RetrogeneDB ID: retro_oruf_9

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 6:22232780..22233818(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI06G22930
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI08G05030
• Aliases: None
• Description: None

Sequence

>retro_oruf_9
ATGAGGACCACGGCGAGGCCAACGGCGGCGGCGACGGCGCTCGCGCTCATCCTCGTCCTGGTGTTCTCGCCGTCCCCCGC
CGCTGCCGCAGCGAGAATGTTCAAGACCATCGACGCCCGACGGAGCCAGCATCTGGACCTCGGCGGATCACTGGTCGGGC
CAGAGAGCGTCGCGTTCGACGGCAAAGGCCGCGGCCCATACAGCGGCGTCTCCGACGGCCGCGTCATGAGGTGGAACGGC
GAGGCGGCTGGCTGGAGCACCTACACGTACAGCCCCAGCTACACGAAAAACAAGTGCGCGGCATCGACTCTCCCCACGGT
TCAAACCGAGAGCAAATGCGGCCGTTCGTTGGGCCTACGGTTTCACTTCAAAACCGGCAACCTGTACATCGCCGACGCCT
ACATGGGATTGATGCGAGTTGGGCCAGGAGGTGGTGAGGCAACAGTGCTAGCCACGAAGGCTGATGGCGTGCCACTTCGC
TTCACCAATGGGGTGGACATTGATCAGGTTACCGGAGATGTTTATTTCACTGACAGCAGCATGAACTACCAACGATCTCA
GCACGAGCAAGTCACGGCGACCAAGGATTCGACCGGACGGCTCATGAAGTATGACCCACGAACTAACCAAGTCACCGTTC
TTCAATCCAACATAACCTACCCGAACGGTGTCGCCATTAGCGCTGACCGAACACATTTGATCGTTGCGTTGACCGGCCCA
TGTAAGTTGAGGTATTGGATTCGAGGTCCAAAGGTTGGTAAGTCCGAACCATTTGTCGACTTGCCAGGCTATCCTGATAA
TGTGAGGCCTGATGAGAAAGGTGGTTACTGGGTAGCGCTCCATCGTGAGAAGTATGAGCTTCCATTTGGTCCGGACAATC
ACTTGGTTGCAATGAGAGTTAGTGCTGGTGGAAAGCTGGTGCAACAGATGAGAGGACCAAAGAGCTTGAGACCAACTGAA
GTGATGGAGAGGAAGGATGGCAAAATATACATGGGAAATGTTGAATTGCCATATGTCGGAGTCGTCAAGAGTATCTAG

Alignment

ORF - retro_oruf_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.2 %
• Parental protein coverage: 80.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PATLVTLLRLVGCLLLAFFLAAPPCAAAQQVKTSHAQFAFHLPLPDGVTGAESLAFDSSNHGPYTGVSDG
          P....T.L.L....L...F...P..AAA...KT..A....HL.L.....G.ES.AFD....GPY.GVSDG
Retrocopy PTAAATALALI---LVLVFSPSPAAAAARMFKTIDARRSQHLDLGGSLVGPESVAFDGKGRGPYSGVSDG

Parental  RVLRWGGAAAGWTTFAHHENYRKIPMCTTPVAPAEETESMCGRPLGLAFHDRTGDLYIADAYKGLMRVGP
          RV.RW.G.AAGW.T......Y.K...C.....P...TES.CGR.LGL.FH..TG.LYIADAY.GLMRVGP
Retrocopy RVMRWNGEAAGWSTYTYSPSYTK-NKCAASTLPTVQTESKCGRSLGLRFHFKTGNLYIADAYMGLMRVGP

Parental  RGGEAEVLAAGADGVPFNFVNGIDVDQATGDVYFTDSSTTYPRRFNSEIMMNADATARLLKYDAATKRVT
          .GGEA.VLA..ADGVP..F.NG.D.DQ.TGDVYFTDSS..Y.R..........D.T.RL.KYD..T..VT
Retrocopy GGGEATVLATKADGVPLRFTNGVDIDQVTGDVYFTDSSMNYQRSQHEQVTATKDSTGRLMKYDPRTNQVT

Parental  VLRAGLPYANGVAVSRDGSHAVVAHTVPCQAFRYWIKGPNAGEYELLADLPGYPDNVRRDANGGYWVALN
          VL.....Y.NGVA.S.D..H..VA.T.PC...RYWI.GP..G..E...DLPGYPDNVR.D..GGYWVAL.
Retrocopy VLQSNITYPNGVAISADRTHLIVALTGPCK-LRYWIRGPKVGKSEPFVDLPGYPDNVRPDEKGGYWVALH

Parental  QEKARL
          .EK..L
Retrocopy REKYEL

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_9 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA028079	1 retrocopy	retro_oind_6,
Oryza glumaepatula	OGLUM08G04830	1 retrocopy	retro_oglu_15,
Oryza meridionalis	OMERI08G04560	1 retrocopy	retro_omer_14,
Oryza punctata	OPUNC08G04420	1 retrocopy	retro_opun_39,
Oryza glaberrima	ORGLA08G0040000	1 retrocopy	retro_ogla_41,
Oryza rufipogon	ORUFI08G05030	1 retrocopy	retro_oruf_9 ,
Oryza sativa japonica	OS08G0175000	1 retrocopy	retro_osat_11,