RetrogeneDB ID: retro_olon_20

Retrocopy location

• Organism: Longstamen rice (Oryza longistaminata)
• Coordinates: KN539151.1:52374..53142(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: KN539151.1_FG015
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: KN538837.1_FG036
• Aliases: None
• Description: None

Sequence

>retro_olon_20
ATGGCTCTGCAGCAGAGCATGGCGATGCCGATGATGGTGGTGTCTGGCCTTGGCGCCGCTCCTCGGTCATCGCCGATGGT
TCAGCTGCAGAGGAGGATGAGGAAGCAGCTGGTGGTGGCGGCGGCGTTCAAGAGCAGGACCAAGGCTCCCAGCAAGTCGT
CGTCGAACAAGAAGAAGTCGATCGTGGAGGACGGCATCTTCGGCACCTCCGGCGGCATCGGGTTCACCAAGGAGAACGAG
CTGTTCGTGGGGAGGGTGGCCATGCTGGGGTTCGCGGCGTCCCTCCTCGGCGAGGCGGTCACCGGCAAGGGCATCCTGGC
GCAGCTCAACCTGGAGACGGGCATCCCCATCTACGAGGCCGAGCCGCTGCTCCTCTTCTTCATCCTCTTCACGCTGCTGG
GCGCCATCGGCGCGCTGGGCGACCGGGGGCGCTTCGTGGACGACGCCACGGGGCTGGAGCGCGCCGTGATCCCGCCGGGG
AAGGGGTTCCGCGCGGCGCTGGGGCTCAGCGAGGGTGGCCCGCTGTTCGGGTTCACCAAGGCGAACGAGCTCTTCGTGGG
TCGCCTCGCGCAGCTGGGGATCGCCTTCTCCCTCATCGGCGAGATCATCACCGGGAAGGGCGCGCTGGCGCAGCTCAACA
TCGAGACCGGCGTCCCCATCAACGAGATCGAGCCGCTCCTCCTCTTCAACATCCTCTTCTTCTTCTTCGCCGCCATCAAC
CCCGGAACCGGCAAGTTCGTCACCGACGACAACGACGGCGACCAATGA

Alignment

ORF - retro_olon_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.33 %
• Parental protein coverage: 80.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VALFGRSKTKAAPARKAEPKPKFKTEDGIFGTSGGIGFTKENELFVGRVAMLGFAASILGEAITGKGILA
          VA....S.TKA.P......K.K...EDGIFGTSGGIGFTKENELFVGRVAMLGFAAS.LGEA.TGKGILA
Retrocopy VAAAFKSRTKA-PSKSSSNKKKSIVEDGIFGTSGGIGFTKENELFVGRVAMLGFAASLLGEAVTGKGILA

Parental  QLNLETGIPIYEAEPLLLFFILFTLLGAIGALGDRGSFVDDQPVTGLDKAVIAPGKGFRSALGLSEGGPL
          QLNLETGIPIYEAEPLLLFFILFTLLGAIGALGDRG.FVDD...TGL..AVI.PGKGFR.ALGLSEGGPL
Retrocopy QLNLETGIPIYEAEPLLLFFILFTLLGAIGALGDRGRFVDD--ATGLERAVIPPGKGFRAALGLSEGGPL

Parental  FGFTKANELFVGRLAQLGIAFSIIGEIITGKGALAQLNIETGVPINEIEPLVLFNVVFFFIAAINPGTGK
          FGFTKANELFVGRLAQLGIAFS.IGEIITGKGALAQLNIETGVPINEIEPL.LFN..FFF.AAINPGTGK
Retrocopy FGFTKANELFVGRLAQLGIAFSLIGEIITGKGALAQLNIETGVPINEIEPLLLFNILFFFFAAINPGTGK

Parental  FVSDDDE
          FV.DD..
Retrocopy FVTDDND

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza longistaminata was not studied using ChIP-Seq data.

EST

Oryza longistaminata was not studied using EST data.

TSS

Oryza longistaminata was not studied using FANTOM5 data.

Lab

retro_olon_20 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza longistaminata 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA004881	1 retrocopy	retro_oind_4,
Oryza longistaminata	KN538837.1_FG036	1 retrocopy	retro_olon_20 ,
Oryza barthii	OBART01G38720	1 retrocopy	retro_obar_4,
Oryza nivara	ONIVA01G43550	1 retrocopy	retro_oniv_35,
Oryza glaberrima	ORGLA01G0325500	1 retrocopy	retro_ogla_5,
Oryza rufipogon	ORUFI01G42080	1 retrocopy	retro_oruf_10,
Oryza sativa japonica	OS01G0869800	1 retrocopy	retro_osat_18,
Triticum aestivum	TRAES3BF044200210CFD_g	1 retrocopy	retro_taes_14,