RetrogeneDB ID: retro_obra_19

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 2:18308435..18309509(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB02G32480
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB03G24650
• Aliases: None
• Description: None

Sequence

>retro_obra_19
ATGGGCCTAATTCTTTCTTGCCACACAAGCAAGGCCCAAGACGACAAGCCACCGCAGGAAAAAGAACACCAACCCCACCA
CTCCACCGAGAAAAAAGATCCAAGCCGAGGCGCACCGTCTCGACTTCTCTCCCCTCTCGCCCTATCCGTTCCTCGTTATA
ACTTGGCTGCCTCACCATCTCGTCCCCAGATTTCCATTCCTCCGCCGTTCGCCTCGAATCCAATCCGGCAGCNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNGTCGTCGCCCGCGCCGTACCAGCCGCCGCAGCAGCCGGCGGGGTACTCGTCGCACCAGGCGTTCGGGCTGGTGC
CCATGGTCATCGAGACGACCTCGCGCGGGGAGCGGGCGTACGATATCTTCTCGCGCCTGCTCAAGGAGCGGATCGTGCTC
ATCCACGGCCCAATCGCCGACGAGACCGCCTCCCTCGTCGTCGCGCAGCTGCTCTTCCTCGAGTCCGAGAACCCGCTCAA
GCCGGTCCACCTCTACATCAACTCCCCCGGGGGCGTCGTCACGGCGGGGCTCGCGATCTACGACACCATGCAGTACATCC
GCTGCCCCGTCACCACGCTCTGCATCGGCCAGGCCGCGTCCATGGGCTCGCTCCTGCTCGCCGCCGGCGCCCGCGGGGAG
CGCAGGGCGCTGCCCAACGCGCGGGTCATGATTCACCAGCCCTCCGGCGGGGCACAGGGCCAGGCCACCGACATCGCCAT
CCAGGCCAAGGAGATTCTCAAGCTGCGTGACCGCCTCAACAAGATCTACCAGAAGCACACCGGGCAGGAAATCGACAAAA
TCGAGCAGTGCATGGAGCGCGATCTGTTCATGGACCCTGAGGAGGCTCGTGACTGGGGGCTCATCGACGAGGTCATTGAG
AACCGCCCCGCTTCCCTGGTGCCCGAGGGCGTCGGTGGTGGCGTTGACCTGCCTATCCACAGCGGCGGCGTCGGCGGAAG
GGGCAGAGATGTCGAGGAGCCCTCCGCGGTGTGA

Alignment

ORF - retro_obra_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.89 %
• Parental protein coverage: 65.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERFQSVVSQLFQHRIIRCGGPVEDDMANIIVAQLLYLDAIDPNKDIIMYVNSPGGSVTAGMAIFDTMKHI
          ER.....S.L...RI....GP..D..A...VAQLL.L....P.K....Y.NSPGG.VTAG.AI.DTM..I
Retrocopy ERAYDIFSRLLKERIVLIHGPIADETASLVVAQLLFLESENPLKPVHLYINSPGGVVTAGLAIYDTMQYI

Parental  RPDVSTVCIGLAASMGAFLLSGGTKGKRYSLPNSRIMIHQPLGGAQGQETDLEIQANEMLHHKANLNGYL
          R..V.T.CIG.AASMG..LL..G..G.R..LPN.R.MIHQP.GGAQGQ.TD..IQA.E.L.....LN...
Retrocopy RCPVTTLCIGQAASMGSLLLAAGARGERRALPNARVMIHQPSGGAQGQATDIAIQAKEILKLRDRLNKIY

Parental  AYHTGQPLDKINVDTDRDYFMSAKEAKEYGLIDGVIMNPLKALQP
          ..HTGQ..DKI.....RD.FM...EA...GLID.VI.N....L.P
Retrocopy QKHTGQEIDKIEQCMERDLFMDPEEARDWGLIDEVIENRPASLVP

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_19 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00045p00165520	1 retrocopy	retro_atri_13,
Oryza brachyantha	OB03G24650	1 retrocopy	retro_obra_19 ,
Oryza glaberrima	ORGLA03G0142400	1 retrocopy	retro_ogla_20,
Triticum aestivum	Traes_4AS_C67AE6944	1 retrocopy	retro_taes_83,