RetrogeneDB ID: retro_oniv_22

Retrocopy location

• Organism: Indian wild rice (Oryza nivara)
• Coordinates: 1:379325..380318(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ONIVA01G00510
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ONIVA02G32440
• Aliases: None
• Description: None

Sequence

>retro_oniv_22
ATGAATAGGAGGAAGAGGTGCGCGGCGTGCTATAGGGAGTTCAACAAGAAGGAGCACCTGGTGGAGCACATGCGGACGTC
GCTGCATTCGGCGCACGACCCTCGCTGCGGCGTGTGCGGCAAGCACTGCCGCTCCCTCGACGCCCTCCGCGACCACCTCA
CCGGCGCCCTCCCCAAGCCGGAGTGCGCCGCCGCCTTCGCCTCCCGCGGCTGCCCCCTCTGCCTCCACGTAGTCCTCCCG
CCCACCGCCGCCGCCCACTCCTGCCCCGCGGCCGCGCCACCGCTCGGCGGCGTCCTCGCCCTGGGGTGCAAGATGGTGGG
CGCCGGCAGCGACGGGTCCCTGGACGTGTGCGCCCGCGTGTGCGTGGTGGACGAGCAGGAGCGCGTGGTGTTGGACACCT
TCGTCAAGCCGCACATCCCCGTCACGCACTACCGCTACGACACCACCGGCATCCGCCCCGAGCACCTGCGCGACGCCATG
ACGCCCAAGCAGGCGGCGCGCCGGGTGCAGGAGCTGCTGCTCAACGGCGAGGCGGCGTGGAAGGCGCGGAGCAGCCGCGG
CAGGGCTCGGATCCTGGTGGGGCACGGCCTGGACCACGACCTCGAGTCGCTGGGCATGGACTACCCGGAGTACCTGAAGC
GGGACACGGCGAGGTACCCGGCGCTGATGAAGACGAGCAACAGCCGCCTCAGCAACTCGCTCAAGTACCTCACCCTCGCC
TACCTCGGCTACCACATCCAGCTCGCCGGCCGCCACCACCACCCCTACGACGACTGCGTCGCCGCGCTGCGACTCTACCG
CCGGATGCGTGGCGCGCGGCCGCACACCTGCAGGGACGCAGGCGTGGGGCCGCACGCGCCGCCGCCGACGCCGGCGGAGG
CGTTCCCGGCGTGGAGGCAGCGGGAGCTGGAGCGCATGTCGCCGGAGGAGCTCCTCCAGCTCTCCACCTCGGACTACTAC
TGCTGGTGCCTCGACGCCAGTGCCACCGACTAA

Alignment

ORF - retro_oniv_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.07 %
• Parental protein coverage: 51.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GRAVAMACKMVGGGSDGSLDICARVCLIGEDENVIFQTYVKPTTTVTNYRYEMTGIRPEYLRDAMPLKLV
          G...A..CKMVG.GSDGSLD.CARVC...E.E.V...T.VKP...VT.YRY..TGIRPE.LRDAM..K..
Retrocopy GGVLALGCKMVGAGSDGSLDVCARVCVVDEQERVVLDTFVKPHIPVTHYRYDTTGIRPEHLRDAMTPKQA

Parental  QRRIQDILCNGEPLWKIRPRSSGRARILVGHGLEHELERLGLEYPAFMIRDTAKYPPLMKT--SKLSNSL
          .RR.Q..L.NGE..WK.R..S.GRARILVGHGL.H.LE.LG..YP....RDTA.YP.LMKT..S.LSNSL
Retrocopy ARRVQELLLNGEAAWKAR-SSRGRARILVGHGLDHDLESLGMDYPEYLKRDTARYPALMKTSNSRLSNSL

Parental  KYLTQAYLGYDIHTG--IQDPYEDCVAAMRLYIRMR
          KYLT.AYLGY.I........PY.DCVAA.RLY.RMR
Retrocopy KYLTLAYLGYHIQLAGRHHHPYDDCVAALRLYRRMR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryza nivara was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza nivara was not studied using ChIP-Seq data.

EST

Oryza nivara was not studied using EST data.

TSS

Oryza nivara was not studied using FANTOM5 data.

Lab

retro_oniv_22 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza nivara 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,