RetrogeneDB ID: retro_oruf_1

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 11:16365549..16367823(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI11G14180
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI02G09610
• Aliases: None
• Description: None

Sequence

>retro_oruf_1
ATGAGAGGCGCCGTGTTGGTGGCCGTGGCGGCCGCCATCGGCAACTACCTGCAGGGATGGGACAACGCCACCATCGCCGG
CGCCGTGCTGTACATCAAGCGGGAGTTCGCCCTCGAGACCCAGCCCGCCGTGGAGGGCCTCGTCGTCGCCATGTCCCTCA
TCGGCGCCACCATCATCACCACCTTCTCCGGCCCCGTCTCCGACCTCGTCGGCCGCCGCCCCATGCTCATCGCCTCCTCC
CTCCTCTACTTCGCCGGCGGCCTCATCATGCTCTGGTCCCCCAACGTCTACGTCCTCCTCCTCGCCCGCCTCGTCGACGG
CTTCGGCGTCGGCCTCGCCGTCACCCTCGTCCCCGTCTACATCTCCGAGACCTCCCCGCCGGAGATCCGCGGCCGCCTCA
ACACGCTGCCGCAGTTCACCGGCTCCGGCGGCATGTTCATGTCCTACTGCATGATCTTCGCCATGACGCTCTCGCCCTCG
CCCAACTGGCGCATCATGCTCGGCGTCCTCTTCGTCCCCTCGCTGCTCTACCTGTTCGTCACCGTCTTCTACCTCCCGGA
GTCGCCGCGGTGGCTCGTCAGCAAGGGGCGCATGAAGGAGGCCAGGGTTGTGCTCGAGATGCTGCGCGGCCGCGAGGACG
TCTCCGGCGAGATGGCGCTGCTCGTCGAGGGCCTCGGCACCGGCGGCGACACCGAGATCGAGGACTACGTCGTCGGCCCG
TCCGAGGGCGACGCCGGCGAGAACGAGCAGGCGAGGGACACCGTCACGCTGTACGGGCCGGAGCAGGGGCTTTCGTGGGT
GGCGCAGCCGGTCGCCGGCGGCCGCGGCAGCATGCTGGGGAGCTCGCTGGGGCTGCAGGCGTCGCGCCATGGCAGCATGT
ACGAGCAGATGAAGGACCCCGTGGTGGCGCTTCTCGGGAGCGTCCACGAGCGGCTGCCGGAGTCCGGCGGCGGCGCCACC
GGCAGCATGAGGGGGAGCACGCTGTTCCCCAACCTCGGGAGCATGCTTAGCGTCAACGATAGGCCCGGCGGCAGCAGCTG
GGACGAGGAGAACGTGCAGCCTGGCGACGACGACCTCGACGAGGAGGAGGAGGAGTACCTCTCCGACGACGGCAAGGACG
ACGACGACGGCGGCGGCCTGCAGGCACCGCTGCTGTCGCGGCAGAGCACCGACGTGGAGACCAAGAACGAGCCCGCCTCC
GGCCAGGTGGCGATGCAGCGGCACAGCAGCATCGGCGGCGGCGGCGGCGTCGAGACGGCGAGCACCATGGGCATCGGCGG
CGGGTGGCAGCTGGCGTGGAAGTGGACGGAGAACGTGGGCCCCGACGGCGTCAAGCGCGGCGCGGTGAAGCGCATGTACC
TGCACGAGGAGTCCGAGGCCGCGCCCGGCGGTGACTCGGGCGCCGCCGGCGACGCGCAGTCCACGGCGTACGTCCACGCG
GCGGCGCTGGTGAGCCGGTCGATGCTGTACACCAAGGACGTCCTGATCGGGCAGAGCCCCACCGAGCCGGCGTTCGCGAA
CCCGCCGGAGGCGGTGGCGGCGGCGGCGTCGACGGGCCCGGCGTGGCGCGAGCTGCTCGAGCCGGGCGTCCGCCACGCCC
TCTTCTGCGGCGTCACCATCCAGATCCTCCAGCAATTCTCCGGCATCAACGGCGTGCTCTACTACACCCCGCAGATCCTC
GACCAGGCCGGCGTCAGCGTCCTCCTCGCCAGCCTCGGCCTCTCCGGCGACTCCACCTCCATCCTCATCAGCGGCCTCAC
CACGCTCCTCATGCTCCCGTCCATCGGCGTCGCCATGCGCCTCATGGACGCCTCGGGCCGCCGCGCCCTCCTCCTCTGGA
CGCTGCCCGTCCTCGTCGCGTCCCTCGCCGTGCTCGTGGTGGCGAACGTCGTGCCCATGGCGGCGACCGCGCACGCGGCG
CTGTCGACGGGGAGCGTCATCGTCTACTTCTGCTGCTTCGTCATGGGGTTCGGCCCCATCCCCAACATCCTCTGCGCCGA
GATCTTCCCGACGAGGGTGAGGGGACTCTGCATTGCCATCTGCTCGCTGACGTTCTGGCTCGGCGACATCGCCGTCACGT
ACAGCCTCCCCGTCATGCTCAGCTCCGTGGGGCTCGCCGGCGTGTTCTCCTTCTACGCCGCCGTGTGCTGCGTCGCGCTC
GTGTTCGTGGCGCTCAAGGTGCCCGAGACCAAGGGCCTCCCGCTCGAGGTCATCATCGAGTTCTTCAACGTCGGCGCCAA
GGCCGGCACGTTGCCTGACGAAGAGTTCCACTGA

Alignment

ORF - retro_oruf_1 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.34 %
• Parental protein coverage: 61.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSGAALVAIAASIGNLLQGWDNATIAGAVLYIKKEFKLESEPTVEGLIVAMSLIGATIITTFSGPVSDWI
          M.GA.LVA.AA.IGN.LQGWDNATIAGAVLYIK.EF.LE..P.VEGL.VAMSLIGATIITTFSGPVSD..
Retrocopy MRGAVLVAVAAAIGNYLQGWDNATIAGAVLYIKREFALETQPAVEGLVVAMSLIGATIITTFSGPVSDLV

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

Parental  GSGGMFLSYCMVFGMSLLPSPDWRIMLGVLAIPSLFFFGLTIFYLPESPRWLVSKGRMAEAKKVLQKLRG
          GSGGMF.SYCM.F.M.L.PSP.WRIMLGVL..PSL.....T.FYLPESPRWLVSKGRM.EA..VL..LRG
Retrocopy GSGGMFMSYCMIFAMTLSPSPNWRIMLGVLFVPSLLYLFVTVFYLPESPRWLVSKGRMKEARVVLEMLRG

Parental  REDVSGEMALLVEGLEVGADTSIEEYIIGPAIEPADEHVVDGDKDQITLYGPEEGQSWIARPSKG--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.D..P..
Retrocopy LGSSLGLQASRHGSMYEQ---MKDPVVALLGSVHERLPESGGGATGSMRGSTLFPNLGSMLSVNDR-PGG

Parental  DQWDEENLHRDD---EEYASDGAGGDYEDNVHSPLLSRQTTSAEGKDIAHHAHRGSALSMRRRSLLEEGG
          ..WDEEN....D....E........D..D......L.....S....D........S......R.....GG
Retrocopy SSWDEENVQPGDDDLDEEEEEYLSDDGKDDDDGGGLQAPLLSRQSTDVETKNEPASGQVAMQRHSSIGGG

Parental  EAVSSTGIGG---GWQLAWKWSEREGEDGKKEGGFKRIYLHQEE--VPGSRRGS
          ..V......G...GWQLAWKW.E..G.DG.K.G..KR.YLH.E....PG...G.
Retrocopy GGVETASTMGIGGGWQLAWKWTENVGPDGVKRGAVKRMYLHEESEAAPGGDSGA

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza rufipogon was not studied using ChIP-Seq data.

EST

Oryza rufipogon was not studied using EST data.

TSS

Oryza rufipogon was not studied using FANTOM5 data.

Lab

retro_oruf_1 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza rufipogon 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,