RetrogeneDB ID: retro_oruf_18

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 5:15161629..15163639(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI05G14920
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI02G01160
• Aliases: None
• Description: None

Sequence

>retro_oruf_18
ATGGCGCGCGGCGCAACGTGGACGCGGCGGCTGCACCTGCACGGCCTCTTCCTCGCCGTGCTCCTCCTCCTCACGTTGCC
GGCGGGCTCCACCGCGGCCGCCGGCGGCGGCGGCGGCACCGTGATCGGGATCGACCTCGGCACCACCTACTCGTGCGTTG
GTGTCTACCGGAATGGCCACGTCGAGATCATCGCCAACGACCAGGGGAACCGGATCACACCCTCGTGGGTCGCCTTCACC
GGCGGCGGCGAGCGGCTCATCGGCGAGGCCGCCAAGAACCAGGCGGCGGCGAACCCGGGGCGGACGGTGTACGACGCCAA
GCGCCTCATCGGCCGCCGGTTCGCCGACGCCGAGGTGCAGCGCGACATGAGGCTGCTGCCGTTCGCTGTCGTCGACAAGG
GCGGCAAGCCGCACGTCCGCGTCGAGGTGAGGGGCGGCGACGTGCGGCTGCTCAGCCCCGAGGAGGTGAGCGCCATGGTG
CTCGCCAGGATGAAGGAGACGGCGGAGGCCTACCTCGGGGAGGAGGTCACCCGCGCCGTCGTCACCGTGCCGGCCTACTT
CAACGACGCGCAGCGGCAGGCCACCAAGGACGCCGCCACCATCGCCGGCCTCGCCGTCGAGCGCATCCTCAACGAGCCCA
CCGCCGCCGCGCTCGCCTATGGCGTCGGCAAGGAGGGCGCCGGCGGGAAGAACGTCCTCGTCTTCGACCTCGGCGGCGGC
ACGTTCGACGTCAGCGTCCTCGCCATCGACGGCGGCGTGTACGAGGTCCTCGCCACCAACGGCGACACCCACCTCGGCGG
CGAGGACTTCGACCAGCGCGTCATGGAGCACTTCGTGGAGCTCGTCAGGCGCAAGCACGGCCGCGACATCGCCGGCGACG
CGCGCGCGCTCGGCAAGCTCCGCCGCGAGTGCGAGCGCGCCAAGCGCGCGCTCAGCATCCAGCACCAGGTGCGCGTCGAG
GTGGAGTCTCTGTTCGACGGCGTCGACCTGTCGGAGCCGCTGTCCAGGGCGCGGTTCGAGGAGCTCAACAACGACCTGTT
CCGGAAGACGATGGCGCCGGTGAGGAAGGCCATGGCGGACGCCAGGCTGAGCAATGCCGACATCGACGAGATCGTCCTCG
TCGGCGGCAGCACGAGGATCCCCAAGGTGAGGCAGCTGCTCAGGGACTACTTCGGCGGCAAGCAGCCCAACCAGGGCGTC
AACCCCGACGAGGCCGTGGCCTACGGCGCCGCCATCCAGGCCAACATCGTCGGCGGCGACACCGACAACAAAACCCGCGA
CATGGTCGTCCTCGACGTCACGCCGCTCACCCTCGGCCTCGAGACCGCCGGCGGCGTCATGGCCACCCTGATCCCGCGCA
ACACGCCGGTGCCGACGAAGAGGGCGCAGCTGTTCTCCACCTACAAGGACAAGCAGACGACGGTGACCGTCAAGGTGTTC
GAGGGCGAGCGGAGCATGACGAGGGACAACCGGCTGCTCGGCAGGTTCGACCTCGCCGGCATCGCGCCGGCGCCGCGCGG
CGCGCCGCAGATCGAGGTGGCGTTCGAGGTGGACGCGGACGGCATCCTCAGCGTGAGCGCCGCCGACAGGGCCACCGGCA
GGTCGGAGAGGATCACCATCTCCGGCGACGACCGCAAGACCAGCCGGGAGGAGATCGACCGGATGCTGGGCGAGGCGGAG
GAGTTCGCCGACGAGGACCGCCACCACAGGGAGCGCGCCGGCGCCCGGAACAGCCTGGAAGCCTACGTCTACGGCGTCAA
GAACGCCGTGGTGGGCGGCGAGATGGCGGGCGCCATGGACGGCGGCGAGAAGGAGAAGGTGGAGGCGGCGGTGATGGAGG
CGTACGAGTGGCTCGACGGCAACCAGGACGTCGGCAAGGAGGAGTACGAGGAGAAGCTCCGGGAGCTGGAGGACGTGTGC
AACCCGGTCATGTCGGCGGTGTACCAGAGGTCCGGCGGCTCACGGCGAGATGGCGACGGCGGCGGCGACGACGATCACGA
TGAGCTTTAG

Alignment

ORF - retro_oruf_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.08 %
• Parental protein coverage: 95.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GTVIGIDLGTTYSCVGVYKNGHVEIIANDQGNRITPSWVAFTDS-ERLIGEAAKNQAAVNPERTIFDVKR
          GTVIGIDLGTTYSCVGVY.NGHVEIIANDQGNRITPSWVAFT...ERLIGEAAKNQAA.NP.RT..D.KR
Retrocopy GTVIGIDLGTTYSCVGVYRNGHVEIIANDQGNRITPSWVAFTGGGERLIGEAAKNQAAANPGRTVYDAKR

Parental  LIGRKFEDKEVQRDMKLVPYKIVNKDGKPYIQVKIKDGENKVFSPEEVSAMILGKMKETAEAYLGKKIND
          LIGR.F.D.EVQRDM.L.P...V.K.GKP...V....G.....SPEEVSAM.L..MKETAEAYLG.....
Retrocopy LIGRRFADAEVQRDMRLLPFAVVDKGGKPHVRVEVRGGDVRLLSPEEVSAMVLARMKETAEAYLGEEVTR

Parental  AVVTVPAYFNDAQRQATKDAGVIAGLNVARIINEPTAAAIAYGLDKKG-GEKNILVFDLGGGTFDVSILT
          AVVTVPAYFNDAQRQATKDA..IAGL.V.RI.NEPTAAA.AYG..K.G.G.KN.LVFDLGGGTFDVS.L.
Retrocopy AVVTVPAYFNDAQRQATKDAATIAGLAVERILNEPTAAALAYGVGKEGAGGKNVLVFDLGGGTFDVSVLA

Parental  IDNGVFEVLATNGDTHLGGEDFDQRIMEYFIKLIKKKYSKDISKDNRALGKLRREAERAKRALSNQHQVR
          ID.GV.EVLATNGDTHLGGEDFDQR.ME.F..L...K...DI..D.RALGKLRRE.ERAKRALS.QHQVR
Retrocopy IDGGVYEVLATNGDTHLGGEDFDQRVMEHFVELVRRKHGRDIAGDARALGKLRRECERAKRALSIQHQVR

Parental  VEIESLFDGTDFSEPLTRARFEELNNDLFRKTMGPVKKAMDDAGLEKSQIHEIVLVGGSTRIPKVQQLLR
          VE.ESLFDG.D.SEPL.RARFEELNNDLFRKTM.PV.KAM.DA.L....I.EIVLVGGSTRIPKV.QLLR
Retrocopy VEVESLFDGVDLSEPLSRARFEELNNDLFRKTMAPVRKAMADARLSNADIDEIVLVGGSTRIPKVRQLLR

Parental  DYFEGKEPNKGVNPDEAVAYGAAVQGSILSGEGGDETKDILLLDVAPLTLGIETVGGVMTKLIPRNTVIP
          DYF.GK.PN.GVNPDEAVAYGAA.Q..I..G.....T.D...LDV.PLTLG.ET.GGVM..LIPRNT..P
Retrocopy DYFGGKQPNQGVNPDEAVAYGAAIQANIVGGDTDNKTRDMVVLDVTPLTLGLETAGGVMATLIPRNTPVP

Parental  TKKSQVFTTYQDQQTTVSIQVFEGERSMTKDCRLLGKFDLSGIPAAPRGTPQIEVTFEVDANGILNVKAE
          TK..Q.F.TY.D.QTTV...VFEGERSMT.D.RLLG.FDL.GI..APRG.PQIEV.FEVDA.GIL.V.A.
Retrocopy TKRAQLFSTYKDKQTTVTVKVFEGERSMTRDNRLLGRFDLAGIAPAPRGAPQIEVAFEVDADGILSVSAA

Parental  DKGTGKSEKITITNEKGRLSQEEIDRMVREAEEFAEEDKKVKERIDARNQLETYVYNMKNTVGDKDKLAD
          D..TG.SE.ITI.......S.EEIDRM..EAEEFA.ED....ER..ARN.LE.YVY..KN.V......A.
Retrocopy DRATGRSERITISGDDRKTSREEIDRMLGEAEEFADEDRHHRERAGARNSLEAYVYGVKNAVVG-GEMAG

Parental  KLESEEKEKVEEALKEALEWLDENQTAEKEEYEEKLKEVEAVCNPIISAVYQRTGGAPGGGADGEGGVDD
          .....EKEKVE.A..EA.EWLD.NQ...KEEYEEKL.E.E.VCNP..SAVYQR.GG......DG.GG.DD
Retrocopy AMDGGEKEKVEAAVMEAYEWLDGNQDVGKEEYEEKLRELEDVCNPVMSAVYQRSGGS---RRDGDGGGDD

Parental  EHDEL
          .HDEL
Retrocopy DHDEL

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_18 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI3G01477	1 retrocopy	retro_bdis_30,
Aegilops tauschii	F775_27431	1 retrocopy	retro_atau_11,
Oryza longistaminata	KN538684.1_FG046	1 retrocopy	retro_olon_13,
Hordeum vulgare	MLOC_55999	1 retrocopy	retro_hvul_1,
Oryza nivara	ONIVA01G37420	1 retrocopy	retro_oniv_8,
Oryza rufipogon	ORUFI02G01160	1 retrocopy	retro_oruf_18 ,
Sorghum bicolor	Sb04g001140	1 retrocopy	retro_sbic_39,
Triticum aestivum	Traes_6DS_A593093E1	1 retrocopy	retro_taes_72,