RetrogeneDB ID: retro_oruf_8

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 6:26841252..26842323(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI06G28930
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI06G18690
• Aliases: None
• Description: None

Sequence

>retro_oruf_8
ATGCTGTCGTCTTCCACCTCCACCCACCGCCTCCACCAGCCGCCGCCGCCGCCGCCGCCGCCGGCGAGCCACCAATTCCG
GTCGGCCGCCGCGTTCCGCCGCCCTCCGTCTCCGGCGGCGGCGCCCCTCCGCGCGCGGCCGCAGCGCGGGGGCGGCACCA
CCATCCGCGCCATCGACGCAGCCCAGCCGTTCGACTACGAGTCCCGCGCGGCGGGGCTCCTGGAGGAGCGGCAGCGGCTC
AAGATCGCCATCGTCGGGTTCGGCAACTTCGGCCAGTTCCTCGCCCGCACCTTCGCGCGGCAGGGCCACACGCTGCTCGC
CCACTCCCGCTCCGACTACTCCTCCCTCGCCGCCTCCGTCGGCGCGTCCTACTTCCAGGACCCGCACGACCTCTGCGAGT
GCCACCCGGATGTGGTGCTCCTCGCCACCTCCATCCTCTCCGCCGAGGCCGTCCTCCGCTCGCTCCCCGTCCACCGCCTC
CGCCGCAACACCCTCTTCGTCGACGTGCTCTCCGTCAAGGAGTTCCCCAGGAACCTCCTCCTCGGCTCGCTCCCGCCGGA
CTTCGACGTCATCTGCACCCACCCCATGTTCGGCCCGGAGTCGGCGCGCGACGGCTGGGACGGCCTCCCCTTCGTGTTCG
ACAAGGTCCGCGTCGGCGACTGCCCCGCGCGCCGCGCCCGCGCCGAGGCCTTCCTCAACATCTTCGAGCGGGAGGGGTGC
CGCATGGTGGAGATGACCTGCGCCGAGCACGACGCGCACGCCGCCGAGACGCAGTTCCTCACCCACACCGTCGGCCGGAT
GCTCGCCATGCTGGAGCTCCGGTCCACGCCGATCAACACCAAGGGGTACGAGACGCTGCTCCGCCTCGTCGACAACACCT
GCAGCGACAGCTTCGACCTCTACAATGGCCTCTTCATGTACAACAAGAACTCCACCGAGCTGCTCAATCGCCTCGAATGG
GCCATGGATTCCGTCAAGAAGAAGCTCTTCGATGGCCTCCACGACGTGCTCCGGAAGCAGCTCTTCGAGGGCTCGCCGCA
CGCTCCCAACAACACCCCCGTCAGGAAGTAG

Alignment

ORF - retro_oruf_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.19 %
• Parental protein coverage: 68.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRVGIVGFGNFGQFIAGGIQRQGHAVLATSRSDYSGYCARHGIRFFATADELCEAGPDVLLVCSSILSTE
          L...IVGFGNFGQF.A....RQGH..LA.SRSDYS...A..G...F.....LCE..PDV.L...SILS.E
Retrocopy LKIAIVGFGNFGQFLARTFARQGHTLLAHSRSDYSSLAASVGASYFQDPHDLCECHPDVVLLATSILSAE

Parental  AVVRAIPFRKLRPGTLVADVLSVKQFPRNLLLEILPPGFGIVCTHPMFGPESGKHGWSGLPFVYDKVRVA
          AV.R..P...LR..TL..DVLSVK.FPRNLLL..LPP.F...CTHPMFGPES...GW.GLPFV.DKVRV.
Retrocopy AVLRSLPVHRLRRNTLFVDVLSVKEFPRNLLLGSLPPDFDVICTHPMFGPESARDGWDGLPFVFDKVRVG

Parental  KEGDQAAKCEQFLSIFEREGCRMVEMLCEEHDRYAAGSQFITHTIGRILSQLNLESTPINTKGYETLLQL
          ......A..E.FL.IFEREGCRMVEM.C.EHD..AA..QF.THT.GR.L..L.L.STPINTKGYETLL.L
Retrocopy DCPARRARAEAFLNIFEREGCRMVEMTCAEHDAHAAETQFLTHTVGRMLAMLELRSTPINTKGYETLLRL

Parental  TKNTISDSFDLYYGLFMYN
          ..NT.SDSFDLY.GLFMYN
Retrocopy VDNTCSDSFDLYNGLFMYN

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_8 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 brachyantha	OB06G25340	1 retrocopy	retro_obra_15,
Oryza rufipogon	ORUFI06G18690	1 retrocopy	retro_oruf_8 ,
Setaria italica	Si006643m.g	1 retrocopy	retro_sita_25,