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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGACAGGACAGGCGGACGCGAGCGTCGTCCTCTTCGTTTCGCTTCTCCTCCTCCTCCTCCGCCTCCGCTCTCGCGAGATCTCCTGATCGACTCGCTCCGgtgagggttctctccctcgcctcgcctccggtagagtaggatcggttgctgcgtgtgcgcgtggtgcggtttggttgggttgtctgtgtggcggcgtcgt...

Basic information

species Oryza sativa
transcript LOC_Os02g47600.1
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|33823829|gb|CF337721.1|CF337721
EST:     CCTTCTCCTCCGCCTCCGCTCTCGCGAGATCTCCTGATCGACTCGCTCCG                         CCATGGCTGGAGAAGCTGATGGAAAAGCCCCACTGGGATCAAGATACCCCC
genomic: CCTCCTCCTCCGCCTCCGCTCTCGCGAGATCTCCTGATCGACTCGCTCCGgtgagggttc ... atttatatagCCATGGCTGGAGAAGCTGATGGAAAAGCCCCACTGGGATCAAGATACCCCC
EST: gi|58600675|gb|CK011203.1|CK011203
EST:     CCTCCTCCTCCGCCTCCGCTCTCGCGAGATCTCCTGATCGACTCGCTCCG                         CCATGGCTGGAGAAGCTGATGGAAAAGCCCCACTGGGATCAAGATACCCCC
genomic: CCTCCTCCTCCGCCTCCGCTCTCGCGAGATCTCCTGATCGACTCGCTCCGgtgagggttc ... atttatatagCCATGGCTGGAGAAGCTGATGGAAAAGCCCCACTGGGATCAAGATACCCCC
EST: gi|163919836|gb|EG714898.1|EG714898
EST:     CCTCCTCCTGGGCCTCCGCTCTCGCGAGATCTCCTGATCGACTCGCTCCG                         CCATGGCTGGAGAAGCTGATGGAAAAGCCCCACTGGGATCAAGATACCCCC
genomic: CCTCCTCCTCCGCCTCCGCTCTCGCGAGATCTCCTGATCGACTCGCTCCGgtgagggttc ... atttatatagCCATGGCTGGAGAAGCTGATGGAAAAGCCCCACTGGGATCAAGATACCCCC
EST: gi|88308785|gb|CI653672.1|CI653672
EST:     CCCCCTCCTCCGCCTCCGCTCTCGCGAGATCTCCTGATCGACTCGCTCCG                         CCATGGCTGGAGAAGCTGATGGAAAAGCCCCACTGGGATCAAGATACCCCC
genomic: CCTCCTCCTCCGCCTCCGCTCTCGCGAGATCTCCTGATCGACTCGCTCCGgtgagggttc ... atttatatagCCATGGCTGGAGAAGCTGATGGAAAAGCCCCACTGGGATCAAGATACCCCC
EST: gi|58667772|gb|CK056458.1|CK056458
EST:     CCTCCTCCTCCG-CTCCG-TCTCGCGAGATCTCCTGATCGACTCGCTCCG                         CCATGGCTTGGAGAAGCTTGATGGAAAAGCCCCACTGGGATCAAGATACCC
genomic: CCTCCTCCTCCGCCTCCGCTCTCGCGAGATCTCCTGATCGACTCGCTCCGgtgagggttc ... atttatatagCCATGGC-TGGAGAAGC-TGATGGAAAAGCCCCACTGGGATCAAGATACCC
EST: gi|58586822|gb|CF985130.1|CF985130
EST:     CCTCCTCCTCCG-CTCCG-TCTCGCGAGATCTCCTGATCGACTCGCTCCG                         CCATGGCTGGAGAAGCTGATGGAAAAGCCCCACTGGGATCAAGATACCCCC
genomic: CCTCCTCCTCCGCCTCCGCTCTCGCGAGATCTCCTGATCGACTCGCTCCGgtgagggttc ... atttatatagCCATGGCTGGAGAAGCTGATGGAAAAGCCCCACTGGGATCAAGATACCCCC
EST: gi|58676589|gb|CK065276.1|CK065276
EST:     CCTCCTCCTCCGGCTCCG-TCTCGCGAGATCTCCTGATCGACTCGCTCCG                         CCATGNGCTGGAGAAGCTTGATGGAAAAGCCCCACTGGGATCAAGATACCC
genomic: CCTCCTCCTCCGCCTCCGCTCTCGCGAGATCTCCTGATCGACTCGCTCCGgtgagggttc ... atttatatagCCATG-GCTGGAGAAGC-TGATGGAAAAGCCCCACTGGGATCAAGATACCC
EST: gi|163929548|gb|EG709315.1|EG709315
EST:     TCTCGCGAGATCTCCTGATCGACTCGCTCCG                         CCATGGCTGGAGAAGCTGATGGAAAAGCCCCACTGGGATCAAGATACCCCC
genomic: TCTCGCGAGATCTCCTGATCGACTCGCTCCGgtgagggttc ... atttatatagCCATGGCTGGAGAAGCTGATGGAAAAGCCCCACTGGGATCAAGATACCCCC

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: 75 (upstream exon), 74 (downstream exon)
Score: 211

TAGACAGGACAGGCGGACGCGAGCGTCGTCCTCTTCGTTTCGCTTCTCCTCCTCCTCCTCCGCCTCCGCTCTCGCGAGATCTCCTGATCGACTCGCTCCGgtgagggttc ... atttatatagCCATGGCTGGAGAAGCTGATGGAAAAGCCCCACTGGGATCAAGATACCCCCCTGCTGCTCTCAACGAGCGCATCCTTTCTTCCATGTCTCAAAAACATGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGACAGGACAGGCGGACGCGAGCGTCGTCCTCTTCGTTTCGCTTCTCCTCCTCCTCCTCCGCCTCCGCTCTCGCGAGATCTCCTGATCGACTCGCTCCGgtgagggttctctccctcgcctcgcctccggtagagtaggatcggttgctgcgtgtgcgcgtggtgcggtttggttgggttgtctgtgtggcggcgtcgt

- - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctcgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgcctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtgcgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcggcg