RetrogeneDB ID: retro_opun_39

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 1:31206739..31207771(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC01G27550
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC08G04420
• Aliases: None
• Description: None

Sequence

>retro_opun_39
ATGAGGAGACCCATGGCTCGGGATTTTACGGCGACGTTTTTTCTTCTGCTCAGCCTTGCATCGCTGCTGGTGATCTCGCC
GTGCGCGGCCCAGCAGATCAAGACCACCGACACGCGGTGGACCTACCACCTCCCGCTTCCCGACGGAATTAGCGGCGCCG
AGAGCCTCGCCTTCGACGGCAAGGACAGGCTCTACACCGGCGTCTCGGACGGCCGCGTGCTCAAGTGGGGTGGCAGCGCC
GCCGGTTGGACCACCTACGCGTACAACGCGAACTACAGGAGAATCCCTCTGTGCTCGTCGTCCGAGGTGCCACCGGAGGA
GAGGGAGAGCATCTGCGGGCGCCCGCTGGGGGTCCGGTTCTTTAGGAAGACCGGCGAGCTCTACATCGCCGACGCGTACA
AGGGGCTGATGAAGGTCGGGCCCGACGGCGGCGAGGCCCAGGTGGTCGCGACCGAGGCGGACGGCGTCCCCTTCCACTTC
CTCAATGGCCTTGACGTCGACCAAGCTACGGGCGATGTCTACTTCACCGACAGCAGCAGCACGTACACCCGCAGGTTCAA
CGGCGAGATCACGATGAACGCCGACGCGACAGGGCGGCTGCTCAAGTACGACGCGCGGACGCGGCGGGTCACCGTGCTGA
AGACCGATCTGCCGTACCCGAACGGCGTCGCCGTCAGCCGCGACAGGACGCACCTCGTCGTGGCGCACACCGTGCCGTGC
CAGGCGTTCCGGTACTGGCTGCGGGGCCCCAACGCCGGCGAGTACGAGCTCTTCGCCGACCTCCCCGGCTACCCCGACAA
TGTGAGGCGCGACACCAAGGGAGGCTACTGGGTGGCGCTCAACCAGGAGAGGATGCGGTTGGGCGCGGCGCCCGCGGCCA
AGCACCTGGTCGGCGTACGGCTCAACCCCGACGGCGTGGAGGTGGAGGAGTTGACGGCTGCCAAGGGCGTCACGCTCAGC
GAGGTGGCGGAGCAGAAGGGCAAGCTGTGGTTGGGCTCCGTCGAACTCGATTACATAGGCATGTTTACTTGA

Alignment

ORF - retro_opun_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.97 %
• Parental protein coverage: 97.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGFPASTLLLLLVSCLLVFLGAAQQLQVKTSHAQFAFHLPLPDGVTGAESLAFDTANHGPYTGVSDGRVL
          R.F.A...LLL....LLV....A.Q.Q.KT.......HLPLPDG..GAESLAFD......YTGVSDGRVL
Retrocopy RDFTATFFLLLSLASLLVISPCAAQ-QIKTTDTRWTYHLPLPDGISGAESLAFDGKDR-LYTGVSDGRVL

Parental  RWGGAAAGWTTFAHHQDYRKIPMCTTPVAPPEETESMCGRPLGLAFHNETGDLYIADAYKGLMRVGPGGG
          .WGG.AAGWTT.A....YR.IP.C.....PPEE.ES.CGRPLG..F...TG.LYIADAYKGLM.VGP.GG
Retrocopy KWGGSAAGWTTYAYNANYRRIPLCSSSEVPPEERESICGRPLGVRFFRKTGELYIADAYKGLMKVGPDGG

Parental  EAEVLAAGADGVPFNFVNGIDVDQATGDVYFTDSSTTYPRRFNSEIMMNADATARLLKYDAATKQVAVLR
          EA.V.A..ADGVPF.F.NG.DVDQATGDVYFTDSS.TY.RRFN.EI.MNADAT.RLLKYDA.T..V.VL.
Retrocopy EAQVVATEADGVPFHFLNGLDVDQATGDVYFTDSSSTYTRRFNGEITMNADATGRLLKYDARTRRVTVLK

Parental  AGLPYANGVAVSHGGEHVVVAHTVPCQAFRYWIKGAKAGEYELFADLPGYPDNVRRDAKGGYWVALNQEK
          ..LPY.NGVAVS....H.VVAHTVPCQAFRYW..G..AGEYELFADLPGYPDNVRRD.KGGYWVALNQE.
Retrocopy TDLPYPNGVAVSRDRTHLVVAHTVPCQAFRYWLRGPNAGEYELFADLPGYPDNVRRDTKGGYWVALNQER

Parental  VRLDAAAAVVPPAKHLVGVRLNGDGVEVEELTAAKGVTLSEVVEKGGKLWLGSVELDFIGL
          .RL.AA....P.AKHLVGVRLN.DGVEVEELTAAKGVTLSEV.E..GKLWLGSVELD.IG.
Retrocopy MRLGAA----PAAKHLVGVRLNPDGVEVEELTAAKGVTLSEVAEQKGKLWLGSVELDYIGM

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_39 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA028079	1 retrocopy	retro_oind_6,
Oryza glumaepatula	OGLUM08G04830	1 retrocopy	retro_oglu_15,
Oryza meridionalis	OMERI08G04560	1 retrocopy	retro_omer_14,
Oryza punctata	OPUNC08G04420	1 retrocopy	retro_opun_39 ,
Oryza glaberrima	ORGLA08G0040000	1 retrocopy	retro_ogla_41,
Oryza rufipogon	ORUFI08G05030	1 retrocopy	retro_oruf_9,
Oryza sativa japonica	OS08G0175000	1 retrocopy	retro_osat_11,