVEKCLEVEGLTVEQALADGRLFILDHHDHFMPYLLDANHQPDTFVYATRTL

Parental  LFLRDDDTLKPLAIELSLPHIEGNLTTAKS--KVHTPASSGIESWVWQLAKAYVAVNDSGWHQLISHWLN
          LF.R.D.TL.P.AIELSLP..E...T...S...V.TPAS.G.E...WQLAKAYV.VND..WHQL.SHWLN
Retrocopy LFHRNDGTLQPAAIELSLPRFEAGSTLISSVGEVYTPASDGVEGHIWQLAKAYVTVNDYSWHQLVSHWLN

Parental  THAVMEPFVIATNRQLSVTHPVYKLLQPHYRDTMTINALARQTLINGGGIFEQTVFPGKHALAMSSAVYK
          THAVMEPF.IAT.RQLSV.HP..KLL.PHYRD...INAL.RQ.LIN.GG..E.TVF.GK..L.M.S.VY.
Retrocopy THAVMEPFAIATHRQLSVAHPIHKLLHPHYRDNLFINALGRQSLINAGGSSENTVFLGKYGLSMTSEVYR

Parental  NWNFTEQGLPDDLIKRGIAIKDPSSPSKVKLLIKDYPYATDGLAIWQAIEQWVTEYCAIYYPNDGVLQGD
          NWNFTEQ.LP.DLIKRGIA.....S.....LLIKDYPYA.DGLAIW.AIE.WV..YCAIYY..D...QGD
Retrocopy NWNFTEQALPEDLIKRGIAKR--RSNGELELLIKDYPYAVDGLAIWSAIETWVRDYCAIYYADDAAVQGD

Parental  VELQAWWKEVREVGHGDLKDADWWPKMQSLPELTKACTTIIWIASALHAAVNFGQYPYAGYLPNRPTISR
          .ELQ.WWK.VRE.GHGDLKD..WWP.M....EL...C.TIIWIASALHAAVNFGQY.YAGY.PNRP..SR
Retrocopy AELQSWWKDVREEGHGDLKDHKWWPEMKTVAELVQSCATIIWIASALHAAVNFGQYMYAGYVPNRPSVSR

Parental  RPMPEPGSKEYTELDENPEKFFIRTITSQFQTILGVSLIEILSKHSADEIYLGQRDTPEWTSDPKALEAF
          RPMP.PG...Y.EL...PEK.F..TIT.Q...I.G..L.E.LS.HS.DE.YLGQRD.P.WTSD..A..AF
Retrocopy RPMPKPGTDLYRELELHPEKEFLLTITKQDLSIAGIALVELLSSHSDDEVYLGQRDSPNWTSDLDAMNAF

Parental  KRFSRQLVEIESKVLNMN-KDPLLKNRVGPANFPYTLMFPNTSDNKGAAEGITARGIPNSISI
          .RF...L.E.E......N.K....KNR.GP.N.PY.L.FP..S....A..G.T..GIPNS.SI
Retrocopy DRFRERLLEVEKNIVAKNDKGSGFKNRTGPVNIPYNLLFPYASGDAEANTGVTGKGIPNSASI

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_7 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza nivara	ONIVA03G32120	1 retrocopy	retro_oniv_7 ,