RetrogeneDB ID: retro_obra_17

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 12:3499033..3499945(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB12G15110
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB12G14670
• Aliases: None
• Description: None

Sequence

>retro_obra_17
ATGCTCGTCTTCGGCGCCCTCGAGATCGTCTTCTCGCAGATCCCCAACTTCCATGAGATCTGGTGGCTGTCCATCGTCGC
CGCCGTCATGTCCTTCACCTACTCCAGCATCGGCCTCGGCATCGGCATCGCCAACACCGTCGCCAATGGTGGGTTCCGTG
GCACCATCGCCGGCGCCACCAACGTGACCGCGATGCAGAAGGTGTGGCGGTCGTTGCAGGCGCTGGGCAACATCGCCTTC
GCCTTCGCCTTCTCCAACGTGCTCACCGAGATCCAGGACACGATCAAGGCGCCGCCGCCGTCGGAGTCGGCGGTGATGAA
GAAGGCCACGAGGATGAGCGTCGTGGCGACGTCGGTGTTCTACGCGCTGTGCGGGTTCATGGGCTACGCGGCGTTCGGCA
ACGCGGCGCCGGACAACCTCCTCACCGGCTTCGGCTTCTACGAGCCCTTCTGGCTCGTCGACGCCGCCAACGTCGCCATC
GCCGTGCACCTCGTCGGCGCCTACCAGGTGTTCGTCCAGCCCATCTTCGCCTTCGTGGAGAGGCGGGTGTCCCAGAGGTG
GCCGGACAGCGGCTTCGTCAACAACGAGCTCCGCCTGGGCCCGTTCTGCATCAGCGCGTTCCGGCTGCTGTGGCGGTCGC
TGTTCGTGTGCTTCACCACGGTGGTCGCCATGGCGCTGCCCTTCTTCGGCGTCGTCGTCGGCCTCCTCGGCGCCATCTCC
TTCTGGCCGCTCACCGTTTACCTCCCCTCAGAGATGTACATCGCGCAGCGCAATGTGCGGCGAGGCAGCGCGCTGTGGAT
CGGCCTCAAGCTGTTCGCCGCCCTGGGCCTCATCGTCTCCGTCGCCGCCACCACCGGATCCGTCGCCGGCTTCGTCGGCG
AATTCAACAAGTTCCGCCCCTTCAGCGGCTAG

Alignment

ORF - retro_obra_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.24 %
• Parental protein coverage: 75.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MILFGAVQIVFSQIPDFDQIWWLSIVAAVMSFTYSGIGLSLGIAQTVANGGIQGSLTGISIGAGVSSTQK
          M..FGA..IVFSQIP.F..IWWLSIVAAVMSFTYS.IGL..GIA.TVANGG..G...G......V...QK
Retrocopy MLVFGALEIVFSQIPNFHEIWWLSIVAAVMSFTYSSIGLGIGIANTVANGGFRGTIAGAT---NVTAMQK

Parental  VWRSLQAFGDIAFAYSFSNILIEIQDTIKAPPPSEAKVMTRATRLSVATTTVFYMLCGCMGYAAFGDAAP
          VWRSLQA.G.IAFA..FSN.L.EIQDTIKAPPPSE..VM..ATR.SV..T.VFY.LCG.MGYAAFG.AAP
Retrocopy VWRSLQALGNIAFAFAFSNVLTEIQDTIKAPPPSESAVMKKATRMSVVATSVFYALCGFMGYAAFGNAAP

Parental  DNLLTGFGFYEPFWLLDVANVAIVVHLVGAYQVFVQPIFAFVERWASRRWPDSGFIARELRVGPFALSLF
          DNLLTGFGFYEPFWL.D.ANVAI.VHLVGAYQVFVQPIFAFVER..S.RWPDSGF...ELR.GPF..S.F
Retrocopy DNLLTGFGFYEPFWLVDAANVAIAVHLVGAYQVFVQPIFAFVERRVSQRWPDSGFVNNELRLGPFCISAF

Parental  RLTWRSAFVCLTTVVAMLLPFFGNVVGLLGAVSFWPLTVYFPVEMYIAQRGVARGSPRWVSLKTLSACCL
          RL.WRS.FVC.TTVVAM.LPFFG.VVGLLGA.SFWPLTVY.P.EMYIAQR.V.RGS..W..LK...A..L
Retrocopy RLLWRSLFVCFTTVVAMALPFFGVVVGLLGAISFWPLTVYLPSEMYIAQRNVRRGSALWIGLKLFAALGL

Parental  VVSIAAAAGSIADVIDALKVYRPFSG
          .VS.AA..GS.A.........RPFSG
Retrocopy IVSVAATTGSVAGFVGEFNKFRPFSG

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_17 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA037101	1 retrocopy	retro_oind_7,
Oryza brachyantha	OB12G14670	1 retrocopy	retro_obra_17 ,
Oryza glumaepatula	OGLUM12G05640	1 retrocopy	retro_oglu_3,
Oryza nivara	ONIVA12G04480	1 retrocopy	retro_oniv_32,
Oryza punctata	OPUNC12G04770	1 retrocopy	retro_opun_43,
Triticum aestivum	Traes_5DL_BB10A3B4B	2 retrocopies	retro_taes_215, retro_taes_217,