RetrogeneDB ID: retro_osat_80

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 5:12982210..12982664(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OS04G0473025
• Aliases: None
• Description: None

Sequence

>retro_osat_80
CAAAAAGATAGACCTTGGTTCTATTTCATCTCTTCAACAAGTTTAGTAATAAGCATAACGGCCCTATTGTTCCGATGGAG
AGAAGAACCTATAATTAGCTTTTCGGGAAATTTCCAAATGAACAATTTCAACAAAATCTTTCAATTTCTTATTTTATTAT
TCAACTTTATGTATTCCTCTATCCGTAGAGTACATTGAATGTACAGAAATGGCTATAACAGAGTTTCTGTTATTCGTATT
AACAGCTACTCTAGGGGGAATGTTTTTATGTGGTGCTAACGATTTAATAACTATCTTTGTAGCTCCAGAATGTTTCAGTT
TATGTTCCTACCTATTGTCTGGATATACCAAGAGAGATCTACGGTCTAATGAGGCTACTATGAAATATTTACTCATGGGT
GGGGCAAGCTCTTCTATTCTGGTTCATGGTTTCTCTTGGCTATATGGTTCATCT

Alignment

ORF - retro_osat_80 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.05 %
• Parental protein coverage: 92.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKKYPARYWVFLAFLSSKIAILLIPKARLPIISFSGNFQTNNFNEIFQ-FLILLCSTLCIPLSVEYIECT
          .K..P..Y......L...I..LL......PIISFSGNFQ.NNFN.IFQ.FL....STLCIPLSVEYIECT
Retrocopy QKDRPWFYFISSTSLVISITALLFRWREEPIISFSGNFQMNNFNKIFQ>FLFYY-STLCIPLSVEYIECT

Parental  EMAITEFLLFVLTATLGGMFLCGANDLITIFVAPECFSLCSYLLSGYTKRDLRSNEATMKYLLMGGASSS
          EMAITEFLLFVLTATLGGMFLCGANDLITIFVAPECFSLCSYLLSGYTKRDLRSNEATMKYLLMGGASSS
Retrocopy EMAITEFLLFVLTATLGGMFLCGANDLITIFVAPECFSLCSYLLSGYTKRDLRSNEATMKYLLMGGASSS

Parental  ILVHGFSWLYGSS
          ILVHGFSWLYGSS
Retrocopy ILVHGFSWLYGSS

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_80 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 1 parental gene, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa japonica	OS04G0473025	16 retrocopies	retro_osat_52, retro_osat_54, retro_osat_55, retro_osat_56, retro_osat_57, retro_osat_66, retro_osat_67, retro_osat_71, retro_osat_73, retro_osat_74, retro_osat_75, retro_osat_76, retro_osat_77, retro_osat_80 , retro_osat_87, retro_osat_90,