RetrogeneDB ID: retro_opun_26

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 3:38564999..38566091(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC03G38590
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC05G14950
• Aliases: None
• Description: None

Sequence

>retro_opun_26
ATGGTGCAGCAGCAGCAGGTGGTGTTCGACGCCGCCGTGCTGAGCGGGCAGACGGACATCCCATCCCAGTTCATCTGGCC
GCCGGACGAGAGCCCCGGCCCCGTGGCCGCCGAGGAGCTAGACGTGCCGCTCATCGACGTGGGCGCGGGGGCGGACCGCG
GCGAGGTGGTCCGGCTGGTGGGCGAGGCGTGCCAGAGGCACGGCTTCTTCCTGGTGGTGAACCACGGCATCGAGGCGGCG
CTGCTGGAGGAGGCGCACCGGTGCATGGACGCCTTCTTCACGCTGCCGCTGGGCGAGAAGCAGCGGGCGCAGCGGCGCGC
CGGCGAGAGCTGCGGGTACGCGAGCAGCTTCACGGGGCGGTTCGCGTCGAAGCTGCCGTGGAAGGAGACGCTGTCGTTCC
GGTACTCGGCGGCGGGCAGCGGCGAGGGCGTGGCGGAGTACCTGGTGAGGAAGGTGGGTCCCGAGCACGGGCGGCGGCTG
GGCGACGTGTACTCGCGGTACTGTGAGGAGATGAGCCGGCTGTCGCTGGAGCTGATGGAGGTGCTGGGGGAGAGCCTGGG
CGTTGCGGGCGGCGACGGCGAGCAGCACTGCTACTTCCGGCGATTCTTCGAGCGGAACGACTCCATCATGCGGCTCAACT
ACTACCCGGCGTGCCAGAGGCCACTGGAGACGCTGGGGACGGGGCCGCACTGCGACCCGACGTCGCTGACCATCCTCCAC
CAGGACGACGTGGGCGGGCTGGAGGTGTGGGCGGAGGGGCGGTGGCGCGCCGTCCGGCCGCGCGCGGGGGCGCTGGTTGT
CAACGTCGGCGACACCTTCATGGCGCTCTCCAACGGCAGGTACCGGAGCTGCCTGCACCGGGCGGTGGTGAACAGCAGGG
CGGCGCGGCGGTCGCTGGCCTTCTTCCTCTGCCCGGAGATGGACACGGTGGTGCGGCCGCCGGAGGAGCTGGTCGACGAC
GACAACCCGAGGGTTTACCCGGACTTCACGTGGCGGGCGCTGCTGGACTTCACGCAGCGCCACTACAGGGCCGACATGCG
CACGCTTCAGGCCTTCTCCGACTTCCAAACCATCCATGCATCCATCGTTTAA

Alignment

ORF - retro_opun_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.62 %
• Parental protein coverage: 73.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QPKIPAPFVWPRADVALPSSPTRELDVPVVDLAAALRDAAGMRRAVAQVAAACASHGFFQVSGHGVPPSL
          Q..IP..F.WP......P.....ELDVP..D..A.....A.....V..V..AC..HGFF.V..HG....L
Retrocopy QTDIPSQFIWPPDESPGPVA-AEELDVPLIDVGAG----ADRGEVVRLVGEACQRHGFFLVVNHGIEAAL

Parental  ARAALDGAAGFFRLPLAAKQRARRAPGTVTGYTAAHADRFVSNLPWKETLSFGHRHANAAGNNNSSVADY
          ...A......FF.LPL..KQRA.R..G...GY......RF.S.LPWKETLSF.......A......VA.Y
Retrocopy LEEAHRCMDAFFTLPLGEKQRAQRRAGESCGYASSFTGRFASKLPWKETLSFRY----SAAGSGEGVAEY

Parental  FSSTLGDSF-KHLGEVYQEYCEAMEEVTKTIMAVLGESLGVGGGGG----YYREFFEDSSSIMRCNYYPP
          .....G......LG.VY..YCE.M.......M.VLGESLGV.GG.G....Y.R.FFE...SIMR.NYYP.
Retrocopy LVRKVGPEHGRRLGDVYSRYCEEMSRLSLELMEVLGESLGVAGGDGEQHCYFRRFFERNDSIMRLNYYPA

Parental  CPEPERTLGTGPHCDPSALTVLLQDGDVDGLQVLVGGAWRPVRPEPGAFVVNIGDTFMALTNGRYKSCLH
          C..P..TLGTGPHCDP..LT.L.QD.DV.GL.V...G.WR.VRP..GA.VVN.GDTFMAL.NGRY.SCLH
Retrocopy CQRPLETLGTGPHCDPTSLTILHQD-DVGGLEVWAEGRWRAVRPRAGALVVNVGDTFMALSNGRYRSCLH

Parental  RAVVHREQERRSLAFFLCPREDRVVRPP
          RAVV.....RRSLAFFLCP..D.VVRPP
Retrocopy RAVVNSRAARRSLAFFLCPEMDTVVRPP

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_26 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	OPUNC05G14950	1 retrocopy	retro_opun_26 ,