RetrogeneDB ID: retro_oruf_46

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 8:18363623..18365201(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI08G17110
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI02G33530
• Aliases: None
• Description: None

Sequence

>retro_oruf_46
ATGGCGGCGGCGATGACAATGTGCGCCGCGGTGGCGGTGCTCCTCGTTCTGACGTCGACAATGGCGGCCGCCGCCGGCGA
TGGCGGTGGCTTCGACTACAAGAAGGCGCTGCACAGCGGGCTGCTCTACTTCGAGGCGCAGCGGTCGGGGCACCTGCTGT
ACAACCAGCGGGTGCGGTGGCGCGGCCACTCGGGGCTCGCCGACGGGCTGCAGCAAGGGGTGGACCTCGTCGGCGGCTAC
TACGACGCCGGCGACAACGTGAAGTTCGGCCTGCCCATGGCGTTCACGATGACGATGCTGTCGTGGGCCGCGGCGGAGTT
CTGGGACGAGATCGCCGCCGCCGGCGAGCGGCGGCACGTGCTGGAGGCCATCAAGTGGGGCACCGACTACCTCGTGAAGG
CGCACACCGCCGCCGACGAGCTGTGGGCCGAGGTCGGCGACGGCGACACCGACCACTACTGCTGGCAGCGGCCGGAGGAC
ATGACGACGTCGAGGCAAGCCTACAAGGTGGACCGCGACAACCCCGGCTCCGACGTCGCCGGCGAGACCGCCGCCGCGCT
CGCCGCCGCGTCCATCGTGTTCCGCCGCTCCAAGCCCCGCTACTCCCGCCTCCTCCTCCGCCACGCCGAGCAGCTGTTCG
ACTTCGGCGACAGGTACAGGGGCAAGTACGACAGCAGCATCGGCGAGGTGAGGGCGTACTACGCGTCGGTGAGCGGCTAC
GGCGACGAGCTGCTGTGGGCGGCGCTGTGGCTGCACCGCGCCACCGGCCGCCGCGGCTACCTCGACTACGCCGTCGCCAT
GGCCGACGAGCTCGGCGGCGTCGGCTGGGCCGTCACCGAGTTCAGCTGGGACGTCAAGTACGCCGGCCTCCAGATCCTCG
CCGCCAAGGTGCTCATGGACGGCGGCGACCACCCGGCGGCGCACGCGGCGACGCTGGAGCAGTACAGGTCCAAGGCGGAG
CACTACCTCTGCGCCTGCCTCGGCAAGAACGCCGCCGCCGGCGACAACGTCAACCGCACCGCCGGCGGCATGCTGTTCGT
CCGCCGCTGGAACAACATGCAGTACGTCACCAACGCCGCCTTCCTCCTCACCGTCTACTCCCGCTACCTCCGCGACTCCG
GCGGCGACACCATCCGGTGCTCCGGTGGGGCTATGGCAACCGGCGACGAGTTGGCGGCGATGGCGAGGGCGCAGGCGGAC
TACGTGCTGGGCGACAACCCGGCGGGGGTGAGCTACATGGTCGGGTACGGGCGGCGGTTCCCGCGGCGGGTGCACCACCG
CGGGGCGTCCATGGTGTCGCACCGCGCGGACGGGCGGTTCGTGGGGTGCGTGCAGGGGTACGACCGCTGGTTCCGGCGCG
GCGGCGCGAACCCGAACGTGGTCGCCGGAGCCATCGTCGGCGGGCCGGACGACCGCGACAGGTTCAGGGACAGCCGCGAC
AACTACATGCAGACGGAGGCGTGCACGTACAACACCGCGCCCATGGTCGGCGTCTTCGCGCACCTGCACGCCCAGAAGAT
GGCGGCGAGGACTGCTAATAATAATGCCGATCGATCGATGATTAAACGAGTGGATTGA

Alignment

ORF - retro_oruf_46 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.17 %
• Parental protein coverage: 88.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLLAAAGGAGAAATERKAHNYEDALRKSLLYFEAQRSGRLPHNQRVAWRDHSGLTDGLEQGVDLVGGYYD
          .LL.......AAA.......Y..AL...LLYFEAQRSG.L..NQRV.WR.HSGL.DGL.QGVDLVGGYYD
Retrocopy VLLVLTSTMAAAAGDGGGFDYKKALHSGLLYFEAQRSGHLLYNQRVRWRGHSGLADGLQQGVDLVGGYYD

Parental  AGDHVKFGLPMAFTVTMLSWSMIEYGDDVEAAGELGHALEAIKWGTDYFIKAHTKPNELWAEVGDGDTDH
          AGD.VKFGLPMAFT.TMLSW...E..D...AAGE..H.LEAIKWGTDY..KAHT...ELWAEVGDGDTDH
Retrocopy AGDNVKFGLPMAFTMTMLSWAAAEFWDEIAAAGERRHVLEAIKWGTDYLVKAHTAADELWAEVGDGDTDH

Parental  YCWQRPEDMTTSRQAYKVDRERPGSDVAGETAAAMAAASIVFRKSNPHYASLLLHHAQQLFEFADKYRGK
          YCWQRPEDMTTSRQAYKVDR..PGSDVAGETAAA.AAASIVFR.S.P.Y..LLL.HA.QLF.F.D.YRGK
Retrocopy YCWQRPEDMTTSRQAYKVDRDNPGSDVAGETAAALAAASIVFRRSKPRYSRLLLRHAEQLFDFGDRYRGK

Parental  YDSSIAEVKSYYASVSGYKDELLWAALWLHRATGKAHYLDYVVDNADCFGGTGWAITEFSWDVKYAGVQI
          YDSSI.EV..YYASVSGY.DELLWAALWLHRATG...YLDY.V..AD..GG.GWA.TEFSWDVKYAG.QI
Retrocopy YDSSIGEVRAYYASVSGYGDELLWAALWLHRATGRRGYLDYAVAMADELGGVGWAVTEFSWDVKYAGLQI

Parental  LAARLLL-RGEHEERHRSTLEQYRAKAEHYVCGCLGRNADGGADANVERSPGGMLYVRQWNNMQYVTNAA
          LAA..L...G.H...H..TLEQYR.KAEHY.C.CLG.NA..G...NV.R..GGML.VR.WNNMQYVTNAA
Retrocopy LAAKVLMDGGDHPAAHAATLEQYRSKAEHYLCACLGKNAAAG--DNVNRTAGGMLFVRRWNNMQYVTNAA

Parental  FLLAAYADYLGDDADGAVSCAGGETAGAGEVAALARAQVDYVLGTNPRGISYLVGYGAKYPNRVHHRAAS
          FLL..Y..YL.D.......C.GG..A...E.AA.ARAQ.DYVLG.NP.G.SY.VGYG...P.RVHHR.AS
Retrocopy FLLTVYSRYLRDSGGDTIRCSGGAMATGDELAAMARAQADYVLGDNPAGVSYMVGYGRRFPRRVHHRGAS

Parental  IVPYKHSKEFIGCTQGFDHWFGRRSSNPNVLVGAIVGGPDRRDRFRDNRENYMQTEACTYNTAPMVGMFA
          .V.......F.GC.QG.D.WF.R...NPNV..GAIVGGPD.RDRFRD.R.NYMQTEACTYNTAPMVG.FA
Retrocopy MVSHRADGRFVGCVQGYDRWFRRGGANPNVVAGAIVGGPDDRDRFRDSRDNYMQTEACTYNTAPMVGVFA

Parental  KLN
          .L.
Retrocopy HLH

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_46 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA009019	1 retrocopy	retro_oind_14,
Oryza barthii	OBART02G31860	1 retrocopy	retro_obar_24,
Oryza glaberrima	ORGLA02G0273700	1 retrocopy	retro_ogla_39,
Oryza rufipogon	ORUFI02G33530	1 retrocopy	retro_oruf_46 ,
Oryza sativa japonica	OS02G0738600	1 retrocopy	retro_osat_30,