RetrogeneDB ID: retro_oruf_41

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 1:1219844..1220411(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI01G01650
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI01G01660
• Aliases: None
• Description: None

Sequence

>retro_oruf_41
ATGGCTGCTGCTTCCATCCTGTTCTTCCTCCTCGCCGGCCTCGCCGCCGCCGCCCACGGCAGCACAGAGGACGACACCAC
GACCACCACCAACACCATACGCCTCCCGAGCGACGGAGGGACACTGGCGGCCACCAGGAGGACGAGGCCGTGGAAGTGCT
GCGACAACATCGAGCAGCTGCCGGTGAGGACCAACCCGCCGCAGTGGCGCTGCAACGACGAGCTGGAGCCCGGGCAGTGC
TTCCGCCAGTGCGAGGCGTGCCGGGATCCGCCGGGGCGGCCGTTCCCCGGCCGGCCGCTCATCTGCGACGACGTCTTCTG
GGGCGACGACCCGGGCACCTCGTGCGCGCCGTCGTCGGAGTGGCCGTGGGGGCCGTGCTGCGACTTCGCCATCTGCACCA
AGTCCATCCCTCCCATCTGCCACTGCTCCGACGAGGTGGAGTCGTGCGCCGCCGCGTGCGGGCAGTGCGAGATGGTGGAC
TCGTGGTCGTGGCGCCCTCTCTTCGTCTGCCGTGACTCCTTCACCGGGGAACCAGGCCCCAGGTGCACACCTGAAATGCA
CAACTAA

Alignment

ORF - retro_oruf_41 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.47 %
• Parental protein coverage: 73.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATSTLLFLLLAG---AAHGAPED---TTTKTIRLPTDGGSAQQAPTTKRPWKLL--AQRLPTKTNPPQW
          MA....LF.LLAG...AAHG..ED...TTT.TIRLP.DGG.......T.RPWK.......LP..TNPPQW
Retrocopy MAAASILFFLLAGLAAAAHGSTEDDTTTTTNTIRLPSDGGTLAATRRT-RPWKCCDNIEQLPVRTNPPQW

Parental  RCNDELEPSQCVAQCEVCQEAPG-PFPG-PLICSDVYWGADPGPFCTPR---PWGDCCTNTTCTRSIPPI
          RCNDELEP.QC..QCE.C...PG.PFPG.PLIC.DV.WG.DPG..C.P....PWG.CC....CT.SIPPI
Retrocopy RCNDELEPGQCFRQCEACRDPPGRPFPGRPLICDDVFWGDDPGTSCAPSSEWPWGPCCDFAICTKSIPPI

Parental  CRCNDRVKKCAAACKDCKRVKS-SKPPRYVCQDQFTGQPGPKC
          C.C.D.V..CAAAC..C..V.S.S..P..VC.D.FTG.PGP.C
Retrocopy CHCSDEVESCAAACGQCEMVDSWSWRPLFVCRDSFTGEPGPRC

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_41 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza rufipogon	ORUFI01G01660	1 retrocopy	retro_oruf_41 ,