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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCCGCCTTTTTTCTACTCAGTCCCACTACGCCGACCGCCTCGCACAAGCAgtcagtctctctacccccccccatctcaatatactccctccgtttcaaaatgtctgacaccgttgactttttagtatgtgtttgaccattcgtcttattc...

Basic information

species Oryza sativa
transcript LOC_Os02g58590.1
intron # 2
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|58675685|gb|CK064372.1|CK064372
EST:     TCCGCCTTTTTTCTACTCAGTCCCACTACGCCGACCGCCTCGCACAAGCA                         GAAAAATCCGAAAACCAATGCACCAGTCAACTCCGCTCCTTGATCGATCAA
genomic: TCCGCCTTTTTTCTACTCAGTCCCACTACGCCGACCGCCTCGCACAAGCAgtcagtctct ... tgcaatttagGAAAAATCCGAAAACCAATGCACCAGTCAACTCCGCTCCTTGATCGATCAA
EST: gi|33795166|gb|CF323456.1|CF323456
EST:     TCCGCCTTTTTTCTACTCAGTCCCACTACGCCGACCGCCTCGCACAAGCA                         GAAAAATCCGAAAACCAATGCACCAGTCAACTCCGCTCCTTGATCGATCAA
genomic: TCCGCCTTTTTTCTACTCAGTCCCACTACGCCGACCGCCTCGCACAAGCAgtcagtctct ... tgcaatttagGAAAAATCCGAAAACCAATGCACCAGTCAACTCCGCTCCTTGATCGATCAA
EST: gi|29626072|gb|CB631083.1|CB631083
EST:     TCCGCCTTTTTTCTACTCAGTCCCACTACGCCGACCGCCTCGCACAAGCA                         GAAAAATCCGAAAACCAATGCACCAGTCAACTCCGCTCCTTGATCGATCAA
genomic: TCCGCCTTTTTTCTACTCAGTCCCACTACGCCGACCGCCTCGCACAAGCAgtcagtctct ... tgcaatttagGAAAAATCCGAAAACCAATGCACCAGTCAACTCCGCTCCTTGATCGATCAA
EST: gi|117216832|gb|CT845224.1|CT845224
EST:     TCCGCCTTTTTTCTACTCAGTCCCACTACGCCGACCGCCTCGCACAAGCA                         GAAAAATCCGAAAACCAATGCACCAGTCAACTCCGCTCCTTGATCGATCAA
genomic: TCCGCCTTTTTTCTACTCAGTCCCACTACGCCGACCGCCTCGCACAAGCAgtcagtctct ... tgcaatttagGAAAAATCCGAAAACCAATGCACCAGTCAACTCCGCTCCTTGATCGATCAA
EST: gi|58672011|gb|CK060697.1|CK060697
EST:     TCCGCCTTTTTTCTACTCAGTCCCACTACGCCGAACGCCTCGCACAAGCA                         GAAAAATCCGAAAACCAATGCACCAGTCAACTCC
genomic: TCCGCCTTTTTTCTACTCAGTCCCACTACGCCGACCGCCTCGCACAAGCAgtcagtctct ... tgcaatttagGAAAAATCCGAAAACCAATGCACCAGTCAACTCC
EST: gi|29628398|gb|CB633409.1|CB633409
EST:     TCCGCCTTTTTTCTACTCAGTCCCACTACGCCGACCGCCTCGCACAAGCA                         GAAAAATCCGAAAACCAATGCACCAGTCAACTCCGCTCCTTGATCGATCAA
genomic: TCCGCCTTTTTTCTACTCAGTCCCACTACGCCGACCGCCTCGCACAAGCAgtcagtctct ... tgcaatttagGAAAAATCCGAAAACCAATGCACCAGTCAACTCCGCTCCTTGATCGATCAA
EST: gi|29635787|gb|CB640796.1|CB640796
EST:     TCCGCNNNNNNNCTACTCAGTCCCACTACGCCGACCGCCTCGCACAAGCA                         GAAAAATCCGAAAACCAATGCACCAGTCAACTCCGCTCCTTGA
genomic: TCCGCCTTTTTTCTACTCAGTCCCACTACGCCGACCGCCTCGCACAAGCAgtcagtctct ... tgcaatttagGAAAAATCCGAAAACCAATGCACCAGTCAACTCCGCTCCTTGA
EST: gi|58674189|gb|CK062875.1|CK062875
EST:     TCCGCCTTTTTTCTACTCAGTCCCACTACGCCGACCGCCTCGCACAAGCA                         GAAAAATCCGAAAACCAATGCACCAGTCAACTCCGCTCCTTGACTCGATCA
genomic: TCCGCCTTTTTTCTACTCAGTCCCACTACGCCGACCGCCTCGCACAAGCAgtcagtctct ... tgcaatttagGAAAAATCCGAAAACCAATGCACCAGTCAACTCCGCTCCTTGA-TCGATCA
EST: gi|29666803|gb|CB663078.1|CB663078
EST:     TCCGCCTTTTTTCTACTCAGTCCCACTACGCCGACCGCCTCGCACAAGCA                         GAAAAATCCGAAAACCAATGCACCAGTCAACTCCGCTCCTTGATCGATCAA
genomic: TCCGCCTTTTTTCTACTCAGTCCCACTACGCCGACCGCCTCGCACAAGCAgtcagtctct ... tgcaatttagGAAAAATCCGAAAACCAATGCACCAGTCAACTCCGCTCCTTGATCGATCAA
EST: gi|29633686|gb|CB638695.1|CB638695
EST:     TCCGCCTTTTTTCTACTCAGTCCCACTACGCCGACCGCCTCGCACAAGCA                         GAAAAATCCGAAAACCAATGCACCAGTCAACTCCGCTCCTTGATCGATCAA
genomic: TCCGCCTTTTTTCTACTCAGTCCCACTACGCCGACCGCCTCGCACAAGCAgtcagtctct ... tgcaatttagGAAAAATCCGAAAACCAATGCACCAGTCAACTCCGCTCCTTGATCGATCAA
EST: gi|29681006|gb|CB677281.1|CB677281
EST:     GCCTCGCACAAGCC                         TTAAAATCCGAAAACCAATGCACCAGTCAACTCCGCTCCTTGATCGATCAA
genomic: GCCTCGCACAAGCAgtcagtctct ... tgcaatttagGAAAAATCCGAAAACCAATGCACCAGTCAACTCCGCTCCTTGATCGATCAA

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: 74 (upstream exon), 39 (downstream exon)
Score: 38

GTCCGCCTTTTTTCTACTCAGTCCCACTACGCCGACCGCCTCGCACAAGCAgtcagtctct ... tgcaatttagGAAAAATCCGAAAACCAATGCACCAGTCAACTCCGCTCCTTGATCGATCAAGTCAGCTCTCAGCAGGAGAAGATTGTCGCGTTGGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCCGCCTTTTTTCTACTCAGTCCCACTACGCCGACCGCCTCGCACAAGCAgtcagtctctctacccccccccatctcaatatactccctccgtttcaaaatgtctgacaccgttgactttttagtatgtgtttgaccattcgtcttattc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctccg