RetrogeneDB ID: retro_oniv_30

Retrocopy location

• Organism: Indian wild rice (Oryza nivara)
• Coordinates: 1:11934021..11934903(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ONIVA01G14890
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ONIVA05G02220
• Aliases: None
• Description: None

Sequence

>retro_oniv_30
ATGGACGCGCCGTGTGGATGGACGACGTCGGCGGCGGCGGCGGTGGCGGAGGAGGAGGATGTTCGGAGAGGGCCGTGGAC
GGTGGAGGAGGACGCGGTGCTGGCCGGGTACGTGGCGGCGAACGGCGAGGGGCGGTGGAACGAGCTGGCGCGGGCGGCGG
GGCTGAGGCGCACGGGGAAGAGCTGCCGCCTCCGGTGGCTCAACTACCTCCGCCCCGACGTGCGCCGCGGTGACTTCACC
CCGCAGGAGCAGCTGCTCATCCTCGAGCTCCACTTCCGGTGGGGGAACCGCTGGTCCAGGATCGCGCAGCACATGCCGGG
GAGGACGGACAACGAGATCAAGAACTACTGGCGGACCAGGGTGCAGAAGCACGCCAAGCAGCTCGGCTGCGACGTCAATA
GCCGCCAGTTCAAGGACGTCATGAGGCACCTCTGGATGCCGCGCCTCGTCGAGAGGATCCACGCCGCCGCCGCCTCGTCG
GAACGCGCCGCGCCGCCGCCGTGTGCCGCCGCGCCGGCTAGTCACAGCGGCATGTGCCACTCACCTGACCCGTCAACCAC
GACGTCGAGCACGGCAGGGTCGTCGGTGACGCACGGCGAGCAGTTCCCGTCGTCGACGAACCACCACCTGATGACCATGG
CCAGCGTCACCACCGCAGCGGCAGATTGGTCCAGCGAGCAATGCGGCAGCGGCAGCGCCACCAGCACGAGCGTTGGGATC
AGTTATGACATGTTCGAGGGGAGCTGGTCGGAGCTCCTCGCCCGCGCCTACGACGACGACGGCGCCGATTCTTCGCTGCT
GCCGGACTTCCAAATGGCAGACACCGGAGACAACTGCTGGTGGAGTAATTTGGAGGACATCTGGTCACAGCAGCCGTACT
GA

Alignment

ORF - retro_oniv_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.83 %
• Parental protein coverage: 52.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TAAAAASEDEGDLRRGPWTVEEDMLLVDYIANHGEGRWNSLARCAGLRRTGKSCRLRWLNYLRPDVRRGN
          T.AAAA...E.D.RRGPWTVEED..L..Y.A..GEGRWN.LAR.AGLRRTGKSCRLRWLNYLRPDVRRG.
Retrocopy TSAAAAVAEEEDVRRGPWTVEEDAVLAGYVAANGEGRWNELARAAGLRRTGKSCRLRWLNYLRPDVRRGD

Parental  ITADEQLLILDLHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQKHAKQLRCDVNSKEFRDVVRHVWMPR
          .T..EQLLIL.LH.RWGNRWS.IAQ..PGRTDNEIKNYWRTRVQKHAKQL.CDVNS..F.DV.RH.WMPR
Retrocopy FTPQEQLLILELHFRWGNRWSRIAQHMPGRTDNEIKNYWRTRVQKHAKQLGCDVNSRQFKDVMRHLWMPR

Parental  LVERIQADAAAAGEVAAPAPVSAA
          LVERI.A.AAA..E.AAP.P..AA
Retrocopy LVERIHA-AAASSERAAPPPCAAA

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_30 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.

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza brachyantha	OB05G12230	1 retrocopy	retro_obra_10,
Oryza glumaepatula	OGLUM05G02350	1 retrocopy	retro_oglu_19,
Oryza nivara	ONIVA05G02220	1 retrocopy	retro_oniv_30 ,
Oryza punctata	OPUNC05G02190	1 retrocopy	retro_opun_37,
Oryza glaberrima	ORGLA05G0022200	1 retrocopy	retro_ogla_43,
Oryza rufipogon	ORUFI05G02420	1 retrocopy	retro_oruf_21,