RetrogeneDB ID: retro_oruf_29

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 8:7341220..7342144(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI08G08070
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI04G26070
• Aliases: None
• Description: None

Sequence

>retro_oruf_29
ATGGCCGTGGACCTCATGGGCTTCAGCCCGCGCGGCGGCTGCCGCCCGTCCGTGGAGACGGAGCAGCTCGCTTTCCAGGA
GGCCGCCGCCGCGGGGCTCCGCAGCCTCGAGCTGCTCGTCTCGTCGCTCTCCGCCGGGGGGGAGCACCACCACCGCCGCC
GCCCGCAGGAGAAGCAGTCTTCGCCGCCGCTGGGGGAGATCGCGGACCAGGCGGTGTCCAGGTTCAGGAAGGTGATCTCG
ATTCTTGACCGGACCGGCCACGCCCGCTTCCGCCGTGGCCCTGTCGTCGGAGCGGCAGCTGCGGAGGCGGCTGCCGCGGC
GGCGTCGGCGTCACCGTCGTCGTCTCCTGTCTCGCCGCCTCTCCCGCCGGTGACGACGCAGCCGGCGGCCGCCGTGAAGA
GCCTGACGCTGGACTTCACGAATCCCGCCAAGGTCGCGGCGGCGTCGGTGACCTCGACGTCGTTCTTCTCGTCGGTCACC
GCCGGCGGAGACGGCAGCGTGTCCAAGGGCCGGAGCCTGGTCTCCTCCGGGAAGCCCCCGCTCGCCGGCGGCGTCAAGCG
CAAGCACCCGCACCCGCCCTGCGCCGCCGCCGGCGACGGCCACGGCCACGGCGCAGGCCACGCGCACGCGCACGGCGGGT
GCCACTGCTCCAAGAAGCGGAAGCAGCGGGTTCGGCGCACGGTGCGCGTGGCGGCGGCGAGCGCGCGGGTGGCGGACATC
CCCGCCGACGAGTACTCGTGGCGCAAGTACGGGCAGAAGCCGATCAAGGGGTCCCCCTACCCGCGCGGCTACTACCGGTG
CAGCACCGTCAAGGGTTGCCCCGCCCGGAAGCACGTCGAGCGCGCCGCCGACGACCCCGCCACCCTCGTCGTCACCTACG
AGGGCGACCACCGCCACTCGCCGCCGCCGCCGCCGCTTGTTTAA

Alignment

ORF - retro_oruf_29 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.55 %
• Parental protein coverage: 90.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GCYAPRRADDQLAIQEAATAGLRSLEMLVSSLSSSSQAAGAHKASPQQQ----PFGEIADQAVSKFRKVI
          GC..P.....QLA.QEAA.AGLRSLE.LVSSLS........H...PQ......P.GEIADQAVS.FRKVI
Retrocopy GC-RPSVETEQLAFQEAAAAGLRSLELLVSSLSAGGEHH--HRRRPQEKQSSPPLGEIADQAVSRFRKVI

Parental  SILDRTGHARFRRGPVESSAPAAPVAAAPPPPPPPPAPVAAALAPTSSQP----QTLTLDFTKPNLTMSA
          SILDRTGHARFRRGPV...A.AA..AAA.....P...PV...L.P...QP......LTLDFT.P.....A
Retrocopy SILDRTGHARFRRGPVVGAA-AAEAAAAAASASPSSSPVSPPLPPVTTQPAAAVKSLTLDFTNP--AKVA

Parental  ATSVTSTSFFSSVTA-GEGSVSKGRSLLSSGKPPLSGH-KRK----PCAG---GHSEATANG---GRCHC
          A.SVTSTSFFSSVTA.G.GSVSKGRSL.SSGKPPL.G..KRK....PCA....GH..........G.CHC
Retrocopy AASVTSTSFFSSVTAGGDGSVSKGRSLVSSGKPPLAGGVKRKHPHPPCAAAGDGHGHGAGHAHAHGGCHC

Parental  SKRRKNRVKRTIRVPAISSKIADIPPDEYSWRKYGQKPIKGSPYPRGYYKCSTVRGCPARKHVERATDDP
          SK.RK.RV.RT.RV.A.S...ADIP.DEYSWRKYGQKPIKGSPYPRGYY.CSTV.GCPARKHVERA.DDP
Retrocopy SKKRKQRVRRTVRVAAASARVADIPADEYSWRKYGQKPIKGSPYPRGYYRCSTVKGCPARKHVERAADDP

Parental  AMLVVTYEGEHRHTPGPLP
          A.LVVTYEG.HRH.P.P.P
Retrocopy ATLVVTYEGDHRHSPPPPP

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_29 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Leersia perrieri	LPERR04G20020	1 retrocopy	retro_lper_26,
Oryza punctata	OPUNC04G21880	1 retrocopy	retro_opun_5,
Oryza rufipogon	ORUFI04G26070	1 retrocopy	retro_oruf_29 ,
Oryza sativa japonica	OS04G0605100	1 retrocopy	retro_osat_10,