RetrogeneDB ID: retro_obra_9

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 7:1000438..1001728(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB07G11710
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB09G11880
• Aliases: None
• Description: None

Sequence

>retro_obra_9
ATGGACGCCTTCCTGCGCCGGTTCTTTCCGGACGTGTACCGGCGGATGCACGGCGGCGGTGAAGGGGAGGGCGTGAGCAA
CTACTGCCGGTTCGTCTCCCGGGGGGGCGCCTCCACCCCCGCCGCGGCGAACATCGCCATGCTCATCGTGGGCCGCGTCC
TGCTCGGCGTCGGCATCGGGTTCGGCAACCAGGCCGTGCCGCTCTACCTCTCGGAGATGGCCCCGCCGTCGCGCCGTGGC
GCGTTCAGCAACGGCTTCCAGCTCTGCGTCAGCGTCGGGGCGTTCGTGGCGCAGCTGGTCAACTTCGGCACCGAGAAGAT
CGCCGGCGGCTGGGGGTGGCGCGTGTCGCTCGCCGTCGCGGCCGTCCCCGCCGCGTTCCTCGCCGTCGGCGCGCTCTTCC
TCCCGGAGACGCCCAACAGCCTCATCCAGCAGGGCGAAGACCATGACAAAGTGAGAGCGCTCCTGAGCAAGATCCGAGGC
AACGACGGCGCCGGAGTCGAGGACGAGCTGGACGACATCGTCGCTGCGGACAGGTCCAAGGTCACGGCGAGGCGCGGGCT
GGCGATGATGCTCACCCAGCGGCGCTACCGCCCGCAGCTGGTGTTGGCCGTGATGATCCCCTTCTTCCAGCAGATGACCG
GGATCAACGCCATCGCGTTCTACGCGCCGGTGCTGCTCCGCACCGTCGGGATGGGCGAGAGCGCGGCGCTCCTCGCGGTG
GTCGTCAAGCAGGTGGCCGGCGTCGCCGCGACGCTCGCCTCGATGTTCGCCGTGGACCGGTTCGGGCGCCGCACCCTGTT
CCTCGCCGGCGGCGCCCAGATGGTGGTGTCGCAGGTCCTGATCGGGGCCATCATGGCGGCGCAGCTCGGCGACGACGGCG
GGCTGAGCAGGGCGAGCGCGCTGCTGCTCATCGTGCTCGTCGCCGTCTACGTGACCGGGTTCGCGTGGTCGTGGGGTCCC
CTGGGCTGGCTGGTGCCGAGCGAGATCTTCCCGCTGGAGGTGAGGTCGGCGGGGCAGAGCATCGCGGTGGCGGTGAACTT
CCTGCTGACGACGGCGGTGGCGCAGTCGTTCCTGGCGATGCTGTGCCACATGAAAGCCGGCATCTTCTTCTTCTTCGCGG
CGTGGCTGGTGGCCATGACCACCTTCGTGTACCTCCTGCTGCCGGAGACCAAGGGACTGCCCATCGAGCAGGTCGGGAAG
CTGTGGGCGCATCACTGGTTCTGGAAGAGGTTCGTCACCGACTCCGGCGACGACGACGAATGTAGAGCCATCGGCGTCGA
CAAGCTCTGA

Alignment

ORF - retro_obra_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.54 %
• Parental protein coverage: 76.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSAIGGTAVNLSMVILGRVLLGVGLGFGNQAVPLYMSEMAPPLHRGAFSNGFQLCVGIGPPPPRLTNFFT
          G.A....A.N..M.I.GRVLLGVG.GFGNQAVPLY.SEMAPP..RGAFSNGFQLCV..G.....L.NF.T
Retrocopy GGASTPAAANIAMLIVGRVLLGVGIGFGNQAVPLYLSEMAPPSRRGAFSNGFQLCVSVGAFVAQLVNFGT

Parental  QKIRQGWGWRVSLAAAAVPGGFLTLGALFLPETPNSVLQQGKDHDTVRVLLRKIRGIHD--VEDELNDIA
          .KI..GWGWRVSLA.AAVP..FL..GALFLPETPNS..QQG.DHD.VR.LL.KIRG.....VEDEL.DI.
Retrocopy EKIAGGWGWRVSLAVAAVPAAFLAVGALFLPETPNSLIQQGEDHDKVRALLSKIRGNDGAGVEDELDDIV

Parental  AANRERASSRRGMHMIVTQRQYRPQLAMAIMIPFFQQVTGINAISFYAPVLLRTIGMGESASLLSVVVTG
          AA.R.....RRG..M..TQR.YRPQL..A.MIPFFQQ.TGINAI.FYAPVLLRT.GMGESA.LL.VVV..
Retrocopy AADRSKVTARRGLAMMLTQRRYRPQLVLAVMIPFFQQMTGINAIAFYAPVLLRTVGMGESAALLAVVVKQ

Parental  LVGTTSTLLSMFLVDRFGRRTLFLVGGVQMLASQLMIGGIMTTQLGDHGQVSRTCAFVLIFLIAVYVAGF
          ..G...TL.SMF.VDRFGRRTLFL.GG.QM..SQ..IG.IM..QLGD.G..SR..A..LI.L.AVYV.GF
Retrocopy VAGVAATLASMFAVDRFGRRTLFLAGGAQMVVSQVLIGAIMAAQLGDDGGLSRASALLLIVLVAVYVTGF

Parental  AWSWGPLGWLVPSEIFPLEVRSAGQSITVAVNFLMTTAVAQLFLPVLCRMKAGIFFFFAAWLVAMTAFVY
          AWSWGPLGWLVPSEIFPLEVRSAGQSI.VAVNFL.TTAVAQ.FL..LC.MKAGIFFFFAAWLVAMT.FVY
Retrocopy AWSWGPLGWLVPSEIFPLEVRSAGQSIAVAVNFLLTTAVAQSFLAMLCHMKAGIFFFFAAWLVAMTTFVY

Parental  LLLPETKGLPIEQVGRLWSQHWFWRRFVTASDGEQAELEPVTKVDKL
          LLLPETKGLPIEQVG.LW..HWFW.RFVT.S.G...E......VDKL
Retrocopy LLLPETKGLPIEQVGKLWAHHWFWKRFVTDS-GDDDECRAI-GVDKL

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_9 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza brachyantha	OB09G11880	1 retrocopy	retro_obra_9 ,