RetrogeneDB ID: retro_oniv_27

Retrocopy location

• Organism: Indian wild rice (Oryza nivara)
• Coordinates: 8:19806466..19808857(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ONIVA08G18360
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ONIVA09G14620
• Aliases: None
• Description: None

Sequence

>retro_oniv_27
ATGGCGTCGTCGGCGTCCCGCACTCTCCTGCTGCTGCTGGTGGTGGTGGTTGTGGCCGCTGCCGTTGGAGGAGTGTTGGG
TGGGGGAGGGGAGGAGAGGACGTTCATCGTGCGGGTGGATGCGGACGCGAAGCCCTCGGCGTTCCCGACGCACGCGCACT
GGTACGAGGCGGCGGTGATGGCAGCGGAGGGTGGTGGTGGTGGAGGGGAGTGGCGGGAGGGGGGCCCGCTGATCCACACC
TACTCCGCCGCCTTCCACGGCTTCTCCGCGCGGATGTCGCCGGCTGCGGCGGCGGCGCTGGCGGAGGCTCCCGGGGTGGC
GGCGGTGGTGCCGGAGCGGGTCCGGCAGCTCGCCACCACCCGCTCGCCGCGGTTCCTTGGGCTGCTGTCGTCCCCGCCGT
CGGCGCTCCTCGCGGACTCGGATTTTGGTTCCGACCTCGTCATCGCCATCATCGACACCGGCATCTCCCCCACCCACCGC
AGCTTCCACGACCGTGGGCTTGGTCCGGTGCCGTCCAAGTGGCGCGGGGTGTGCTCGTCGGGGCCTGGGTTCCCGCCCAA
CTCCTGCAATCGCAAGCTCGTCGGCGCGCGGTTCTTCTCCGCCGGGTATGAGGCCACCTCTGGCCGCATGAACGAGACGG
CGGAGGTCAGGTCGCCGCTCGACACCGATGGGCACGGGACCCACACGGCCTCCATCGCCGCCGGCCGCTACGTGTTCCCG
GCGTCCACCCTCGGCTACGCCCGGGGCGTGGCTGCCGGGATGGCGCCCAAGGCACGCCTCGCCGCGTACAAGGTGTGCTG
GGTGGGCGGCTGCTTCGACTCCGACATCCTTGCGGCTTTCGATGCCGCCGTCGCCGACGGCGTCGATGTCGTGTCCCTCA
GCGTCGGTGGCGTCGTCGTGCCGTACTACCTTGACGCCATTGCCATTGGGGCATTCGGGGCGACGGAGGCTGGGATTGTT
GTTTCGGCTTCGGCCGGCAATGGCGGCCCTGGTGGGCTCACTGTGACCAATGTGGCTCCCTGGATGGCCACCGTTGGCGC
TGGGTCCATGGACCGCGCCTTCCCGGCCAACGTGCAGCTCGGCAATGGTCAAGTGCTCGACGGTGTCAGCGTGTACGGCG
GGCCAGCGCTCCAATCCGGCAAGATGTATGAGCTTGTATATGCTGGAGCAAGCAGCGGCGCTGCCTCGTCTGCGGCTGAC
GGCTACTCGGCGTCCATGTGCCTCGACGGCTCGCTCGACCCCGCCGCGGTGCGGGGCAAGATCGTGGTGTGCGACCGCGG
CGTGAACTCGCGCGCCGCCAAGGGCGACGTGGTTCACCGCGCGGGCGGCATCGGGATGGTGCTCGCCAACGGGGTGTTCG
ACGGGGAGGGCCTCGTCGCCGACTGCCACGTTCTGCCAGCCACAGCCGTCGGCGCGGCCGCTGGCGACAAGCTCCGTAAG
TACATTGGGTCGTCGACGCGGCAGGCGCCGGCCACCGGCACCATCTTGTTCGAAGGCACCCACCTCGGCGTGCATCCGGC
GCCTGTGGTGGCCGCGTTCTCCGCGCGTGGCCCCAATCCCCAATCCCCGGAGATACTCAAGCCAGACCTGATTGCCCCCG
GCCTAAACATCCTCGCCGCATGGCCCAGCGGCGTCGGGCCGGCCGGCATCCCCTCCGACGGCCGCCGCACGGAATTCAAC
ATCCTCTCGGGCACGTCCATGGCTTGCCCGCACATCTCCGGCCTCGCCGCATTGCTCAAGGCGGCGCATCCTACCTGGAG
CCCCGCGGCGATCAAGTCAGCGCTCATGACCACCGCCTACATCAAGGACAACAGCAACGGCACCATGGTGGACGAGTCCA
CGGGCGTCGTGGCCGACGTGTTCGACTTCGGCGCAGGGCACGTTGACCCGATGCGCGCCATGGACCCTGGTCTCGTCTAC
GACATCACCCCCGTGGACTACGTCAACTTCCTCTGCAACCTGAACTACACCGAGCAGAACATCCGGGCGATCACGCGGCG
CCCCGCGGACTGCCGCGGCGCGCGGCGCGCGGGGCACGCCGGGAACCTCAACTACCCGTCCATGTCCGCCACGTTCGCCG
CGGACGGCACCAGGGCGACGATGAAGACCCACTTCATCCGGACGGTGACCAACGTCGGCGGCGGGCGCGCGGTGTACCGC
GCGACGGTGAGGTCGCCCGAGGGGTGCGCGGTGACCGTGCAGCCGCGGCAGCTGGCGTTCCGGCGCGACGGGCAGAAGCT
GAGCTTCACGGTGCGGGTGGAGGCCGCGGCGCCGGCCAAGAAGATGGAGCCCGGGAGCTCGCAGGTGAGGAGCGGCGCGG
TGACGTGGAGCGACGGGAGGCACGCCGTGAACACCCCGGTCGTCGTGACAGTGCAAGCGCCGCTGCAGTAA

Alignment

ORF - retro_oniv_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.41 %
• Parental protein coverage: 57.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CNRKLIGARYFNKGYLSTVGQAANPASTR---DTDGHGTHTLSTAAGRFVPGANLFGYGNGTAKGGAPGA
          CNRKL.GAR.F..GY..T.G.....A..R...DTDGHGTHT.S.AAGR.V..A...GY..G.A.G.AP.A
Retrocopy CNRKLVGARFFSAGYEATSGRMNETAEVRSPLDTDGHGTHTASIAAGRYVFPASTLGYARGVAAGMAPKA

Parental  HVAAYKVCWRPVNGSECFDADIIAAFDAAIHDGVDVLSVSLGGAPAGYLRDGVAIGSFHAVRRGVTVVCS
          ..AAYKVCW..V.G..CFD.DI.AAFDAA..DGVDV.S.S.GG....Y..D..AIG.F.A...G..V..S
Retrocopy RLAAYKVCW--VGG--CFDSDILAAFDAAVADGVDVVSLSVGGVVVPYYLDAIAIGAFGATEAGIVVSAS

Parental  AGNSGPGAGTVSNTAPWLVTVGASTMDREFPAYLVLGNNKKIKGQSL-SPVRLAGGKNYPLI---SSEQA
          AGN.GPG..TV.N.APW..TVGA..MDR.FPA...LGN.....G.S......L..GK.Y.L.....S..A
Retrocopy AGNGGPGGLTVTNVAPWMATVGAGSMDRAFPANVQLGNGQVLDGVSVYGGPALQSGKMYELVYAGASSGA

Parental  RAANATASQARLCMEGSLERGKVEGRIVVCMRGKNARVEKGEAVRRAGGAGLVLANDEATGNEMIADAHV
          ....A....A..C..GSL....V.G.IVVC.RG.N.R..KG..V.RAGG.G.VLAN....G....AD.HV
Retrocopy ASSAADGYSASMCLDGSLDPAAVRGKIVVCDRGVNSRAAKGDVVHRAGGIGMVLANGVFDGEGLVADCHV

Parental  LPATHVTYSDGVALLAYL-NSTRS--PSGFITVPDTALDTKPAPFMAAFSSQGPNTVTPQILKPDITAPG
          LPAT.V....G..L..Y...STR.....G.I....T.L...PAP..AAFS..GPN...P.ILKPD..APG
Retrocopy LPATAVGAAAGDKLRKYIGSSTRQAPATGTILFEGTHLGVHPAPVVAAFSARGPNPQSPEILKPDLIAPG

Parental  VSILAAFTGQAGPTGLAFDSRRVLFNAESGTSMSCPHVAGVAGLLKALHPDWSPAAIKSAIMTTARVKDN
          ..ILAA.....GP.G...D.RR..FN..SGTSM.CPH..G.A.LLKA.HP.WSPAAIKSA.MTTA..KDN
Retrocopy LNILAAWPSGVGPAGIPSDGRRTEFNILSGTSMACPHISGLAALLKAAHPTWSPAAIKSALMTTAYIKDN

Parental  MRRPM-SNSSFLRATPFSYGAGHVQPGRAADPGLVYDMNDTDYLGFLCALGYNSSVI
          ....M...S....A..F..GAGHV.P.RA.DPGLVYD....DY..FLC.L.Y....I
Retrocopy SNGTMVDESTGVVADVFDFGAGHVDPMRAMDPGLVYDITPVDYVNFLCNLNYTEQNI

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_27 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza barthii	OBART09G14060	1 retrocopy	retro_obar_23,
Oryza nivara	ONIVA09G14620	1 retrocopy	retro_oniv_27 ,
Sorghum bicolor	Sb02g027810	1 retrocopy	retro_sbic_11,