RetrogeneDB ID: retro_oruf_11

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 6:539146..540058(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI06G00620
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI09G10540
• Aliases: None
• Description: None

Sequence

>retro_oruf_11
ATGGCGGGAATCGTAGAAAAAGAAGGCGAGACGGGTCACCTCACCTCACCAACCGCGCCAACTTTAACCACACCAACCAA
CCAAGCCTTCGTCAATATAATAACAGTACTGATGATGGTGAGCTTGATGGAGGAAGAGGCCATGGCCATGGAGACGATGG
CGACGACGACGACCAAGAGGATGTCGGTGGCGGAGGTGTCTCTGGTGGAGGCCGTGCTGTTCGACATCGACGGCACCATG
TGCGTCTCCGACCCGTTCCACCACAGGGCCTTCTCCGAGCTCCTCCAGGCCCTCGGCTACAACTCCGGCGTCCCCATCAC
GCCGGAGTTCGGCATGGCCCACATGGCCGGCCGGAGCAACCACCAGATCGGCAGCTTCCTCTTCCCGGACTGGCCCCAGC
ACCGCCTCGACGCCTTCTTCGCCGACAAGGAGGCCCTCTTCGCGCGCTACGCCGCCGAGGGCCTCCGCGAGGTCGCCGGC
CTCACCGACCTCTGCCGGTGGGCCGCCGCCCGCGGCCTCAAGCGCGCCGCCGTCACCAACGCGCCGCGGGCCAACGCCGA
CCTCATGATCTCCATCCTCGGCCTCTCCGACTTCTTCCAGGTCATCGTCGCCGCTGCCGACGACTGCGACCTCCCCAAGC
CCTCGCCGGAGCCCTACCTCCGGGCGCTCAGCCTGCTCGGCGCGTCTCCCCGTCACACGCTCGTCTTCGAGGACTCGGTG
GTCGGGGTGCAGGCCGGCGTCGCCGCCGGGATGCCGGTGATCGCCGTCGCGGAGGAGGCCCGGGAGGCCAAGGTCGTCGC
CGCCGGAGCGTCCCTCGTCATCAGGGACTACAAAGACCACAAGCTCTGGGCGGCATTAGACAAGCTCCAAGCAGCAGCAG
CAGCTCAATCCAATGGACAACTTGGAGCATAG

Alignment

ORF - retro_oruf_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.65 %
• Parental protein coverage: 89.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IEAVLFDIDGTLCDSDPLHHVAFQEMLLEIGYNNGVPIDEEFFINNIAGRSDVEAAQNLFPDWPLEKGLK
          .EAVLFDIDGT.C.SDP.HH.AF.E.L...GYN.GVPI..EF.....AGRS.......LFPDWP......
Retrocopy VEAVLFDIDGTMCVSDPFHHRAFSELLQALGYNSGVPITPEFGMAHMAGRSNHQIGSFLFPDWPQHRLDA

Parental  FLEDKEAKYRSLAKERLEPVKGLAKVVQWVKYHGYKRAAVTNAPRINSELMISLLGLTDFFQAVIVGG-E
          F..DKEA.....A.E.L..V.GL.....W....G.KRAAVTNAPR.N..LMIS.LGL.DFFQ........
Retrocopy FFADKEALFARYAAEGLREVAGLTDLCRWAAARGLKRAAVTNAPRANADLMISILGLSDFFQVIVAAADD

Parental  CEKPKPAPFPYLKALKELQVSADHTFIFEDSASGTRAGVAAGIPVVAVATRNPEKSLLDAGATLIIKDYE
          C..PKP.P.PYL.AL..L..S..HT..FEDS..G..AGVAAG.PV.AVA....E.....AGA.L.I.DY.
Retrocopy CDLPKPSPEPYLRALSLLGASPRHTLVFEDSVVGVQAGVAAGMPVIAVAEEAREAKVVAAGASLVIRDYK

Parental  DPKLWSALEEIDREEA
          D.KLW.AL.......A
Retrocopy DHKLWAALDKLQAAAA

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_11 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
Oryza sativa indica	BGIOSGA029783	1 retrocopy	retro_oind_12,
Oryza barthii	OBART09G09890	1 retrocopy	retro_obar_14,
Oryza glumaepatula	OGLUM09G10170	1 retrocopy	retro_oglu_30,
Oryza meridionalis	OMERI09G07660	1 retrocopy	retro_omer_18,
Oryza punctata	OPUNC09G08360	1 retrocopy	retro_opun_16,
Oryza glaberrima	ORGLA09G0073400	1 retrocopy	retro_ogla_33,
Oryza rufipogon	ORUFI09G10540	1 retrocopy	retro_oruf_11 ,
Oryza sativa japonica	OS09G0407700	1 retrocopy	retro_osat_26,