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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGGTCGGTCGTCTTGCTGGTGGCTGGAGGGCACGGAGGAGTTGGAGGAGGAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttccttcgctcgatcttgggctttcttgacttgaccctcttttgtgttgccgtggtttcgtgttagggggaagatccaagaggaggaggaggagg...

Basic information

species Oryza sativa
transcript LOC_Os02g05630.1
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|5003494|gb|AU068643.1|AU068643
EST:     CGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: CGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|5803440|gb|AI978410.1|AI978410
EST:     CGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: CGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|29668036|gb|CB664311.1|CB664311
EST:     GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|29639786|gb|CB644795.1|CB644795
EST:     GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|58670044|gb|CK058730.1|CK058730
EST:     GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|29666851|gb|CB663126.1|CB663126
EST:     GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|29688008|gb|CB684283.1|CB684283
EST:     GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|88445125|gb|CI589603.1|CI589603
EST:     GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|33675133|gb|CF303372.1|CF303372
EST:     GCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: GCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|29686520|gb|CB682795.1|CB682795
EST:     GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|44671917|gb|CR285351.1|CR285351
EST:     GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|29640127|gb|CB645136.1|CB645136
EST:     GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
EST: gi|29662047|gb|CB658322.1|CB658322
EST:     GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAG                         TGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC
genomic: GAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGC

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: 64 (upstream exon), 73 (downstream exon)
Score: 41

CGGGTCGGTCGTCTTGCTGGTGGCTGGAGGGCACGGAGGAGTTGGAGGAGGAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttcct ... ctgttgacagTGAAAACGGCAAGTTCAGTTATGGGTATGCAAGTGCTCCTGGGAAAAGGGCTTCAATGGAGGATTTCTACGAGACGAGAATCGATGGTGTTGATGGAGAG




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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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGGTCGGTCGTCTTGCTGGTGGCTGGAGGGCACGGAGGAGTTGGAGGAGGAGATGGGGTTTGCCGGGGACTGCTCGCCGGTCAGCGGTGGCGGGCTCAGgtgcgttccttcgctcgatcttgggctttcttgacttgaccctcttttgtgttgccgtggtttcgtgttagggggaagatccaagaggaggaggaggagg

- - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggggaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaggagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaggag