RetrogeneDB ID: retro_opun_40

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 1:46080035..46081019(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC01G44890
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC03G36000
• Aliases: None
• Description: None

Sequence

>retro_opun_40
ATGGAGGAGGAGCGGCGCGTGCTCGTGACCGGCGGCAATGGTTTCATCGGATCCTGGATCGTGCGGATCCTTCTCGCACG
CGGGTATGCCGTGACCGCAACCTACCAGCCGGGCACAGATGCCGTCCACCTCCTCGCCCTCGACGATGAAAGGCTCCTCC
TGCTCCCCGCCGATCTGCTTGATGCGGGCGCCATCTCCGCCGCGGCGGCAGCGGGCGGGGGCTGCCGGGCGGGCGTGCTG
CACGTGGCCTCACCGTGCACGCTGGATGACCCGCGAGATCCGCAGGCCGAGCTGGTGGAGCCGGCGGTGCGGGGCACGCT
GCACGTGCTGGAGGCGGCGCGGGGCGCGGGAGCGCGGCGCGTGGTGGTGACGTCGTCCATCTCAGCCATGGTGCCCAACC
CAGGGTTGGCGGCGGGAGAGCTCGTCGACGAGCGAAGCTGGACGGACATGGAATTCTGCAAGGCCCGGGGCAAGTGGTAC
CCGGTGTCCAAGACGCTCGCCGAGAGGGCGGCGTGGGAGTACGCGGCGCGGTGGCCCGGCTTCGAGTTGGCGACCATCCT
TCCGTCGACATGCCTCGGCCCGCTCCTGCAGCCCACCCTGAACGCCAGCTCTGCCGTGCTGCAGCGCCTCTTGCAGGGGT
CCACGGACGACCAAGCGGACTACTGGCTCGGCGCCGTCCACGTCCGTGACGTCGCCGCCGCCCACCTCCTGCTGCTCGAG
GCTCCCACCGTGTCCGGGAGGTACCTTTGCACCAACGGCATCTACCAGTTCAGCGACTTCGCACGGCTAGCTGCCAGGAT
CTGCCCGGCGTACGCCCACGCCATCCATCGCTTCGAGGAGGGGAGTACACAACCGTGGCTCGTGCCGCGCGACGGCCGTG
ACGCAGCACGCCGGCTCCTCGACCTGGGCCTCGTCCTCACTCCCCTCGAGGAGGCTATCAAGGACGCGGAGAAGAGTCTC
ACCGACAAATGCTTCCTTCCTTGA

Alignment

ORF - retro_opun_40 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.69 %
• Parental protein coverage: 84.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TDHLHALAAAGEGRLSVFPGDLLDGAALLAAAR---GC-SGVFHLASPCIVDRVLDPQAQLMVPAVEGTL
          TD..H.LA...E.RL...P.DLLD..A..AAA....GC..GV.H.ASPC..D...DPQA.L..PAV.GTL
Retrocopy TDAVHLLALDDE-RLLLLPADLLDAGAISAAAAAGGGCRAGVLHVASPCTLDDPRDPQAELVEPAVRGTL

Parental  NVLRAAKDAGGVRRVVVTSSISAIVPSPGWPAGEVRDERCWTDLDYCEKNGVWYPASKTLAEKAAWRFAE
          .VL.AA..AG..RRVVVTSSISA.VP.PG..AGE..DER.WTD...C...G.WYP.SKTLAE.AAW..A.
Retrocopy HVLEAARGAGA-RRVVVTSSISAMVPNPGLAAGELVDERSWTDMEFCKARGKWYPVSKTLAERAAWEYAA

Parental  E-NGLDVVVVNPGTVMGPVIPPTINASMAMLVRLLEGCTEEYADFYMGPVHVEDVALAHILLYENPSASG
          ...G.......P.T..GP...PT.NAS.A.L.RLL.G.T...AD...G.VHV.DVA.AH.LL.E.P..SG
Retrocopy RWPGFELATILPSTCLGPLLQPTLNASSAVLQRLLQGSTDDQADYWLGAVHVRDVAAAHLLLLEAPTVSG

Parental  RHLCVQSIAQWSDFASKVAELYPEY--KVPKFPK-DTQPGLVRAEA--ASKKLIALGLQFSPMEKIIRDS
          R.LC...I.Q.SDFA...A...P.Y......F....TQP.LV......A...L..LGL...P.E..I.D.
Retrocopy RYLCTNGIYQFSDFARLAARICPAYAHAIHRFEEGSTQPWLVPRDGRDAARRLLDLGLVLTPLEEAIKDA

Parental  VESLKSRGFI
          ..SL....F.
Retrocopy EKSLTDKCFL

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_40 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA013825	1 retrocopy	retro_oind_13,
Oryza punctata	OPUNC03G36000	1 retrocopy	retro_opun_40 ,
Oryza sativa japonica	OS03G0818200	1 retrocopy	retro_osat_21,