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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTCTTCTCCGAGACCGAGATGGCACTCGACTCTGTTCCATCCTACCCCAGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatctatggctaccattcttttctcctccatcgatttcttgcttgcagcaaagagcctccccatgtgtatgtgtagttcttgatctgtttctctcctttcttcaatttgtggtgggttctgtgatgtgccattgattctgatatggtagccccag

Basic information

species Oryza sativa
transcript LOC_Os12g02420.2
intron # 1
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|58602862|gb|CK013390.1|CK013390
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|58602862|gb|CK013390.1|CK013390
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|58602862|gb|CK013390.1|CK013390
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|58602862|gb|CK013390.1|CK013390
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|58602862|gb|CK013390.1|CK013390
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|58602862|gb|CK013390.1|CK013390
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|218480411|gb|FG951142.1|FG951142
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         GAAGGAGGAGCGGACATGGACGACCGACACCTACGCGCCGTACGACGACGG
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccagGAAGGAGGAGCGGACATGGACGACCGACACCTACGCGCCGTACGACGACGG
EST: gi|33822052|gb|CF336835.1|CF336835
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|33822052|gb|CF336835.1|CF336835
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|33822052|gb|CF336835.1|CF336835
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|33822052|gb|CF336835.1|CF336835
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|33822052|gb|CF336835.1|CF336835
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|33822052|gb|CF336835.1|CF336835
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|88327524|gb|CI646713.1|CI646713
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|88327524|gb|CI646713.1|CI646713
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|88327524|gb|CI646713.1|CI646713
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|88327524|gb|CI646713.1|CI646713
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|88327524|gb|CI646713.1|CI646713
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|88327524|gb|CI646713.1|CI646713
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|33803500|gb|CF327625.1|CF327625
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|33803500|gb|CF327625.1|CF327625
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|33803500|gb|CF327625.1|CF327625
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|33803500|gb|CF327625.1|CF327625
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|33803500|gb|CF327625.1|CF327625
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|33803500|gb|CF327625.1|CF327625
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|33691269|gb|CF319508.1|CF319508
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         GAAGGAGGAGCGGACATGGACGACCGACACCTACGCGCCGTACGACGACGG
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccagGAAGGAGGAGCGGACATGGACGACCGACACCTACGCGCCGTACGACGACGG
EST: gi|58600345|gb|CK010873.1|CK010873
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|58600345|gb|CK010873.1|CK010873
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|58600345|gb|CK010873.1|CK010873
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|58600345|gb|CK010873.1|CK010873
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|58600345|gb|CK010873.1|CK010873
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|58600345|gb|CK010873.1|CK010873
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|33693069|gb|CF321308.1|CF321308
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|33693069|gb|CF321308.1|CF321308
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|33693069|gb|CF321308.1|CF321308
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|33693069|gb|CF321308.1|CF321308
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|33693069|gb|CF321308.1|CF321308
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-
EST: gi|33693069|gb|CF321308.1|CF321308
EST:     AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAG                         C
genomic: AGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccag-

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: 72 (upstream exon), 63 (downstream exon)
Score: 5

GCTTCTTCTCCGAGACCGAGATGGCACTCGACTCTGTTCCATCCTACCCCAGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatct ... gtagccccagGAAGGAGGAGCGGACATGGACGACCGACACCTACGCGCCGTACGACGACGGCCACCAGTGGAGGAAGTACGGCGAGAAGAAACTCTCCAATTCCAACTTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTCTTCTCCGAGACCGAGATGGCACTCGACTCTGTTCCATCCTACCCCAGCGATCTTGGATCCAGCAGGGCCAGGACGCCGCAGCAGCAAAGGGTCAGgtacatatctatggctaccattcttttctcctccatcgatttcttgcttgcagcaaagagcctccccatgtgtatgtgtagttcttgatctgtttctctcctttcttcaatttgtggtgggttctgtgatgtgccattgattctgatatggtagccccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG