RetrogeneDB ID: retro_opun_24

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 7:14013860..14015099(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC07G10440
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC01G40860
• Aliases: None
• Description: None

Sequence

>retro_opun_24
ATGGGCTCCTCGCCGCTGCGGACGCAGATGAAGCGGTCCACTCCGCACATGTTGGTGGCGGCGCTCGTCTTTCTCGTCCT
CATGTTCGTCGCCGGCGCGGCCGTCACGGTACACCACAAGGACCGGCGCCCGATCAGCCCGTCGACTTCACCGGCGGCAG
CCGACAAGATCACCCTGTCGCGGAAGATGCTGCGCGACAAGCGAGCTGAAGCGCCAGTCGCGTCCAGCGACGGCGGCGGC
CGTAGCGAGCCTCTCCCCAGGGGCATCGTGCAGGGCGAGTCCAACCTGGAGATGGAGTCCATGGTCGGCGACCCGGAGCA
CGGCCGGCAGAAGGCGTCGAAGAGCCTCCTGGCGATCCCCGTCGGGATCAAGAACAAGGCGGCCGTCAACAAGCTCGTGT
CCAAGTTCCCCGCCGAGGAGTTCGCGTTGATGCTGTTCCACTACGACGGCGCGGTCGAGCAGTGGGGCGACCTTGAGTGG
CACGGACGCGCGGTGCACGTGGCGGCGGCGGGGCAGACCAAGTGGTGGTTCGCCAAGCGCTTCCTCCACCCGGACGTGGT
GGCCGAGTACGACTACGTCTTCCTCTGGGACGAGGACGTCGAGGTCGACGCCTTCGACCCCACCCGCTACCTCGCCATCG
TCAGGAGGGAGGGGCTCGAGGTCTCGCAGCCGGCGCTGGCGCGCGGCTCGGAGATCCACCACGGCATCACCGCCCGACAA
AACGTGGCCGGAGGAGGAGGCCACGTGCACCGGCGGTTCTACAGGCGAGCCAGGCCGCGGTGCGACGAGGGCAGCACGGC
GCCGCCGTGCACGGGGTGGGTCGAGATGATGGTGCCGGTGTTCTCCCGCGCGGCGTGGCGGTGCACCTGGGGCATGGTGC
AGAACGACCTCGTCCACGGGTGGGGGCTCGACTACAAGCTCGGGTACTGCGCGCAGGGCGACCGGACGATGAAGGTCGGC
GTCGTCGACAACGAGTACGTCATGCACAGGGGCATCCCCTCGCTCGGCGGCAGCGTCGGCGGCGGGAGGTCGGCGTCGGC
CAGCCGGATCGCGGTGAGGCGGCGATCCTTCGCCGAGATGCAGATATTCAACCGGAGGTGGAAGGAGGCCGTGGCGGCGG
ACGCGTCGTGGGCCGACCCGTACCCGGAAACCGCAGCTGCTAGCTTGATCAACGCCGGCCGGCTGGCGCGCCGTCTCTGC
ATGCATGGCACGAGCCACGAGGCCTTGCTTGGATCTTAG

Alignment

ORF - retro_opun_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.34 %
• Parental protein coverage: 59.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RPAKSLLAIPVGIKQKAVVDKLVSKFPGDRFTVMLFHYDGEVDGWRELRWSHRAIHVAAMDQTKWWFGKR
          ...KSLLAIPVGIK.KA.V.KLVSKFP...F..MLFHYDG.V..W..L.W..RA.HVAA..QTKWWF.KR
Retrocopy KASKSLLAIPVGIKNKAAVNKLVSKFPAEEFALMLFHYDGAVEQWGDLEWHGRAVHVAAAGQTKWWFAKR

Parental  FLHPDMVAEYEYIFLWDEDIEVDGFDPIRYLRVVRRERLEISQPALDHRSQIHHRLTLR---ARKGQVHR
          FLHPD.VAEY.Y.FLWDED.EVD.FDP.RYL..VRRE.LE.SQPAL...S.IHH..T.R...A..G....
Retrocopy FLHPDVVAEYDYVFLWDEDVEVDAFDPTRYLAIVRREGLEVSQPALARGSEIHHGITARQNVAGGGGHVH

Parental  RFYKTRGGGRCDGNSTGPPCTGWVEMMVPVFSRAAWRCSWHMIQNDLIYAWGLDFKLGYCAGGDRSLAVG
          R....R...RCD..ST.PPCTGWVEMMVPVFSRAAWRC.W.M.QNDL...WGLD.KLGYCA.GDR...VG
Retrocopy RRFYRRARPRCDEGSTAPPCTGWVEMMVPVFSRAAWRCTWGMVQNDLVHGWGLDYKLGYCAQGDRTMKVG

Parental  IVDSEYVLHRGIPTLGDGGKPARPSSSSKAATDR
          .VD.EYV.HRGIP.LG......R..S.S..A..R
Retrocopy VVDNEYVMHRGIPSLGGSVGGGRSASASRIAVRR

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_24 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza brachyantha	OB01G50760	1 retrocopy	retro_obra_21,
Oryza punctata	OPUNC01G40860	1 retrocopy	retro_opun_24 ,