RetrogeneDB ID: retro_opun_17

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 11:17594937..17597199(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC11G11260
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC02G08590
• Aliases: None
• Description: None

Sequence

>retro_opun_17
ATGAGAGGCGCCGTGTTGGTGGCCGTGGCGGCCGCCGTTGGCAACCTGCTGCAAGGATGGGACAACGCCACCATCGCCGG
CGCCGTGCTGTACATCAAGCGTGAGTTCGCCCTCGAGTCGCAGCCTGCCGTCGAGGGCCTCGTCGTCGCCATGTCCCTCA
TCGGCGCCACCATCATCACCACCTTCTCCGGCCCGGTCTCCGACGTCGTCGGCCGCCGCCCCATGCTCATCGCCTCCTCT
CTCCTCTACTTCGCCGGCGGCCTCATCATGCTCTGGTCACCCAACGTCTATGTCCTCCTCCTCGCCAGGCTCGTCGACGG
CTTCGGCGTCGGCCTCGCCGTCACGCTCGTCCCCGTCTACATCTCCGAGACGTCGCCGCCGGAGATCCGCGGCCGCCTCA
ACACGCTGCCGCAGTTCACCGGGTCGGGTGGCATGTTCATGTCCTACTGCATGATCTTCGCCATGACGCTGTCGCCGTCG
CCCAACTGGCGCGTCATGCTCGGCGTGCTGTTCCTTCCCTCGCTGCTCTACCTGTTCGTCACCGTCTTCTACCTGCCGGA
GTCGCCGCGCTGGCTCGTCAGCAAGGGCCGGATGAAGGAGGCCAGGGTTGTACTTGAGATGCTGCGTGGACGGGAGGACG
TCTCCGGCGAGATGGCGCTCCTCGTCGAGGGCCTTGGCACCGGCGGCGACACCGAGATCGAGGACTACGTCGTCGGGCCG
TCCGAGGGCGACGCGGGCGAGAACGAGCAGGCGAGGGACACCGTCACGCTGTACGGGCCGGAGCAGGGGTTGTCGTGGGT
GGCGCAGCCGGTCGCCGGCGGTCGCGGCAGCATGCTGGGGAGCTCGCTGGGTCTGCAGGCGTCGCGTCACGGCAGCATGT
ACGAGCAGATGAAGGATCCCGTGGTGGCGCTGCTCGGGAGCGTCCACGAGCGGCTGCCGGAGTCCGGCGGCGGCGCCGCC
GGGAGCATGAGGGGGAGCACGCTGTTCCCTAACCTCGGGAGCATGCTGAGCGTCAATGAGAGGCCCGGCGGCGACTGGGA
CGAGGAGAACGTGCAGCCGGCCGACGAGGAGGAGGACGAGGAGTACCTCTCCGACGACGGCAAGGACGAAGACGACGGAC
TGCAAGCGCCGCTGCTGTCGCGGCAGAGCACCGACGTGGAGGTCAAGAACGAGGCCTCCTCTGGCCAGATGACGATGCAG
CGGCACAGCAGCATCGGCGGCGTCGAGACGGCGAGCACGATGGGGATCGGCGGCGGGTGGCAGCTGGCGTGGAAGTGGAC
GGAGAAAGTTGGTCCCGACGGCGTCAAGCGCGGCGCCGTGAAGCGCATGTACCTGCACGAGGAGGCCGAGGCCGCCCCCG
GTGGCGACGCTGGCGGCGGCGGCAGCGGCGACGCGCCACCATCGCCGTACGTGCACGCGGCCGCGCTGGTCAGCCGCTCG
ATGCTGTACACCAAGGACGTTCTTATCGGCCAGAGCCCCACCGAGCCGGCGTTCGCGAACCCGCCGGAGGCGGTGGCGGC
GGCGGCGACGACGGGCCCTGTCTGGCGCGAGCTTCTCGAGCCCGGCGTCCGCCACGCCCTCTTCTGCGGCATCACCATCC
AGATCCTCCAGCAATTCTCCGGCATCAACGGCGTGCTCTACTACACGCCACAGATCCTCGACCAGGCCGGCGTCAGCGTC
CTCCTCGCAAGCCTCGGCCTCTCCGGCGACTCCACCTCCATCCTCATCAGCGGCCTCACCACGCTCCTCATGCTCCCGTC
CATCGGAGTCGCCATGCGCCTCATGGACGTGTCCGGCCGCCGCGCGCTCCTCCTCTGGACGCTGCCCGTCCTCGTCGCGT
CCCTCGCCGTCCTCGTGGTGGCGAACGTCGTGCCCATGGCGGCGACGGCGCACGCCGCGCTGTCGACGGGGAGCGTCATC
GTCTACTTCTGCTGCTTCGTCATGGGGTTCGGACCCATCCCGAACATCCTCTGCGCCGAGATCTTCCCGACGAGGGTGAG
GGGACTCTGCATCGCCATCTGCTCGCTCACGTTCTGGCTCGGCGACATCGCCGTCACCTACAGCCTCCCGGTGATGCTCA
GCTCCGTCGGGCTCGCCGGCGTGTTCGCCTTCTACGCCGCCGTGTGCTGCGTCGCGCTCGTGTTCGTCGCGTTCAAGGTG
CCGGAGACGAAGGGCCTCCCGCTCGAGGTCATCATCGAGTTCTTCAACGTCGGCGCCAAGGCCGGCACGTTGCCTGACGA
TGAGTTCCACGCTGAAACTTGA

Alignment

ORF - retro_opun_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.33 %
• Parental protein coverage: 61.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGAALVAIAASIGNLLQGWDNATIAGAVLYIKKEFKLESEPTVEGLIVAMSLIGATIITTFSGPVSDWI
          M.GA.LVA.AA..GNLLQGWDNATIAGAVLYIK.EF.LES.P.VEGL.VAMSLIGATIITTFSGPVSD..
Retrocopy MRGAVLVAVAAAVGNLLQGWDNATIAGAVLYIKREFALESQPAVEGLVVAMSLIGATIITTFSGPVSDVV

Parental  GRRPMLILSSILYFLSSLIMLWSPNVYVLLLARLIDGFGIGLAVTLVPLYISETAPSEIRGLLNTLPQFS
          GRRPMLI.SS.LYF...LIMLWSPNVYVLLLARL.DGFG.GLAVTLVP.YISET.P.EIRG.LNTLPQF.
Retrocopy GRRPMLIASSLLYFAGGLIMLWSPNVYVLLLARLVDGFGVGLAVTLVPVYISETSPPEIRGRLNTLPQFT

Parental  GSGGMFLSYCMVFGMSLLPSPDWRIMLGVLAIPSLFFFGLTIFYLPESPRWLVSKGRMAEAKKVLQKLRG
          GSGGMF.SYCM.F.M.L.PSP.WR.MLGVL..PSL.....T.FYLPESPRWLVSKGRM.EA..VL..LRG
Retrocopy GSGGMFMSYCMIFAMTLSPSPNWRVMLGVLFLPSLLYLFVTVFYLPESPRWLVSKGRMKEARVVLEMLRG

Parental  REDVSGEMALLVEGLEVGADTSIEEYIIGPATEPADEHVIDGDKDQITLYGPEEGQSWIARPSKG--PSI
          REDVSGEMALLVEGL..G.DT.IE.Y..GP....A.E.......D..TLYGPE.G.SW.A.P..G...S.
Retrocopy REDVSGEMALLVEGLGTGGDTEIEDYVVGPSEGDAGEN--EQARDTVTLYGPEQGLSWVAQPVAGGRGSM

Parental  LGSVLSL-TSRHGSMVNQSVPLMDPIVTLFGSVHENMPHAGG----SMR-STLFPNFGSMFSVTDQHPKV
          LGS.L.L..SRHGSM..Q.....DP.V.L.GSVHE..P..GG....SMR.STLFPN.GSM.SV....P..
Retrocopy LGSSLGLQASRHGSMYEQ---MKDPVVALLGSVHERLPESGGGAAGSMRGSTLFPNLGSMLSV-NERPGG

Parental  DQWDEENL----HRDDEEYASDGAGGDYEDNVHSPLLSRQTTSAEGKDIAHHGHRGSALSMRRRSLLEEG
          D.WDEEN........DEEY.SD..G.D..D....PLLSRQ.T..E.K..A..G.......M.R.S....G
Retrocopy D-WDEENVQPADEEEDEEYLSDD-GKDEDDGLQAPLLSRQSTDVEVKNEASSGQ----MTMQRHSSI-GG

Parental  GEAVSSTGIGGGWQLAWKWSEREGEDGKKEGGFKRIYLHQ--EGVPGSRRG
          .E..S..GIGGGWQLAWKW.E..G.DG.K.G..KR.YLH...E..PG...G
Retrocopy VETASTMGIGGGWQLAWKWTEKVGPDGVKRGAVKRMYLHEEAEAAPGGDAG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryza punctata was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza punctata was not studied using ChIP-Seq data.

EST

Oryza punctata was not studied using EST data.

TSS

Oryza punctata was not studied using FANTOM5 data.

Lab

retro_opun_17 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza punctata 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza punctata	OPUNC02G08590	1 retrocopy	retro_opun_17 ,
Oryza rufipogon	ORUFI02G09610	1 retrocopy	retro_oruf_1,
Oryza sativa japonica	OS02G0229400	1 retrocopy	retro_osat_16,