RetrogeneDB ID: retro_oniv_35

Retrocopy location

• Organism: Indian wild rice (Oryza nivara)
• Coordinates: 4:28491063..28491810(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ONIVA04G29850
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ONIVA01G43550
• Aliases: None
• Description: None

Sequence

>retro_oniv_35
ATGGCGATGCCGATGATGGTGGTGTCTGGCCTTGGCACCGCTCCTCGGTCATCGCCGATGGTTCAGCTGCAGAGGATGAA
GAAGCATCTGGTGGTGGTGGCGGCGTTCAAGAGCAGAACCAAGGCTTCCCCCAAGGTGGACAAGTCGAACAAGAACAAGT
CGATCGTGGAGGACGGCATCTTCGGCACCTCCGGCGGCATCGGGTTCACCAAGGAGAACGAACTGTTCGTGGGGAGGGTG
GCCATGCTGGGGTTCGCGGCGTCCCTCCTCGGCGAGGCGGTCACCGGCAAGGGCATCCTGGCGCAGCTCAACCTGGAGAC
GGGCATCCCCATCTACGAGGCCGAGCCGCTGCTCCTCTTCTTCATCCTCTTCACGCTGCTGGGCGCCATCGGCGCGCTGG
GCGACCGGGGGCGCTTTGTGGACGACGCCACCGGGCTGGAGCGCGCCGTGATCCCGCCGGGGAAGGGGTTCCGCGCGGCG
CTGGGGCTCAGCGAGGGTGGCCCGCTGTTCGGGTTCACCAAGGCGAACGAGCTCTTCGTGGGTCGCCTCGCGCAGCTGGG
GATCGCCTTCTCCCTCATCGGCGAGATCATCACCGGGAAGGGCGCGCTGGCGCAGCTCAACATCGAGACCGGCGTCCCCA
TCAACGAGATCGAGCCGCTCCTCCTCTTCAACATCCTCTTCTTCTTCTTCGCCGCCATCAACCCCGGAACCGGCAAGTTC
GTCACCGACGACAACGACGACCAATGA

Alignment

ORF - retro_oniv_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.83 %
• Parental protein coverage: 86.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SQPSSSLGRAVSVKTVALFGRSKTKAAPARKAEPKPKFKTEDGIFGTSGGIGFTKENELFVGRVAMLGFA
          S.P...L.R......V.....S.TKA.P......K.K...EDGIFGTSGGIGFTKENELFVGRVAMLGFA
Retrocopy SSPMVQLQRMKKHLVVVAAFKSRTKASPKVDKSNKNKSIVEDGIFGTSGGIGFTKENELFVGRVAMLGFA

Parental  ASILGEAITGKGILAQLNLETGIPIYEAEPLLLFFILFTLLGAIGALGDRGSFVDDQPVTGLDKAVIAPG
          AS.LGEA.TGKGILAQLNLETGIPIYEAEPLLLFFILFTLLGAIGALGDRG.FVDD...TGL..AVI.PG
Retrocopy ASLLGEAVTGKGILAQLNLETGIPIYEAEPLLLFFILFTLLGAIGALGDRGRFVDD--ATGLERAVIPPG

Parental  KGFRSALGLSEGGPLFGFTKANELFVGRLAQLGIAFSIIGEIITGKGALAQLNIETGVPINEIEPLVLFN
          KGFR.ALGLSEGGPLFGFTKANELFVGRLAQLGIAFS.IGEIITGKGALAQLNIETGVPINEIEPL.LFN
Retrocopy KGFRAALGLSEGGPLFGFTKANELFVGRLAQLGIAFSLIGEIITGKGALAQLNIETGVPINEIEPLLLFN

Parental  VVFFFIAAINPGTGKFVSDDDEE
          ..FFF.AAINPGTGKFV.DD...
Retrocopy ILFFFFAAINPGTGKFVTDDNDD

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_35 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA004881	1 retrocopy	retro_oind_4,
Oryza longistaminata	KN538837.1_FG036	1 retrocopy	retro_olon_20,
Oryza barthii	OBART01G38720	1 retrocopy	retro_obar_4,
Oryza nivara	ONIVA01G43550	1 retrocopy	retro_oniv_35 ,
Oryza glaberrima	ORGLA01G0325500	1 retrocopy	retro_ogla_5,
Oryza rufipogon	ORUFI01G42080	1 retrocopy	retro_oruf_10,
Oryza sativa japonica	OS01G0869800	1 retrocopy	retro_osat_18,
Triticum aestivum	TRAES3BF044200210CFD_g	1 retrocopy	retro_taes_14,