RetrogeneDB ID: retro_oniv_2

Retrocopy location

• Organism: Indian wild rice (Oryza nivara)
• Coordinates: 9:6194367..6195939(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ONIVA09G04600
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ONIVA07G16940
• Aliases: None
• Description: None

Sequence

>retro_oniv_2
ATGCCGGGCGGCGGCGCGATGGTGGCGGCGAGCGGCGCCGGCCGGCCTGAGTACCCGGGCGGGCTCACCATGTTCGTGTC
CATGGCGTGCCTCGTGGCTGCCACCGGCGGCCTCATCTTCGGCTACGACATCGGCGTCTCCGGCGGCGTCACCTCCATGG
ACCCGTTCCTCAGCAGGTTCTTCCCGTCGGTGTACCGCGCGCAGTCGGCGGCGGCTGCGGCGGCCGGCGGGAACCAGTAC
TGCAGGTTCGACAGCCAGCTGCTGACCATGTTCACCTCGTCGCTCTACCTCGCCGCGCTCGCCTCGTCGCTCGGCGCCGC
CACGGTGACGCGCGTGGCGGGGCGCAAGTGGTCCATGTTCGCCGGCGGGCTAGTGTTCCTCGCCGGGTGCGCGCTCAACG
GCGCGGCGGCGAACGTGGCGATGCTCATCGTCGGCCGCGTCCTGCTCGGCGTCGGCATCGGGTTCGCCAACCAGAGCGTG
CCGGTGTACCTGTCGGAGATGGCGCCGGCGAGGATGCGCGGGATGCTCAACAACGGGTTCCAGATGATGATCACCACCGG
CGTGCTCGCCGCCAACCTCATCAACTACGGCACCGCGAGGATCGCCGGCGGGTGGGGGTGGCGCCTCAGCCTGGCGCTCG
CGGCGGTCCCGGCCGCCGTCATGACCGCCGGCGCGCTGTTCCTCCCGGAGACGCCCAACTCCCTCCTGGAGCGCGGGAGG
CGCGGCGAGGCCAGGCGGATGCTCCAGCGCGTGCGCGGCGAGGGCGTGGACGTGGAGGACGAGTACAACGACCTGGTCGC
CGCCGGCGAGGCGTCCCACGCCGTGGCGAGCCCGTGGCGCGACATCCTGCGCCGCCGCAACCGGCCGCCGCTGGTGATGG
CGGTGGCGATCCCGCTGTTCCAGCAGCTGACCGGCATCAACGTGATCATGTTCTACGCGCCGGTGCTGTTCAGGACGCTG
GGGTTCGGCGGCGGCGCGTCGCTGATGTCGGCGGTGATCACCGGCGGCGTGAACATGGCGGCGACGCTGGTGTCCGTGCT
CGCCGTGGACCGGGTGGGGCGGCGGGCGCTGTTCCTGGAGGGCGGCGCGCAGATGGTAGCGAGCCAGGCGGCGGTGGGGG
CGCTGATCGGGGCGAGGCTGGGGTGGTCGGGGACGGCGGCGATCCCGGCGGGGTACGCGGCGGCTGTGGTGGCGGCCATG
TGCGTGTACGTGGCGGCGTTCGCGTGGTCATGGGGGCCATTGGCGTGGCTGGTGCCGAGCGAGGTGATGCCGCTGGAGGT
GAGGCCGGCGGGGCAGAGCATCACGGTGGCGGTGAACATGGCCATGACGTTCGCCGTCGCGCAGGCCTTCCTGCCGCTGC
TCTGCCGCCTCAGGTTCGTGCTCTTCTTCTTCTTCGCCGGGTGGGTCGCCGCCATGACCGCCTTCGTCGCGCTCTTCGTG
CCGGAGACCAAGGGCGTCCCCATCGAGGACATGGCCGCCGTCTGGAGCGACCACTGGTACTGGAAGCGCTTCGTCGACGG
CGACGGCGACGGCGCACGACGCCGGGGAGACATTGAGATGGGACACAAGTAG

Alignment

ORF - retro_oniv_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.26 %
• Parental protein coverage: 93.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGVVVNNGGGK-DYPGKLTMFVLFACIVAATGGLIFGYDIGISGGVTSMNPFLIKFFPSVYRKEQAAEKN
          G..V...G.G...YPG.LTMFV..AC.VAATGGLIFGYDIG.SGGVTSM.PFL..FFPSVYR...AA...
Retrocopy GAMVAASGAGRPEYPGGLTMFVSMACLVAATGGLIFGYDIGVSGGVTSMDPFLSRFFPSVYRAQSAAAAA

Parental  QS-NQYCKFDSPLLTMFTSSLYLAALVASFFASTVTRVAGRKWSMFGGGVTFLVGAALNGAAKNVLMLIL
          ...NQYC.FDS.LLTMFTSSLYLAAL..S..A.TVTRVAGRKWSMF.GG..FL.G.ALNGAA.NV.MLI.
Retrocopy AGGNQYCRFDSQLLTMFTSSLYLAALASSLGAATVTRVAGRKWSMFAGGLVFLAGCALNGAAANVAMLIV

Parental  GRVLLGVGVGFANQSVPLYLSEMAPARLRGMLNIGFQLMITIGILCANLINYGTAKIKGGWGWRVSLALA
          GRVLLGVG.GFANQSVP.YLSEMAPAR.RGMLN.GFQ.MIT.G.L.ANLINYGTA.I.GGWGWR.SLALA
Retrocopy GRVLLGVGIGFANQSVPVYLSEMAPARMRGMLNNGFQMMITTGVLAANLINYGTARIAGGWGWRLSLALA

Parental  AVPAAIIAVGALFLPDTPNSLIDRGHTDAAKRMLRRVRGTD-DIEEEYNDLVAASEESKLVAHPWRNILQ
          AVPAA....GALFLP.TPNSL..RG....A.RML.RVRG...D.E.EYNDLVAA.E.S..VA.PWR.IL.
Retrocopy AVPAAVMTAGALFLPETPNSLLERGRRGEARRMLQRVRGEGVDVEDEYNDLVAAGEASHAVASPWRDILR

Parental  RRYRPQLTMAIAIPLFQQLTGINVIMFYAPVLFKTLGFADDASLMSAVITGLVNVFATFVSIVTVDRLGR
          RR.RP.L.MA.AIPLFQQLTGINVIMFYAPVLF.TLGF...ASLMSAVITG.VN..AT.VS...VDR.GR
Retrocopy RRNRPPLVMAVAIPLFQQLTGINVIMFYAPVLFRTLGFGGGASLMSAVITGGVNMAATLVSVLAVDRVGR

Parental  RKLFLQGGTQMLACQIVVGSLIGAKFGFSGVADIPKAYAAFVVLFICAYVAGFAWSWGPLGWLVPSEIFP
          R.LFL.GG.QM.A.Q..VG.LIGA..G.SG.A.IP..YAA.VV...C.YVA.FAWSWGPL.WLVPSE..P
Retrocopy RALFLEGGAQMVASQAAVGALIGARLGWSGTAAIPAGYAAAVVAAMCVYVAAFAWSWGPLAWLVPSEVMP

Parental  LEIRSAGQSINVSVNMLFTFIIAQAFLPMLCRFKFILFFFFGAWVVIMTLFVAFFLPETKNVPIEEMVLV
          LE.R.AGQSI.V.VNM..TF..AQAFLP.LCR..F.LFFFF..WV..MT.FVA.F.PETK.VPIE.M..V
Retrocopy LEVRPAGQSITVAVNMAMTFAVAQAFLPLLCRLRFVLFFFFAGWVAAMTAFVALFVPETKGVPIEDMAAV

Parental  WKSHWYWGRFI
          W..HWYW.RF.
Retrocopy WSDHWYWKRFV

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_2 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G24820	1 retrocopy	retro_bdis_38,
Hordeum vulgare	MLOC_55525	1 retrocopy	retro_hvul_80,
Medicago truncatula	MTR_0009s0370	1 retrocopy	retro_mtru_23,
Oryza glumaepatula	OGLUM07G18360	1 retrocopy	retro_oglu_7,
Oryza meridionalis	OMERI07G15470	2 retrocopies	retro_omer_15, retro_omer_8,
Oryza nivara	ONIVA07G16940	1 retrocopy	retro_oniv_2 ,
Oryza punctata	OPUNC07G17520	1 retrocopy	retro_opun_36,
Oryza glaberrima	ORGLA07G0149800	1 retrocopy	retro_ogla_30,
Oryza rufipogon	ORUFI07G19310	1 retrocopy	retro_oruf_45,
Oryza sativa japonica	OS07G0559700	1 retrocopy	retro_osat_29,
Triticum aestivum	Traes_2BS_7DF366FE1	1 retrocopy	retro_taes_36,