RetrogeneDB ID: retro_opun_8

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 7:21534705..21535578(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC07G14970
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC07G14400
• Aliases: None
• Description: None

Sequence

>retro_opun_8
ATGGCCTCGTCGCAGCAGGCGGTGCGCGAGACGGGGAGGGGCAGGGCGGCGCCGTCGTCGGCCGGCGGGAGGAAGGTGAC
CTTCGGTTACCACCTTGTGGAGGGCAAGATGCCCCACGGCATGGAGGACCGCCACGTCGCCGAGTTCCGCCGCCTGGACG
ACGGCAACGAGGTCGGCCTCTTCGCCGTGTTCGACGGCCACTCCGGCGCCGACGTCGCCACCTACCTCCGGGAGCACCTC
TTCGACAACATCCTCCGCGAGCCCGGGTTCTGGACCGACACCATGGCCGCCATCCGCCGCGCCTACCACCGCACCGACCG
GAAGGTGCTGAGGACGACGACGGAGACGGAGGAGGATGACGGCGAGGAGCGGCGGCGCCGCGGCGGGTCGACGGCGGTGA
CGGCGATCCTGATCAACGGCGAGACGCTGGTGGTGGCGAACGTGGGGGACTCCCGCGCCGTGGCGTGCGACCGCGCGGGG
CGGGCGCGGCAGCTGTCCGTGGACCACGAGCCGCTCCGGGAGCGCGACGCCGTCGAGAGCCGCGGCGGGTTCGTGACGGA
GATCCACGGCGACGTGCCACGCGTGGACGCGCAGCTGGCAATGTCGCGCGCGTTCGGCGACCAGCAGATCAAGGAGCACA
TCAGCTCCGACCCGGACGTGACCATCGAGGACGTCGGCGGCGACGGCGACGGTGGCACGGAGTTCGTCGTCCTCGCCAGC
GACGGGGTCTGGACGGTGATGTCGAACCAGGAGGCGGTGGACGCGGTGAGGGGCACGGCGGACGCCCGGAAGGCAGCGGC
GGAGGTCGTCGGCGAGGCCCTCGACCGGGGCAGCAAGGACGACATCGCCTGCGTCGTCGTGCGCCTCCACTGA

Alignment

ORF - retro_opun_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.58 %
• Parental protein coverage: 55.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGGSTAVTAILISSENSVNLVVANVGDSRAVI-SKNGVAKQLSVDHEPNKERPSIEKKGGFVSNLPGDVP
          RGGSTAVTAILI..E....LVVANVGDSRAV.....G.A.QLSVDHEP..ER...E..GGFV....GDVP
Retrocopy RGGSTAVTAILINGET---LVVANVGDSRAVACDRAGRARQLSVDHEPLRERDAVESRGGFVTEIHGDVP

Parental  RVDGQLAVARAFGDRSLKKHLSSEPDVVEEPI----NENTDFLILASDGLWKVMSNQEAVNEIKDFKDAQ
          RVD.QLA..RAFGD...K.H.SS.PDV..E.........T.F..LASDG.W.VMSNQEAV.......DA.
Retrocopy RVDAQLAMSRAFGDQQIKEHISSDPDVTIEDVGGDGDGGTEFVVLASDGVWTVMSNQEAVDAVRGTADAR

Parental  AAAKHLTEQAVNRKSKDDISCIVVK
          .AA......A..R.SKDDI.C.VV.
Retrocopy KAAAEVVGEALDRGSKDDIACVVVR

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza punctata was not studied using ChIP-Seq data.

EST

Oryza punctata was not studied using EST data.

TSS

Oryza punctata was not studied using FANTOM5 data.

Lab

retro_opun_8 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza punctata 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza punctata	OPUNC07G14400	1 retrocopy	retro_opun_8 ,