RetrogeneDB ID: retro_oruf_2

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 12:4577982..4579389(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI12G06230
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI05G18300
• Aliases: None
• Description: None

Sequence

>retro_oruf_2
ATGGTTCAGATCGAGCCGCTCGAGGTGTCACTGGAGGCCGGCAACCAGGCGGACTCGGCGTTGCTCGACGACGACGGGCG
GCCGCGCCGCACCGGCACGTTCTGGACGGCGAGCGCGCACATCATCACCGCCGTGATCGGGTCCGGGGTGCTGTCGCTGC
CGTGGGCGACGGCGCAGCTCGGGTGGGTCGGCGGGCCCGCCGTGATGGTGGTGTTCGGCGGCGTCACCTACTTCACCGCC
ACGCTCCAGGCCGAGTGCTACCGCACCGGCGACGAGGAGACCGGCGCCCGCAACTACACCTACATCGGCGCCGTCCGCGC
CATCCTCGGCGGCGCCAACGCCAAGCTCTGCGGCATCATCCAGTACGCCAACCTCGTCGGCACCGCCGTCGGCTACACCA
TCGCCGCCTCCATCAGCATGCAGGCCATCAAGAGGGCGGGCTGCTTCCACGCCAATGGCCACAACGTCCCGTGCCACATC
TCGAGCACCCCGTACATGCTCATCTTCGGCGCCTTCGAGATCGTCTTCTCGCAGATCCCCGACTTCCACGAGATCTGGTG
GCTGTCCATCGTCGCCGCCGTCATGTCCTTCACCTACTCCGGCGTCGGCCTCGGCCTCGGCATCGCCCAGACCGTCGCCG
ACGGCGGGTTCCGCGGCACGATCGCCGGCGTCACCAACGTCACCGCCACGCAGAAGGCGTGGCGGTCGCTGCAGGCGCTG
GGCAACATCGCCTTCGCGTTCGCCTTCTCCAACGTGTACACCGAGATCCAGGACACGATCAAGGCGCCGCCGCCGTCGGA
GGCGAAGGTGATGAAGCAGGCGTCGCTGCTGAGCATCGTGGCGACGTCGGTGTTCTACGCGCTGTGCGGGTGGATGGGCT
ACGCGGCGTTCGGCAACGCGGCGCCGGACAACCTCCTCACCGGATTCGGCTTCTTCGAGCCGTTCTGGCTCGTCGACGCC
GCCAACGTCGCCATCGCCGTGCACCTCATCGGCGCCTACCAGGTGTACTGCCAGCCGGTCTTCGCCTTCGTCGAGCGCAA
GGCGTCGCGCCGGTGGCCCGACAGCGGCTTCGTCAACAGCGAGCTCCGGGTGTGGCCCTTCGCCATCAGCGCGTTCCGGC
TGGCGTGGCGCTCGGTGTTCGTCTGCTTCACCACCGTGGTCGCCATGGCGCTGCCCTTCTTCGGCGTCATCGTCGGCCTC
CTCGGTGCCATCTCCTTCTGGCCGCTCACCGTCTACCTCCCCACGGAGATGTACATCGCGCAGCGCGGCGTGCGGCGCGG
CAGCGCACTGTGGATCGGGCTCAGGGCGCTCGCCGTCGCCGGCTTCGTCGTGTCGGCCGCCGCCACCACGGGCGCCGTCG
CCAACTTCGTCGGCGACTTCATGAAATTCCGTCCCTTCAGTGGATAG

Alignment

ORF - retro_oruf_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.11 %
• Parental protein coverage: 66.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAAELGHTAGSKLYDDDGRLKRTGTMWTASAHIITAVIGSGVLSLGWAIAQLGWVAGPAVMLLFSFVTYY
          V..E.G..A.S.L.DDDGR..RTGT.WTASAHIITAVIGSGVLSL.WA.AQLGWV.GPAVM..F..VTY.
Retrocopy VSLEAGNQADSALLDDDGRPRRTGTFWTASAHIITAVIGSGVLSLPWATAQLGWVGGPAVMVVFGGVTYF

Parental  TSALLADCYRSGDESTGKRNYTYMDAVNANLSGIKVQVCGFLQYANIVGVAIGYTIAASISMLAIKRANC
          T..L.A.CYR.GDE.TG.RNYTY..AV.A.L.G.....CG..QYAN.VG.A.GYTIAASISM.AIKRA.C
Retrocopy TATLQAECYRTGDEETGARNYTYIGAVRAILGGANAKLCGIIQYANLVGTAVGYTIAASISMQAIKRAGC

Parental  FHVEGHGDPCNISSTPYMIIFGVAEIFFSQIPDFDQISWLSILAAVMSFTYSTIGLGLGVVQVVANGGVK
          FH..GH..PC.ISSTPYM.IFG..EI.FSQIPDF..I.WLSI.AAVMSFTYS..GLGLG..Q.VA.GG..
Retrocopy FHANGHNVPCHISSTPYMLIFGAFEIVFSQIPDFHEIWWLSIVAAVMSFTYSGVGLGLGIAQTVADGGFR

Parental  GSLTGISIGVVTPMDKVWRSLQAFGDIAFAYSYSLILIEIQDTIRAPPPSESRVMRRATVVSVAVTTLFY
          G...G.....VT...K.WRSLQA.G.IAFA...S....EIQDTI.APPPSE..VM..A...S...T..FY
Retrocopy GTIAGVT--NVTATQKAWRSLQALGNIAFAFAFSNVYTEIQDTIKAPPPSEAKVMKQASLLSIVATSVFY

Parental  MLCGCTGYAAFGDAAPGNLLTGFGFYEPFWLLDVANAAIVVHLVGAYQVYCQPLFAFVEKWAQQRWPKSW
          .LCG..GYAAFG.AAP.NLLTGFGF.EPFWL.D.AN.AI.VHL.GAYQVYCQP.FAFVE..A..RWP.S.
Retrocopy ALCGWMGYAAFGNAAPDNLLTGFGFFEPFWLVDAANVAIAVHLIGAYQVYCQPVFAFVERKASRRWPDSG

Parental  YITKDIDV-PLSLS
          .......V.P...S
Retrocopy FVNSELRVWPFAIS

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_2 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	ORUFI05G18300	1 retrocopy	retro_oruf_2 ,