RetrogeneDB ID: retro_opun_28

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 6:33366665..33367622(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC06G24330
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC05G12230
• Aliases: None
• Description: None

Sequence

>retro_opun_28
ATGGACGCCAACATGTTGAACGCGATGATGGCCGCCGTCGGCGGCGACCGAGCGGCGGCGCCGGGCGGCGACAAGCCGCA
GCCGGACTCGTCGGAGCAGATCAACGTCTCCCCTCTCGCCCTCCTCAAGATGCTAAAGCACGGGCGAGCTGGCGTGCCAA
TGGAGGTGATGGGTCTGATGCTGGGTGAGTTCGTCGACGAGTACACGGTGACGGTGACCGACGTGTTCGCCATGCCGCAG
AGCGGCACGGGCGTGAGCGTGGAGGCGGTGGACCACGCGTTCCAGAGCGAGATGCTGGAGATGCTCCGGCAGACGGGGCG
GCCGGAGATGGTGGTGGGGTGGTACCACTCCCACCCGGGCTTCGGCTGCTGGCTCTCCGGCACCGACATGGCCACGCAGC
AGAGCTTCGAGCAGCTCAACCCGCGCGCCGTCGCCGTGGTGATCGACCCGGTGCAGAGCGTCAAGGGGAAGGTGGTCATG
GACGCCTTCCGCCTCGGCGACCACATGGCGATGGTGCTCGGCGGCGGCGGCGGCGGCGGGATGGAGGCGAGGCAGACCAC
GTCCAACGTCGGCGGCATCGCGAAGCCGTCGGTGGTGGCGCTCGTCCACGGCCTGGGGCGACACTACTACTCGCTCGCCA
TCAACTACCGGATGAAGGAGGGGGAGGAGCGGATGCTGGCGTGCCTCAGCCGGAGCGGATGGTCCGACGGGTTCGCGCTC
CGGCGGTTCGGCGCGCACGACGCCGGCAACGAGGAGGCGGTGCGCGGGATGCGGGACCTCGCCGTGAGCTACGAGGCGCA
GGTGAGGGAGGAGGACGAGACGCCGCCGGAGAGGCTCGCCGTCGTCAGGGCGGGCAAGGTGGACGCCAAGGGGAAGCTGG
AGGAGCAAGCCAAGGACGCCATGTCCGCCAACATCCTGCAGACGCTCGGCATGATGCTCGACACCGTCACCTTCTAG

Alignment

ORF - retro_opun_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.26 %
• Parental protein coverage: 52.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GASGMGQPPSDSPLLDSSEQVYISSLALLKMLKHGRAGVPMEVMGLMLGEFVDDYTVRVVDVFAMPQSGT
          G......P..D.P..DSSEQ...S.LALLKMLKHGRAGVPMEVMGLMLGEFVD.YTV.V.DVFAMPQSGT
Retrocopy GGDRAAAPGGDKPQPDSSEQINVSPLALLKMLKHGRAGVPMEVMGLMLGEFVDEYTVTVTDVFAMPQSGT

Parental  GVSVEAVDHVFQTNMLDMLKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALNPRAVAVVIDPIQS
          GVSVEAVDH.FQ..ML.ML.QTGRPEMVVGWYHSHPGFGCWLSG.D..TQQSFE.LNPRAVAVVIDP.QS
Retrocopy GVSVEAVDHAFQSEMLEMLRQTGRPEMVVGWYHSHPGFGCWLSGTDMATQQSFEQLNPRAVAVVIDPVQS

Parental  VKGKVVIDAFRLINPQTMMLG
          VKGKVV.DAFRL.....M.LG
Retrocopy VKGKVVMDAFRLGDHMAMVLG

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_28 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Aegilops tauschii	F775_30029	1 retrocopy	retro_atau_45,
Hordeum vulgare	MLOC_37295	1 retrocopy	retro_hvul_98,
Oryza barthii	OBART05G14050	1 retrocopy	retro_obar_8,
Oryza glumaepatula	OGLUM05G14910	1 retrocopy	retro_oglu_36,
Oryza nivara	ONIVA05G14600	1 retrocopy	retro_oniv_12,
Oryza punctata	OPUNC05G12230	1 retrocopy	retro_opun_28 ,
Oryza glaberrima	ORGLA05G0247800	1 retrocopy	retro_ogla_24,
Oryza rufipogon	ORUFI05G15150	1 retrocopy	retro_oruf_24,
Oryza sativa japonica	OS05G0371200	1 retrocopy	retro_osat_40,