RetrogeneDB ID: retro_oruf_31

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 4:25231077..25233024(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI04G25010
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI02G09480
• Aliases: None
• Description: None

Sequence

>retro_oruf_31
ATGGCAAAATATGCGAGCTTTTCGCGTTTCCGTACGAGCTTTTTTTCCATGCGAATCCGACTAGGATTCGACCTGTCATT
TTCCGCTGTTGACTCCCCGAATCCGACTAGGATTCGAGCTATTGCCTTCCGCTTAGTATATAGGGAGGCAGGCTTCAAGT
CAAGCTCCCATTTGGTCCATTTCTCGCATCCCTCTCCTGAACTTTTCCCTCGCTTTTTGCACCACGCCACCCGATTCGCC
ACCGTGCCGGCGCGCCGCCGATCTGAGCACGAGAGAATGGCTTCCCAGTCGCCACAGTCGCGGGGCGTCGCGGAGCCCAT
CTCGCTCGTCGGCCCGACGCCGGCCGACCTGGAGAGCACGGCGCGGCTGGAGAGGCTCCTCCGCGAGGAGGGCCTGTACG
AGAGCGCCGAGGAGACGGCGGCCCGGGAGGAGGTGCTCCGCGGCCTCCGCGGCGTCGTCGACCGCTGGGTGAAGCGCCTC
ACGCGGCAGCGCGGGTACCCCGACGGCATGGCCGACCGGGCCACCGCCCTGGTGCTCCCCTTCGGCTCCTACCGCCTCGG
CGTCCACGGCCGCGGCTCCGACATCGACGCGCTCGTCGTCGGCCCGTCCTACGTCGACCGCGACCGCGACTTCTTCGGCG
CGCTCGCCGCCGCGCTGGCGGAGACGGCGGCCGTCGCCGAGCTCCAGCCCGTGCCCGGCGCGCACGTTCCCGTGATCAAG
ATGAGGTTCCACGGCGTGCAGGTGGACCTCGTGTACGCCGGCGTGTGCCTCCCCGTGGTGCCCGGCGACCTGGACCTCAG
CGGCCGGTCGGTGCTCCGCGGCCTCGACCTCGCCACCGCGCGCAGCCTCAACGGCGTCCGCGTGGCCGACGAGATCCTGC
GGCTGGTCCCGGACGCCGCCGCGTTCCGCACCACGCTGCGGTGCGTGAAGCACTGGGCCAAGGCGCGGGGCGTCTACTCC
AACGTCGCGGGCTTCCTCGGCGGCGTCGGCTGGGCCATCCTCGTGGCGCGCGTGTGCCTGCTCTACCCCAACGCCTCCCC
CAGCATGCTGCTCCCGCGCTTCTTCCGCGTCTTCGCGCGGTGGAAGTGGCCCAGCCCGGTGATGCTGCGCGCCATCGAGC
ACAACGACGGCGAGCTCGGCCTCAGCCTCCCGGTCTGGGACCCCCGCCGGAATCCGCGGGACAAGATACACCTCATGCCC
ATCGTGACGCCGGCGTACCCGTGCATGAACTCCGGCTACAACGTCTCGCACGCCACCCTGCGCGTCATCACCGAGCAGCT
CGCCGTCGGCGACGCCGTCTGCCAGGAGATCGTCAAGGCCGGCAGCGGCGGCGGCGGGTGGGACAAGCTGTTCCAGCCGT
TCAACTTCTTCGGCGCGTACAAGAGCTACCTCCAGGTGGACGTGACGGTGACCGGCGGGGAGGAGGACGACCTCCGCGAG
TGGAAGGGCTGGGTGGAGTCGCGGCTGAGGCTGCTGTCGGCCAGGGTGGAGGCGGACACGTCCGGGATGCTGCTCTGCCA
CCTGCACCCGCAGCCGTACGCCGCCGAGCCCCACAACGAGCCGCGGCGGCGGCGGCGCACGTCGTCCTTCTTCGTGGGCT
TGTCCAAGCCACCGGCGCAGCCGCAGCAGCAGCAGCATCAGCTGTTCGACCTCCGCGCGACGACAGAGGGGTTCAAGGAG
GAGGTGTACATGTACGACTACTGGAGGCCCGGCATGGAGGTCGCGGTGGCGCACGTCCGCCGGAAGGACCTGCCGTCCTA
CGTGCTGCGGCAGCTGCTTCGCTCGCCTGGCCGCCATGATCAGCTCAAGAGGAAGCGCGCCGACGATGATCCGTCTTCTT
CCCCTGCTGCTTCCGATCACTCCGCTTCGAGCTCGAGCAGCAGGGACGCCAAGAGGCCGGCGGCTGCGCCGGGCAGGATC
GGATCGTCGTTTGAGAAGAAGACGTAG

Alignment

ORF - retro_oruf_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.08 %
• Parental protein coverage: 66.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GADPPLSLAMPTVADLHKTAELEKFLVEAGLYEGEEESAKREEVLREIDQIVKEWVKKVTIQKGYSEQMV
          G...P.SL..PT.ADL..TA.LE..L.E.GLYE..EE.A.REEVLR.....V..WVK..T.Q.GY...M.
Retrocopy GVAEPISLVGPTPADLESTARLERLLREEGLYESAEETAAREEVLRGLRGVVDRWVKRLTRQRGYPDGMA

Parental  KEANAVLFTFGSYRLGVHGPGADIDALCIGPSYVKREEEFFVMLYGALSEMEEVTELQPVPDAHVPVMKF
          ..A.A....FGSYRLGVHG.G.DIDAL..GPSYV.R...FF..L..AL.E...V.ELQPVP.AHVPV.K.
Retrocopy DRATALVLPFGSYRLGVHGRGSDIDALVVGPSYVDRDRDFFGALAAALAETAAVAELQPVPGAHVPVIKM

Parental  KFRGLPIDLLYASVSLPVIPPDFDISQGSVLCDVDEATVRSLNGCRVADQILRLVPNAEIFRKTLRCLKY
          .F.G...DL.YA.V.LPV.P.D.D.S..SVL...D.AT.RSLNG.RVAD.ILRLVP.A..FR.TLRC.K.
Retrocopy RFHGVQVDLVYAGVCLPVVPGDLDLSGRSVLRGLDLATARSLNGVRVADEILRLVPDAAAFRTTLRCVKH

Parental  WAQRRGVYSNVTGLLGGVSWALLVARVCQLYPNAVPSMLVSRFFRVFTQWQWPNPVMLCAIENDD---NL
          WA..RGVYSNV.G.LGGV.WA.LVARVC.LYPNA.PSML..RFFRVF..W.WP.PVML.AIE..D....L
Retrocopy WAKARGVYSNVAGFLGGVGWAILVARVCLLYPNASPSMLLPRFFRVFARWKWPSPVMLRAIEHNDGELGL

Parental  GFAVWDPRKNPRDRSHVMPIITPAYPCMNSSYNVSTSTLRVIMEQFQFGNKICQEIELNKASWSSLFEPF
          ...VWDPR.NPRD..H.MPI.TPAYPCMNS.YNVS..TLRVI.EQ...G...CQEI.............F
Retrocopy SLPVWDPRRNPRDKIHLMPIVTPAYPCMNSGYNVSHATLRVITEQLAVGDAVCQEIVKAGSGGGGWDKLF

Parental  QFFE---AYTRYLVVD--IVADDDDDLRLWKGWIESRLRQLTLKIERDTKGMLQCHPNPCEYA
          Q.F....AY..YL.VD........DDLR.WKGW.ESRLR.L....E.DT.GML.CH..P..YA
Retrocopy QPFNFFGAYKSYLQVDVTVTGGEEDDLREWKGWVESRLRLLSARVEADTSGMLLCHLHPQPYA

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_31 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 sativa indica	BGIOSGA007827	1 retrocopy	retro_oind_15,
Oryza rufipogon	ORUFI02G09480	1 retrocopy	retro_oruf_31 ,
Oryza sativa japonica	OS02G0227400	1 retrocopy	retro_osat_45,