RetrogeneDB ID: retro_obar_13

Retrocopy location

• Organism: Oryza barthii
• Coordinates: 11:2213577..2214126(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OBART11G03450
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OBART02G19160
• Aliases: None
• Description: None

Sequence

>retro_obar_13
ATGGCGCAGATGGCGTTCGAGCCAGACAAGGTGGGTACGGTGACGGTGAACGGCAAGGTGTACAGCTTCAGGCGGGTGCA
CTGGCACGCGCCGTCGGAGCACACCATCAACGGGGAGAAGCACCCGCTGGAGCTCCAGATGGTGCACGCTGCCGCCGACG
GCAGCCTCGCCGTCATCGCCATCCTCTACAAGTACGGCGCCCCGGACTCCTTCTACTTCCAGCTCAAGAGGAAGCTCGCC
GAGCTCGCCGCCGACGGATGCAGCTTCGGCGAGGAGAACGCCCAGGTCGCCCTCGGCCTCGTCCACCTCCGCTCGCTGCA
GAAGCGGACGGGGAGCTACTTCCGCTACGCCGGCTCGCTGACGGCGCCGCCGTGCACCGAGGACGTCATCTGGAGCGTGG
TCGGCAAGATCAGGCAGATCAGCCAGGAGCAGGTCGCCCTCATCACCGCGCTGCTCCCCGCCGGCGGCGCGAGGCCGACG
CAGCCGCTCAACGGCCGCACCGTGCAGTTCTACAACCCGCCCAACAGCACCATCTCCTTCAAGGTCTAG

Alignment

ORF - retro_obar_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.25 %
• Parental protein coverage: 63.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IALRYDTAGTVKVDGKKYKLRQLHWHSPSEHTINGQRFAVELHMVHHSDDGNITVIAVLYRHGKPDPFLF
          .A...D..GTV.V.GK.Y..R..HWH.PSEHTING.....EL.MVH...DG...VIA.LY..G.PD.F.F
Retrocopy MAFEPDKVGTVTVNGKVYSFRRVHWHAPSEHTINGEKHPLELQMVHAAADGSLAVIAILYKYGAPDSFYF

Parental  QIKDKLAALYLEGCK-AEKGEPLPVGLVDMRELKKGADRYFRYVGSLTAPPCTENVIWNIFGEIREMTKE
          Q.K.KLA.L...GC...E.......GLV..R.L.K....YFRY.GSLTAPPCTE.VIW...G.IR....E
Retrocopy QLKRKLAELAADGCSFGEENAQVALGLVHLRSLQKRTGSYFRYAGSLTAPPCTEDVIWSVVGKIRQISQE

Parental  QAAALRAPLHGSYRHNRRPTQPLNGRTVQ
          Q.A...A.L........RPTQPLNGRTVQ
Retrocopy QVALITALLPAG---GARPTQPLNGRTVQ

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza barthii was not studied using ChIP-Seq data.

EST

Oryza barthii was not studied using EST data.

TSS

Oryza barthii was not studied using FANTOM5 data.

Lab

retro_obar_13 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza barthii 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 barthii	OBART02G19160	1 retrocopy	retro_obar_13 ,