RetrogeneDB ID: retro_obar_15

Retrocopy location

• Organism: Oryza barthii
• Coordinates: 1:29880552..29881179(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OBART01G35840
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OBART05G07210
• Aliases: None
• Description: None

Sequence

>retro_obar_15
ATGCCGTACGCCGCCGTACGTCCTTCGCCACCGCCGCAGCTCAGCCGGCCGATCGGCTCCGGAGCCGGCGGCGGTAAGGC
GTGCCCGGCGGTGCCGTGCGAGGTGGCGCGGTACCACGAGCACGCGGTGGGCGCGGGGCAGTGCTGCTCCACCGTGGTGC
AGGCGATCGCGGCGCCGGCGGACGCGGTGTGGTCGGTGGTGCGGAGGTTCGACCGGCCGCAGGCGTACAAGAAGTTCATC
AAGAGCTGCCGCCTCGTGGACGGCGACGGCGGCGAGGTCGGGTCGGTGCGGGAGGTGCGCGTCGTGTCCGGGCTGCCGGC
CACGAGCAGCCGCGAGCGGCTCGAGGTCCTGGACGACGACCGCCGCGTGCTCAGCTTCCGGATCGTCGGCGGCGAGCACC
GCCTCGCCAACTACCGCTCGGTGACCACCGTCCACGAGGCGGCGGCGCCGGCGATGGCCGTGGTGGTCGAGTCGTACGTG
GTGGACGTGCCGCCGGGGAACACCTGGGAGGAGACGCGCGTGTTCGTGGACACGATCGTGCGCTGCAACCTCCAGTCGCT
TGCGCGAACGGTCGAGCGGCTCGCGCCGGAAGCGCCGCGCGCCAACGGATCGATCGATCATGCATGA

Alignment

ORF - retro_obar_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.82 %
• Parental protein coverage: 87.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGAVAAGAAAAAEAEHMRRLHSHAPGEHQCSSALVKHIKAPVHLVWSLVRSFDQPQRYKPFVSRC-VVRG
          G.....G.A..A......R.H.HA.G..QC.S..V..I.AP...VWS.VR.FD.PQ.YK.F...C..V.G
Retrocopy GSGAGGGKACPAVPCEVARYHEHAVGAGQCCSTVVQAIAAPADAVWSVVRRFDRPQAYKKFIKSCRLVDG

Parental  GDLEIGSVREVNVKTGLPATTSTERLELLDDDEHILSVKFVGGDHRLRNYSSIITVHPESIDGRPGTLVI
          ...E.GSVREV.V..GLPAT.S.ERLE.LDDD...LS...VGG.HRL.NY.S..TVH...........V.
Retrocopy DGGEVGSVREVRVVSGLPATSSRERLEVLDDDRRVLSFRIVGGEHRLANYRSVTTVHEAAAPAM--AVVV

Parental  ESFVVDVPDGNTKDETCYFVEAVIKCNLTSLAEVSERLAVQSP
          ES.VVDVP.GNT..ET..FV.....CNL.SLA...ERLA...P
Retrocopy ESYVVDVPPGNTWEETRVFVDTIVRCNLQSLARTVERLAPEAP

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_15 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00107p00103680	1 retrocopy	retro_atri_5,
Oryza brachyantha	OB05G16630	1 retrocopy	retro_obra_18,
Oryza barthii	OBART05G07210	1 retrocopy	retro_obar_15 ,
Prunus persica	PRUPE_ppa012114mg	1 retrocopy	retro_pper_8,