RetrogeneDB ID: retro_obra_15

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 6:20962822..20963956(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB06G34780
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB06G25340
• Aliases: None
• Description: None

Sequence

>retro_obra_15
ATGGCGATGTCGTGCTCTTCCTCCATGCGCCTCCGATTGAATCTAGTGCCCTCCGGCCGCCGACGGGAGGATCCCGGTAA
CGTCCACTTTGTCCGGCGGGCTGGAGTGGTTGCTTCTCCTCTCCGGCTCCGTGCCGCCCGTGCCATGGAGGATGATGCAC
GGCACCCGTTCGACCACGTGCCGCGCGGCGTTGAGGAGGTGGTTGGTGACCAGGAGGAAGACGAGGAGAAGCGGCGGCGG
CGACTCACGATCGCCGTCGTGGGGTTTGGGAACTACGGGCAGTTCCTGACAAGGACGCTGGTGCGGCAGGGGCACACCGT
CCTGGCGCACTCGCGCTCCGACTACTCCGCCGTCGCGGCCGAGTTCGGCGCGTCGTTCTTCGCCGACCCGCACGACCTCT
GCGAGTGCCACCCGGATGTCGTGCTCCTCGTCACCTCCATCCTCTCCGCGGAGGCCGTCCTCCTCTCGCTCCCCGTCCAC
CGCCTCCGCCGCGACACACTCTTCGCCGACGTGCTCTCCGTCAAGGAGTTCCCGAGGAACCTCCTCCTCGGCACGCTCCC
GGAGGAGTTCGACATCATCTGCACCCACCCCATGTTCGGGCCGGAGTCCGCGCGGGACGGATGGGGCGGCCTCCCCTTCG
TGTTCGACAAGGTCCGCGTCGGCGACTGCCCCGCCCGCCGCGCCCGCGCCGAGGCCTTCCTCGACATCTTCGCGCGCGAG
GGGTGCCGCATGGTGGAGATGAGCTGCGCCGAGCACGACGCGCACGCCGCCGAGACGCAGTTCCTCACCCACACCGTCGG
CCGGACACTCGCCATGCTGGAGCTCCAGCCAACCCCGATCAACACCAAGGGCTACGAGACCCTCCTCCGGCTCATCGACA
ACACCTGCAGCGACAGCTTCGACCTCTACAATGGCCTCTTCATGTACAACAACAACTCGACGGAGCTGCTCAACCGCCTC
GAATGGGCCATGGATTCCGTCAAGAAGAAGCTCTTCGACGGCCTCCACGACGTGCTCCGGAGGCAGCTCTTCGAGGCCCC
GTTGGACTCCGCCACCGCCGCGGCCGCGCCGCCGATCGATGACGCACCGATCGATGGCGATCTAGACGGTGACAACGACA
AGGAATCGGAATAA

Alignment

ORF - retro_obra_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.7 %
• Parental protein coverage: 80.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEEERADVAAGALRVGIVGFGNFGQFIARGIQRRGHAVPATSRSDYFGYCARRGIRFFATADALCDAGPD
          ..EE........L....VGFGN.GQF..R...R.GH.V.A.SRSDY....A..G..FFA....LC...PD
Retrocopy DQEEDEEKRRRRLTIAVVGFGNYGQFLTRTLVRQGHTVLAHSRSDYSAVAAEFGASFFADPHDLCECHPD

Parental  VLLLCSSILSTEAVVRAVPFHKLRPDAIVADVLSVKQFPRNLLLEILPPGFGIVCTHPMFGPESGKHGWS
          V.LL..SILS.EAV....P.H.LR.D...ADVLSVK.FPRNLLL..LP..F.I.CTHPMFGPES...GW.
Retrocopy VVLLVTSILSAEAVLLSLPVHRLRRDTLFADVLSVKEFPRNLLLGTLPEEFDIICTHPMFGPESARDGWG

Parental  GLPFVYDKVRVAQEGNQATKCEQFLSIFEEEGCRMVEMSCAEHDRYAAGSQFITHTIGRILAQLNLKSTP
          GLPFV.DKVRV..........E.FL.IF..EGCRMVEMSCAEHD..AA..QF.THT.GR.LA.L.L..TP
Retrocopy GLPFVFDKVRVGDCPARRARAEAFLDIFAREGCRMVEMSCAEHDAHAAETQFLTHTVGRTLAMLELQPTP

Parental  INTKGYETLLKLTENTVSDSFDLYYGLFMYNINATEQMENLEKAFQKVKEMLYGRLHNVLRKQIVE
          INTKGYETLL.L..NT.SDSFDLY.GLFMYN.N.TE....LE.A...VK..L...LH.VLR.Q..E
Retrocopy INTKGYETLLRLIDNTCSDSFDLYNGLFMYNNNSTELLNRLEWAMDSVKKKLFDGLHDVLRRQLFE

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza brachyantha was not studied using ChIP-Seq data.

EST

Oryza brachyantha was not studied using EST data.

TSS

Oryza brachyantha was not studied using FANTOM5 data.

Lab

retro_obra_15 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza brachyantha 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 brachyantha	OB06G25340	1 retrocopy	retro_obra_15 ,
Oryza rufipogon	ORUFI06G18690	1 retrocopy	retro_oruf_8,
Setaria italica	Si006643m.g	1 retrocopy	retro_sita_25,