RetrogeneDB ID: retro_obra_3

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 3:29576752..29577577(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB03G48920
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB0038G10090
• Aliases: None
• Description: None

Sequence

>retro_obra_3
ATGGCGGGTAGCAGCAAGGACTACCACGATCCTCCTCCCACGCCGCTAGTGGACGCCGGCGAGCTGGGAAAGTGGTCCCT
CTACCGTGCCACCATCGCCGAGTTCACCGCCACGCTGCTCTTCGTCTGCATCACTGTGACCACCGTCATTGGCCACAAGC
GCCAGTCGGCTGAGGCCTGCGCCGGCGCCGGCGTGCTTGGCATCGCCTGGGCTTTCGGTGGCATCATCTTCGTGCTCGTG
TACTGCACCGCTGGCATCTCCGGCGGGCACATCAACCCAGCCGTCACCTTCGCCATGCTGCTCGCGCGCAGGGTCTCGCT
GCCGCGCGCTGCGCTCTACATGATCGCGCAGTGCCTCGGCGCCATGTGCGGCGCGGGCCTCGCTAGGGCGCTGCACGGTG
GTCGTCAGTACGCGCGCCACGGCGGCGGTGCCAACGAGCTGGTGGAGGGCTACTCCGCTGGCGCGGGGTTCGCCGCCGAG
ATGGTGGGCACCTTCGTGCTGGTGTACACGGTGTTGTCGGCGACCGACCCGAAGCGCAAGGCACGGGACTCGCACGTGCC
CGTGCTGGCGCCGCTGCCCATCGGGTTGGCGGTGCTGGTGGTGCACCTGGCCACCATCCCCATCACCGGCACTGGCATCA
ACCCGGCGCGCAGCCTGGGGCCGGCCGTCGTTTACAACGGCAGCAAGGCGTGGAAAGAGCAGTGGATGTTCTGGGTGGGG
CCCTTCGCCGGCGCCGGCGCCGCAATACTGTACCACCAGTACATCCTCAGGGGCGCTGCTGCCAAGGCCTTCGCCTCCTC
CTACCTCGCCCATTTTGCTAGCTAG

Alignment

ORF - retro_obra_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.08 %
• Parental protein coverage: 73.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KDYTDPPPAPLFDVGELRLWSFYRALIAEFIATLLFLYITVATVIGYKVQSSADQCGGVGTLGIAWAFGG
          KDY.DPPP.PL.D.GEL..WS.YRA.IAEF.ATLLF..ITV.TVIG.K.QS.A..C.G.G.LGIAWAFGG
Retrocopy KDYHDPPPTPLVDAGELGKWSLYRATIAEFTATLLFVCITVTTVIGHKRQS-AEACAGAGVLGIAWAFGG

Parental  MIFILVYCTAGISGGHINPAVTFGLLLARKVSVIRAVMYIVAQCLGGIVGVGIVKGIMK-HQYNANGGGA
          .IF.LVYCTAGISGGHINPAVTF..LLAR.VS..RA..Y..AQCLG...G.G.........QY...GGGA
Retrocopy IIFVLVYCTAGISGGHINPAVTFAMLLARRVSLPRAALYMIAQCLGAMCGAGLARALHGGRQYARHGGGA

Parental  NVVASGYSNGTALGAEIIGTFVLVYTVFSATDPKRNARDSHVPVLAPLPIGFAVFMVHLATIPITGTGIN
          N....GYS.G....AE..GTFVLVYTV.SATDPKR.ARDSHVPVLAPLPIG.AV..VHLATIPITGTGIN
Retrocopy NELVEGYSAGAGFAAEMVGTFVLVYTVLSATDPKRKARDSHVPVLAPLPIGLAVLVVHLATIPITGTGIN

Parental  PARSIGAAVIYNQKKAWDDHWIFWAGPFIGALAAAAYHQYILRAAAIKALGS
          PARS.G.AV.YN..KAW...W.FW.GPF.GA.AA..YHQYILR.AA.KA..S
Retrocopy PARSLGPAVVYNGSKAWKEQWMFWVGPFAGAGAAILYHQYILRGAAAKAFAS

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_3 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 11 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA009362	1 retrocopy	retro_oind_43,
Oryza longistaminata	KN540828.1_FG001	1 retrocopy	retro_olon_7,
Leersia perrieri	LPERR04G03430	1 retrocopy	retro_lper_22,
Oryza brachyantha	OB0038G10090	1 retrocopy	retro_obra_3 ,
Oryza barthii	OBART04G05050	1 retrocopy	retro_obar_18,
Oryza glumaepatula	OGLUM04G04240	1 retrocopy	retro_oglu_29,
Oryza meridionalis	OMERI04G05010	1 retrocopy	retro_omer_6,
Oryza nivara	ONIVA04G03300	1 retrocopy	retro_oniv_20,
Oryza punctata	OPUNC04G04310	1 retrocopy	retro_opun_34,
Oryza rufipogon	ORUFI04G05780	1 retrocopy	retro_oruf_16,
Oryza sativa japonica	OS04G0233400	1 retrocopy	retro_osat_19,