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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaagtggttacttcctttttttttttttgagaaacaagaggttacttttggtatccagttaggctgtactgaactagtagcagatggtattaaa...

Basic information

species Oryza sativa
transcript LOC_Os02g09460.1
intron # 4
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|88211486|gb|CI211126.1|CI211126
EST:     GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
genomic: GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
EST: gi|86485004|gb|CI127637.1|CI127637
EST:     TACCAGA-GGCACGATCTGCTCCTTGGAAGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
genomic: TACCAGAGGGC-CGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
EST: gi|88435892|gb|CI514031.1|CI514031
EST:     AGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
genomic: AGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
EST: gi|86528104|gb|CI168310.1|CI168310
EST:     GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
genomic: GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
EST: gi|88547724|gb|CI478044.1|CI478044
EST:     GGAAGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAATTCATCAATGTTTGGGTTGTGCC
genomic: GGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGG-TTGTGCC
EST: gi|88293128|gb|CI512893.1|CI512893
EST:     GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
genomic: GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
EST: gi|9866191|gb|AU101941.1|AU101941
EST:     GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCNATGTTTGGTTGTGCCC
genomic: GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
EST: gi|86595369|gb|CI262607.1|CI262607
EST:     GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
genomic: GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
EST: gi|40493973|gb|BX901795.1|BX901795
EST:     GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
genomic: GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
EST: gi|86414523|gb|CI068926.1|CI068926
EST:     GACCGATCTGCTCCTTGGAAGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTCGGTTGTGCCC
genomic: GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
EST: gi|88259596|gb|CI363889.1|CI363889
EST:     GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
genomic: GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
EST: gi|88216643|gb|CI214743.1|CI214743
EST:     GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
genomic: GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
EST: gi|88244910|gb|CI242761.1|CI242761
EST:     GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
genomic: GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
EST: gi|88979867|gb|CI026167.1|CI026167
EST:     GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
genomic: GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
EST: gi|88239487|gb|CI239964.1|CI239964
EST:     GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
genomic: GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
EST: gi|88214348|gb|CI214197.1|CI214197
EST:     GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
genomic: GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
EST: gi|88526829|gb|CI454918.1|CI454918
EST:     CTGCTCCTTGGAAGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
genomic: CTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
EST: gi|88319148|gb|CI513212.1|CI513212
EST:     CCTTGGAAGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
genomic: CCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
EST: gi|86495983|gb|CI138616.1|CI138616
EST:     GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
genomic: GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
EST: gi|88243875|gb|CI242997.1|CI242997
EST:     GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
genomic: GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
EST: gi|58664625|gb|CK053311.1|CK053311
EST:     ACCAGAGGGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
genomic: ACCAGAGGGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
EST: gi|88543260|gb|CI473251.1|CI473251
EST:     GGCCGATCTGCTCCTTGGGAGCACACTGTAGAAG                         GACCTGATNACATGCCAGCACATATTAAATCATCAATGTTTGGTTTGTGCC
genomic: GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGG-TTGTGCC
EST: gi|86483406|gb|CI126039.1|CI126039
EST:     GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
genomic: GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
EST: gi|86835521|gb|CI347978.1|CI347978
EST:     GGCCGATCTGCTCCTTGGAAACACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGCTTGTGCCC
genomic: GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
EST: gi|88213410|gb|CI213259.1|CI213259
EST:     GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTTTGCCC
genomic: GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
EST: gi|55411794|gb|CV724170.1|CV724170
EST:     GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAG                         GACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC
genomic: GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 34 (upstream exon), 71 (downstream exon)
Score: 77

GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaag ... caaattgcagGACCTGATGACATGCCAGCACATATTAAATCATCAATGTTTGGTTGTGCCCTGAC




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCCGATCTGCTCCTTGGAAGCACACTCTAGAAGgttatttaagtggttacttcctttttttttttttgagaaacaagaggttacttttggtatccagttaggctgtactgaactagtagcagatggtattaaa

- - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaacaa