RetrogeneDB ID: retro_oniv_17

Retrocopy location

• Organism: Indian wild rice (Oryza nivara)
• Coordinates: 10:12877820..12880088(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ONIVA10G11910
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ONIVA02G31600
• Aliases: None
• Description: None

Sequence

>retro_oniv_17
ATGGGCGAGGGCGAGTTCGTCGACGTCGAGCGCGGCGTGGTCGCTGAAGGGGCGTTGGACGACGACGCGTCGCCGATCGA
GGAGGTCCGGCTGACGGTTCCGGTCACTGACGACCCGTCCCTTCCGGTGTGGACGTTCCGGATGTGGACACTCGGCCTGC
TCTCGTGCGTGCTCATGAGCTTCCTGAACCAGTTCTTCTCCTACCGCACCGAGCCGCTCATCGTCACCCAGATCACCGTG
CAGGTGGCCTCGCTGCCTCTGGGCCACATCCTCGCCCGCGTGCTGCCGCGCCGCAAGTTCAAGGCCCCCGCGCTGCTCGG
CGGCGGGGAGTGCAGCCTCAACCCGGGGCCCTTCAACATGAAGGAGCACGTGCTCGTCTCCATCTTCGCCAACGCCGGCT
GCGCCTTCGGCAGCGGGTCCGCCTACGCCGTCATGATCGTCGACATCATCCGCGCCTTCTACGGGCGGTCCATCTCCCTC
TTCCCCGCATGGCTCCTCATCACCACCACGCAGGTGCTCGGCTACGGGTGGGCGGGGCTGATGCGCAAGTACGTGGTGGA
GCCGGCGCAAATGTGGTGGCCCGGCACGCTCGTGCAGGTGTCGCTGTTCAGGGCGCTGCACGGGAAGGGGGAAGAGAAGG
AGGAGAATAAGGAGGGCAGCGGCGGCGGGATGTCTCAGGCCAAGTTCTTCCTGATCGCGCTCGCCTGCAGCTTCCTGTGG
TACGCCGTGCCGGGTTACCTGTTCCCGACGCTGACCTCCGTCTCGTGGGTCTGCTGGATCTTCTCCAAGTCCGTCACCGC
GCAGCAGCTGGGCTCCGGCATGAAGGGCCTGGGCCTCGGCGCCTTCACCCTCGACTGGACGGCCGTGTCAGCCTTCCTGT
ACAGCCCGCTGATCTCGCCGTTCTTTGCCACCGCCAACATCTTGGCCGGCTACGTGCTCCTGATGTACGTGGTCGTGCCG
GTGTCGTACTGGGGCCTCGACCTGTACAACGCCCGGAGGTTCCCCATCTTCTCGTCGCACCTGTTCACGGCCACCGGCAG
CACATACGACATCACGGCCATCGTGAACGACCGCTTCGAGATCGACATGGACGGGTACCATCGGATGGGGCGGATCAACA
TGAGCACGTTCTTCGCGCTGTCCTACGGGCTCGGCTTCGCGACGATCGCGGCCACCGTCACGCACGTGGCGCTGTTCCAC
GGGAAGGAGATCTACCGCCGGTTCCGCGCGTCGCAGAGGGACAAGCCCGACGTGCACACGAGGCTGATGAAGAGCTACCG
CGACGTGCCGAGCTGGTGGTTCTACGCGATGCTCGCGCTGTCCATGGCCGTCTCACTCTTGCTCTGCACCGTCCTCAGGT
CGGCGGTGCAGCTCCCGTGGTGGGGTCTCCTCTTCGCCTGCGCCATGGCCTTCGTGTTCACGCTGCCGATCAGCATCATC
ACGGCCACGACCAACCAGACGCCGGGGCTCAACATCATCACCGAGTACGTCATCGGGCTCATGCTTCCGGGCAAGCCCAT
CGCCAACGTCTGCTTCAAGGCGTACGGCTACATGAGCATGTCGCAGGCCGTGTCCTTCCTGTCCGACTTCAAGCTCGGCC
ACTACATGAAGATACCCCCCAAGTCCATGTTCCTCGTGCAGTTGGTCGGCACGGTGGTCGCCTCCACGGTCAACCTCGTG
GTGGCGTACTGGCTGCTGGGTTCCATCCCCAACATCTGCCAGGACGCGCTCCTCCCGGCGGATAGCCCGTGGACGTGCCC
GAACGACCGCGTCTTCTTCGACGCGTCCGTCATCTGGGGCCTCGTCGGGCCGCGCCGCATCTTCGGGCCACTCGGCAACT
ACGGCGCGCTCAATTGGTTCTTCCTCGCTGGCGCCGTGGGACCCGTCATTGTGTACTTGCTCCACAGGGCGTTCCCCAGC
AAGACCTGGATACCGATGATCAACCTGCCGGTGCTCATCGGAGCGACCTCCTACATGCCGCCGGCAACGGCCGTGAACTA
CAACTCCTGGCTGATCATCGGGATCATCTTCAACTTCTTCGTTTTCCGGTACAGGAAGCTGTGGTGGAAGAGGTACAACT
ACATCCTCTCGGCTGCGCTCGACGCCGGCGTCGCGTTCATGGCGGTGCTGCTCTACTTCTCGCTGTCGATGGAGAACCGG
AGCATCAGCTGGTGGGGTACGGCCGGCGAGCACTGCCCGCTGGCCTCATGCCCTACCGCCAAAGGGATAAACTTGGGCGC
TGATAGCGTCTGCCCTGTTGTGTTATAA

Alignment

ORF - retro_oniv_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.58 %
• Parental protein coverage: 99.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RAMRGALHEKDELPHGSRQ-ISRSKFFLVALICSFAWYAVPGYLFPTLTSISWVCWVFSKSVTAQQLGSG
          RA..G...EK.E...GS....S..KFFL.AL.CSF.WYAVPGYLFPTLTS.SWVCW.FSKSVTAQQLGSG
Retrocopy RALHGKGEEKEENKEGSGGGMSQAKFFLIALACSFLWYAVPGYLFPTLTSVSWVCWIFSKSVTAQQLGSG

Parental  LKGLGVGAFSLDWTAISSFLFSPLISPFFATANIFVGFVLFLYVLVPIAYWGFDLYNAKTFPIFSSHLFM
          .KGLG.GAF.LDWTA.S.FL.SPLISPFFATANI..G.VL..YV.VP..YWG.DLYNA..FPIFSSHLF.
Retrocopy MKGLGLGAFTLDWTAVSAFLYSPLISPFFATANILAGYVLLMYVVVPVSYWGLDLYNARRFPIFSSHLFT

Parental  SNGTSYDITAIVNDKFELDIDAYNKLGRINLSVFFALAYGLSFATIASTVTHVGLFYGKEIYHRFRASQK
          ..G..YDITAIVND.FE.D.D.Y...GRIN.S.FFAL.YGL.FATIA.TVTHV.LF.GKEIY.RFRASQ.
Retrocopy ATGSTYDITAIVNDRFEIDMDGYHRMGRINMSTFFALSYGLGFATIAATVTHVALFHGKEIYRRFRASQR

Parental  EKPDIHTRLMKKYDDIPVWWFYSLMALSMTVALILCTVLKHEVQLPWWGLLFACGMAFIFTLPISIISAT
          .KPD.HTRLMK.Y.D.P.WWFY...ALSM.V.L.LCTVL...VQLPWWGLLFAC.MAF.FTLPISII.AT
Retrocopy DKPDVHTRLMKSYRDVPSWWFYAMLALSMAVSLLLCTVLRSAVQLPWWGLLFACAMAFVFTLPISIITAT

Parental  TNQASYTPGLNVITEYAIGLIIPGHPIANVCFKVYGYMSMSQAIAFLSDFKLGHYMKIPPKSMFLVQFIG
          TNQ...TPGLN.ITEY.IGL..PG.PIANVCFK.YGYMSMSQA..FLSDFKLGHYMKIPPKSMFLVQ..G
Retrocopy TNQ---TPGLNIITEYVIGLMLPGKPIANVCFKAYGYMSMSQAVSFLSDFKLGHYMKIPPKSMFLVQLVG

Parental  TIVAGTVNLGVAWWLLGSIHDICQDS-LPADSPWTCPNDRVFFDASVIWGLIGPIRIFGPHGNYSALNWF
          T.VA.TVNL.VA.WLLGSI..ICQD..LPADSPWTCPNDRVFFDASVIWGL.GP.RIFGP.GNY.ALNWF
Retrocopy TVVASTVNLVVAYWLLGSIPNICQDALLPADSPWTCPNDRVFFDASVIWGLVGPRRIFGPLGNYGALNWF

Parental  FLIGAAGPVIVYIFHKMFPNKKWITLINLPVLIGATASMPPATAVNYNSWLLFGTIFNFFVFRYRKKWWE
          FL.GA.GPVIVY..H..FP.K.WI..INLPVLIGAT..MPPATAVNYNSWL..G.IFNFFVFRYRK.WW.
Retrocopy FLAGAVGPVIVYLLHRAFPSKTWIPMINLPVLIGATSYMPPATAVNYNSWLIIGIIFNFFVFRYRKLWWK

Parental  RYNYILSAALDAGVAFMAVLLYFSLSMENRSIDWWGTAGEHCPLATCPTAKGVDLGPTSVCPV
          RYNYILSAALDAGVAFMAVLLYFSLSMENRSI.WWGTAGEHCPLA.CPTAKG..LG..SVCPV
Retrocopy RYNYILSAALDAGVAFMAVLLYFSLSMENRSISWWGTAGEHCPLASCPTAKGINLGADSVCPV

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_17 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA005797	1 retrocopy	retro_oind_42,
Oryza nivara	ONIVA02G31600	1 retrocopy	retro_oniv_17 ,
Oryza sativa japonica	OS02G0695800	1 retrocopy	retro_osat_46,
Setaria italica	Si016420m.g	1 retrocopy	retro_sita_13,