RetrogeneDB ID: retro_osat_23

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 5:29585075..29585909(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OS05G0594100
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OS01G0550300
• Aliases: None
• Description: None

Sequence

>retro_osat_23
ATGGAGGGGTACGACGAGCGTGAGTTCTGGCAGTTCAGCGACCAGCTCCGCCTCCACAACTTCTCCAGCCTCTCCATCGC
CGACTCCATCTGGTCCTCCCCCTCGCCTGCCGCCGTCGATCATAGCAGCAACAAGCTCGCCCTCGCCAACAACAGCAACA
ACAACGCCACCGCCAAGACCTACTTCAACAAGTCCGTCGGCAGGCCGGCCAACAACAACTTCAACTTCAACTACAACAGC
AACAGCGTCGTCGTAGATGCGTTCAACGGGAAGAAGAAGGCCGCTGTCGACGCTCCTGCTGGAGGAGGAGGAGGAGGCAG
GAACAACAACAAGAAGAACAGCAGCAGCAACGACAACAAGATGAGCAGCAGGTTGAAGAAGAGCCAGCTGCCGGCGTCGG
AGTCGGTGCCAAAGGAGGAGGCGATCGGGGGATACATATTCGTGTGCAACAACGAGACGATGGAGGAGAATCTCAAGAGG
CAGCTGTTCGGCCTGCCATCCAGGTACAGGGACTCGGTGAGGGCCATCAGGCCCGGCCTCCCGCTCTTCCTCTACAACTA
CTCCACCCACCAGCTTCACGGCATCTTCGAGGCCACCAGCTTCGGCGGATCCAACATCGATCCCGGCGCTTGGGAGGACA
GCAAGTGCCCCGGCGGCGAGTCCAGGTTCCCAGCGCAGGTTCGGGTGGCCACGCGCAAGATCTGTGAGCCGCTGGAGGAG
GACGCCTTCAGGCCCGTGCTGCACCACTACGACGGCCCCAAGTTCCGCCTCGAGCTCACCGTCGCCGAGGCCCTATCCCT
TCTTGACATCTTCGCCGAGAAGCTCTTCGCCTGA

Alignment

ORF - retro_osat_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.89 %
• Parental protein coverage: 52.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GDGAGGKKKHAKNSDSGAQASDKRFKT--LPASEALPRDEAIGGYIFVCNNDTMEENLKRQLFGLPSRYR
          G.G.GG.....KNS.S.......R.K...LPASE..P..EAIGGYIFVCNN.TMEENLKRQLFGLPSRYR
Retrocopy GGGGGGRNNNKKNSSSNDNKMSSRLKKSQLPASESVPKEEAIGGYIFVCNNETMEENLKRQLFGLPSRYR

Parental  DSVRAIRPGLPLFLYNYSTHQLHGIFEAASFGGTNIDPTAWEDKKCP-GESRFPAQVKVATRKIYDPLEE
          DSVRAIRPGLPLFLYNYSTHQLHGIFEA.SFGG.NIDP.AWED.KCP.GESRFPAQV.VATRKI..PLEE
Retrocopy DSVRAIRPGLPLFLYNYSTHQLHGIFEATSFGGSNIDPGAWEDSKCPGGESRFPAQVRVATRKICEPLEE

Parental  DAFRPILHHYDGPKFRLELSVAEALSLLDIFADK
          DAFRP.LHHYDGPKFRLEL.VAEALSLLDIFA.K
Retrocopy DAFRPVLHHYDGPKFRLELTVAEALSLLDIFAEK

Legend:

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

Expression

RNA-Seq

Oryza sativa japonica was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza sativa japonica was not studied using ChIP-Seq data.

EST

Oryza sativa japonica was not studied using EST data.

TSS

Oryza sativa japonica was not studied using FANTOM5 data.

Lab

retro_osat_23 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza sativa japonica 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Leersia perrieri	LPERR01G16570	1 retrocopy	retro_lper_24,
Oryza sativa japonica	OS01G0550300	1 retrocopy	retro_osat_23 ,