RetrogeneDB ID: retro_oniv_9

Retrocopy location

• Organism: Indian wild rice (Oryza nivara)
• Coordinates: 3:16331..17492(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ONIVA03G00040
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ONIVA02G02120
• Aliases: None
• Description: None

Sequence

>retro_oniv_9
ATGGCCTTCTTCGTCAAGATATCGGCGCCGTGCTCGCTTGCCGGCCATGGCACCACCAGCAGTAGCAGTGGCAGCAGCAG
GTCAAAGAGGGGATTGTTGCTTCCAGTTGGGGCTGGGGCTGGGGCTGGGGCTGGGGCTGGGGCCTACGGCGGCAGGCAGT
ACTCGGACGTGGTCCCGGTGCCAGCGCTATCGCAGGCGCAGGCGAGCTCTAGCGGTGGTCGGCTGCGCATCTTCTCCGGC
ACGGCGAACCCGAGGCTGGCGCAGGAGGTGGCGTGCTACCTGGGGATGGAGCTGGGGAGGGTGAAGATCAAGCGGTTCGC
GGACGGGGAGCTGTACGTGCAGCTGCAGGAGAGCGTGCGTGGGTGCGACGTGTTCCTGGTGCAGCCCACCTGCCCGCCGG
CAAACGAGAACCTGATGGAGCTCCTCATCATGATCGACGCATGCCGCCGCGCCTCCGCCAAGACCATCACCGCCGTCGTG
CCCTACTTCGGGTACGCCCGCGCCGACCGCAAGATGCGCGGCGGCCGGGAGTCGATCGCCGCCAAGCTGGTGGCAAACCT
CATCACGGAGGCCGGCGCCCACCGCGTGCTGGCCTGCGACCTCCACTCGGGGCAGTCCATCGGCTACTTCGACATCCCCG
TGGACCATGTGTACGGGCAGCCGGTGATCCTGGACTACCTGGCCAGCAAGACCATCTGCCCCGACGAGGTGGTGGTGGTG
TCCCCGGACGTGGGTGGCGTCGCCCGGGCCCGCGCCTTCGCCAAGAAGCTGTCGGACGCGCCGCTGGCCATCGTGGACAA
GCGGCGGCAGGGGCACAACCAGTCGGAGGTGGTGCACCTCATCGGCGACGTCAGGGGGAAGGTGGCGGTGATGGTGGACG
ACATGATCGACACTGCGGGGACGGTGTCCCAGGGAGCGGAGCTGCTGCACAGGGAGGGCGCCAGGGCCGTCTACGCCTGC
AGCACCCACGCCGTGCTCAGCCCGCCCGCCGTCGACAGGCTCTCCAGCGGCCTCTTCCAGGAGGTGATCGTCACCAACAC
CGTCCCCGTGCTTCACCACCGGACCTTCCCCCAGCTCACCGTCCTCTCCGTCGCCAATCTCCTCGGCGAGACCATCTGGC
GCGTTCACGACGACTGCTCTGTCAGTAGCATCTTCCAGTGA

Alignment

ORF - retro_oniv_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.42 %
• Parental protein coverage: 78.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RLRIFSGTANPSLSQEIASYLGLELGKINIKRFADGEIYVQLQESVRGCDVFLVQPTCPPANENLMELLI
          RLRIFSGTANP.L.QE.A.YLG.ELG...IKRFADGE.YVQLQESVRGCDVFLVQPTCPPANENLMELLI
Retrocopy RLRIFSGTANPRLAQEVACYLGMELGRVKIKRFADGELYVQLQESVRGCDVFLVQPTCPPANENLMELLI

Parental  MIDACRRASAKNITAVIPYFGYARADRKSQ-GRESIAAKLVANMITEAGANRVLVCDLHSSQAMGYFDIP
          MIDACRRASAK.ITAV.PYFGYARADRK...GRESIAAKLVAN.ITEAGA.RVL.CDLHS.Q..GYFDIP
Retrocopy MIDACRRASAKTITAVVPYFGYARADRKMRGGRESIAAKLVANLITEAGAHRVLACDLHSGQSIGYFDIP

Parental  VDHVYGQPVILDYLASKTICSDDLVVVSPDVGGVARARAFAKKLSDAPLAIVDKRRHGHN---VMNLIGD
          VDHVYGQPVILDYLASKTIC.D..VVVSPDVGGVARARAFAKKLSDAPLAIVDKRR.GHN...V..LIGD
Retrocopy VDHVYGQPVILDYLASKTICPDEVVVVSPDVGGVARARAFAKKLSDAPLAIVDKRRQGHNQSEVVHLIGD

Parental  VRGKVAVMMDDMIDTAGTIAKGAELLHQEGAREVYACCTHAVFSPPAIERLSSGLFQEVIITNTIPLKED
          VRGKVAVM.DDMIDTAGT...GAELLH.EGAR.VYAC.THAV.SPPA..RLSSGLFQEVI.TNT.P....
Retrocopy VRGKVAVMVDDMIDTAGTVSQGAELLHREGARAVYACSTHAVLSPPAVDRLSSGLFQEVIVTNTVPVLHH

Parental  KSFPQLTILSVANLLGETIWRVHDDCSV
          ..FPQLT.LSVANLLGETIWRVHDDCSV
Retrocopy RTFPQLTVLSVANLLGETIWRVHDDCSV

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_9 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Leersia perrieri	LPERR02G02000	1 retrocopy	retro_lper_21,
Oryza brachyantha	OB02G12100	1 retrocopy	retro_obra_24,
Oryza barthii	OBART02G02200	1 retrocopy	retro_obar_2,
Oryza glumaepatula	OGLUM02G02060	1 retrocopy	retro_oglu_34,
Oryza nivara	ONIVA02G02120	1 retrocopy	retro_oniv_9 ,
Oryza punctata	OPUNC02G01640	1 retrocopy	retro_opun_20,
Oryza rufipogon	ORUFI02G02210	1 retrocopy	retro_oruf_33,
Oryza sativa japonica	OS02G0127700	1 retrocopy	retro_osat_35,