RetrogeneDB ID: retro_oniv_10

Retrocopy location

• Organism: Indian wild rice (Oryza nivara)
• Coordinates: 8:3712506..3714066(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ONIVA08G04580
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ONIVA01G47760
• Aliases: None
• Description: None

Sequence

>retro_oniv_10
ATGGCGGGCGGCGCGATGGTCCAGACGGTGGGTGGCAAGACGTACCCGGGGAAGATGACCGCGTTCGTGTTCTTCACCTG
CCTCGTCGCCTCCTCCGGCGGCCTCATCTTCGGCTACGACATCGGCATCTCCGGCGGCGTCACCTCCATGGACTCCTTCC
TCAGCGAGTTCTTCCCGTCGGTGTACGCGCAGGCGAAGGCGAGCAAGGACACCAACCAGTACTGCAAGTTCGACAGCCAG
CTGCTGACGCTCTTCACCTCGTCGCTGTACCTGGCGGCGCTGGCGACGTCGTTCGTGGCGGCGTGGGTCACCCGGGTGTT
CGGCCGGAAGTGGTCCATGTTCTGCGGCGGCGTCACCTTCCTCGCCGGCTCGGCGCTCAACGGCGCCGCCACCGACGTCA
TGATGCTCATCCTCGGCCGCATCCTCCTCGGCATCGGCGTCGGCTTCGCCAACCAGTCCGTGCCGCTCTACCTGTCGGAG
ATGGCGCCGGCGAACCTCCGCGGGATGCTCAACATCGGCTTCCAGCTCATGACCACCATCGGCATCCTCTCCGCCAACCT
CATCAACTACGCGACGTCGAGCATCGAGGGCGGGTGGGGGTGGCGCATCGGCCTCGGCCTCGCCGGCGTGCCCGCGCTCA
TCATCACGCTCGGCGCGCTCGTCCTCCCGGACACCCCAAACTCCCTCATCGCCCGCGGCTACGCCGGCGACGCCAAGCGC
GTCCTCGTCAAGATCCGCGGCACGGACGACGTCCACGACGAGTACGACGACATGGTAGCGGCAAGCGAAGAAGCCGCCTC
GATCGAGCACCCATGGCGGAACATCCTCCATCGCAAGTACCGCCCGCAGCTCACCATCGCCATCCTCATCCCGTGCTTCC
AACAGCTCACCGGCATCAACGTGATCATGTTCTACGCGCCGGTGCTCTTCCTCACCATCGGCTTCGCCGGCGACGCGTCG
CTCATGTCCGCCGTGATCACGGGCCTCGTCAACATGTTCGCCACCGTCGTCTCGATCATCTCCGTGGACCGCCTCGGCCG
CCGAGTGCTGTTCCTCCAGGGCGGCACGCAGATGTTCATCTCCCAGGTGGTGGTCGGGACGCTGATCGCGCTCCAGTTCG
GCGTCGCGGGCGTCGGCGAGATGTCGCGGTCGTACGCCATCTTGCTCGTGCTGTTCATCTGCATGTACGTGGCCGGGTTC
GCGTGGTCGTGGGGGCCCCTGGGGTGGCTGGTGCCGAGCGAGGTGTTCGCGCTGGAGATCAGGTCGGCGGGGCAGAGCAT
CGCGGTGTGCGTCAACATGATGCTGACGTTCGTCATCGGGCAGGCGTTCCTCACCATGCTGTGCCACCTCAAGTTCGGCC
TCTTCTACTTCTTCGCCGGGTGGATGCTGGTCATGACCACCTTCGTCGCGCTCTTCCTGCCGGAGACGAAGGGGGTGCCC
ATCGAGGAGATGAACCACGTCTGGAGCCGGCACTGGTTCTGGGGCAGCTACGTCACCGCCCACGACGTCGCCGCCGCCGG
CGCCGGAGGAGGAGGAAACCGCAGAAGCCACAACGTCTAG

Alignment

ORF - retro_oniv_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.21 %
• Parental protein coverage: 97.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAGGAVVSTGAGKDYPGKLTLFVFFTCVVAATGGLIFGYDIGISGGVTSMDPFLKKFFPEVYRKKQMADK
          MAGGA.V.T..GK.YPGK.T.FVFFTC.VA..GGLIFGYDIGISGGVTSMD.FL..FFP.VY........
Retrocopy MAGGAMVQTVGGKTYPGKMTAFVFFTCLVASSGGLIFGYDIGISGGVTSMDSFLSEFFPSVYAQAKASKD

Parental  NNQYCKYDNQLLQTFTSSLYLAALVSSFFAATVTRVLGRKWSMFAGGLTFLIGAALNGAAENVAMLIVGR
          .NQYCK.D.QLL..FTSSLYLAAL..SF.AA.VTRV.GRKWSMF.GG.TFL.G.ALNGAA..V.MLI.GR
Retrocopy TNQYCKFDSQLLTLFTSSLYLAALATSFVAAWVTRVFGRKWSMFCGGVTFLAGSALNGAATDVMMLILGR

Parental  ILLGVGVGFANQSVPVYLSEMAPARLRGMLNIGFQLMITIGILAAELINYGTAKIKAGWGWRVSLALAAV
          ILLG.GVGFANQSVP.YLSEMAPA.LRGMLNIGFQLM.TIGIL.A.LINY.T..I..GWGWR..L.LA.V
Retrocopy ILLGIGVGFANQSVPLYLSEMAPANLRGMLNIGFQLMTTIGILSANLINYATSSIEGGWGWRIGLGLAGV

Parental  PAAIITLGSLFLPDTPNSLIDRGHPEAAERMLRRIRGSDVDVSEEYADLVAASEESKLVQHPWRNIIRRK
          PA.IITLG.L.LPDTPNSLI.RG....A.R.L..IRG.D.DV..EY.D.VAASEE.....HPWRNI..RK
Retrocopy PALIITLGALVLPDTPNSLIARGYAGDAKRVLVKIRGTD-DVHDEYDDMVAASEEAASIEHPWRNILHRK

Parental  YRAQLTMAICIPFFQQLTGINVIMFYAPVLFDTLGFKSDASLMSAVITGLVNVFATLVSIFTVDRLGRRK
          YR.QLT.AI.IP.FQQLTGINVIMFYAPVLF.T.GF..DASLMSAVITGLVN.FAT.VSI..VDRLGRR.
Retrocopy YRPQLTIAILIPCFQQLTGINVIMFYAPVLFLTIGFAGDASLMSAVITGLVNMFATVVSIISVDRLGRRV

Parental  LFLQGGAQMVVCQVVVGTLIAVKFGTSGIGDIPKGYAAVVVLFICMYVAGFAWSWGPLGWLVPSEIFPLE
          LFLQGG.QM...QVVVGTLIA..FG..G.G.....YA...VLFICMYVAGFAWSWGPLGWLVPSE.F.LE
Retrocopy LFLQGGTQMFISQVVVGTLIALQFGVAGVGEMSRSYAILLVLFICMYVAGFAWSWGPLGWLVPSEVFALE

Parental  IRPAGQSINVSVNMLFTFVIAQAFLTMLCHMKFGLFYFFAGWVVIMTVFIALFLPETKNVPIEEMVLVWK
          IR.AGQSI.V.VNM..TFVI.QAFLTMLCH.KFGLFYFFAGW...MT.F.ALFLPETK.VPIEEM..VW.
Retrocopy IRSAGQSIAVCVNMMLTFVIGQAFLTMLCHLKFGLFYFFAGWMLVMTTFVALFLPETKGVPIEEMNHVWS

Parental  SHWFWRRFIGDHDV
          .HWFW......HDV
Retrocopy RHWFWGSYVTAHDV

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_10 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza nivara	ONIVA01G47760	1 retrocopy	retro_oniv_10 ,