RetrogeneDB ID: retro_opun_30

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 1:364718..365726(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC01G00480
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC02G27250
• Aliases: None
• Description: None

Sequence

>retro_opun_30
ATGGATAAAAAAAATGTTAGGAGGAAGAGGTGCGCGGCGTGCTACAGGGAGTTCAACAAGAAGGAGCACCTGGTGGAGCA
CATGCGCACGTCGCTGCATTCGCCGCACGACCCTCGCTGCGCCGTCTGCGCCAAGCACTGCCGCTCCCTCGACGCCCTCC
GCGACCACCTCACCGGCGCCCTCCCCAAGCCGGAGTGCGCCGCCGCCTTCGCCTCCCGCGGCTGCCCGCTCTGCCTCCAC
GTCCTCCCCACCGCCGCCGCGCTCCGCACCCACTCCTGCCCCACGGCGCCTCCACCGCTGGGCGGCGTCCTCGCCCTGGG
ATGCAAGATGGTCGGCGCCGGCAGCGACGGGTCCCTGGACGTGTGCGGCCGCGTGTGCGTGGTGGACGAGCAGGAGCGCG
TGGTGTTCGAGAGCTTCGTGAAGCCGCACATCCCCGTCACGCACTACCGGTACGACACGACGGGCATCCGGCCGGAGCAC
CTGCGCGACGCCATGACGCCCAAGCAGGCCGCGCGGCGGGTGCAGGAGCTGCTGCTGAACGGCGAGGCGGCGTGGAAGGC
GCGGAGCAGCCGCGGCAGGGCGAGGATCCTGGTCGGGCACGGCCTGGACCACGACCTGGAGTCGCTGGGCATGGACTACC
CGGAATACCTGAAGCGGGACACGGCGAGGTACCCGGCGCTGATGAAGACGAGCAACTGCCGGCTCAGCAACTCGCTCAAG
TACCTCACCCTCGCCTACCTCGGCTACCACATCCAGCCCGCCGGCCGCCACCACCACCCCTACGACGACTGCGTCGCCGC
GCTGCGCCTCTACCGCCGGATGCGTGGCGCGCGCCCGCACACCAGCGACGCCGGCGTGGGGCCGCACGCCCCGCCACCAA
CGCCGGCAGAGGCGTTCCCGGCGTGGAGGCAGCGGGAGCTGGAGCGCATGTCGCCGGAGGAGCTCCTCCACCTGTCCACC
ACGGACTACTACTGCTGGTGCCTCGACGCCACGGACGGACTAAACTAG

Alignment

ORF - retro_opun_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.79 %
• Parental protein coverage: 59.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GRAVAMACKMVGGGSDGSLDICARVCLIGEDENVIFQTYVKPTTTVTNYRYEVTGIRPEYLRDAMPLKLV
          G...A..CKMVG.GSDGSLD.C.RVC...E.E.V.F...VKP...VT.YRY..TGIRPE.LRDAM..K..
Retrocopy GGVLALGCKMVGAGSDGSLDVCGRVCVVDEQERVVFESFVKPHIPVTHYRYDTTGIRPEHLRDAMTPKQA

Parental  QRRIQDILCNGEPLWKIRPRSSGRAKILVGHGLEHELERLGLEYPAFMIRDTAKYPPLMKTS--KLSNSL
          .RR.Q..L.NGE..WK.R..S.GRA.ILVGHGL.H.LE.LG..YP....RDTA.YP.LMKTS...LSNSL
Retrocopy ARRVQELLLNGEAAWKAR-SSRGRARILVGHGLDHDLESLGMDYPEYLKRDTARYPALMKTSNCRLSNSL

Parental  KYLTQAYLGYDIHTG--IQDPYEDCVAAIRLYIRMRSQAHPRDYASGSG
          KYLT.AYLGY.I........PY.DCVAA.RLY.RMR..A.P.....G.G
Retrocopy KYLTLAYLGYHIQPAGRHHHPYDDCVAALRLYRRMRG-ARPHTSDAGVG

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_30 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_16329	1 retrocopy	retro_hvul_65,
Oryza nivara	ONIVA02G32440	1 retrocopy	retro_oniv_22,
Oryza punctata	OPUNC02G27250	1 retrocopy	retro_opun_30 ,
Oryza sativa japonica	OS02G0709000	1 retrocopy	retro_osat_50,