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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGATGAAGATACCCTTCAAGATGTCGTAAACTTGGGTTATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaaacaaatgaactgttcatcctttttaatgatcacattgctgattttagaccattttctag

Basic information

species Oryza sativa
transcript LOC_Os03g17980.1
intron # 7
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|58667418|gb|CK056104.1|CK056104
EST:     ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
genomic: ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
EST: gi|58662658|gb|CK051344.1|CK051344
EST:     ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG                         T
genomic: ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctag-
EST: gi|58662658|gb|CK051344.1|CK051344
EST:     ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG                         T
genomic: ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctag-
EST: gi|58666104|gb|CK054790.1|CK054790
EST:     ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
genomic: ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
EST: gi|58674982|gb|CK063669.1|CK063669
EST:     ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
genomic: ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
EST: gi|29673828|gb|CB670103.1|CB670103
EST:     CTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
genomic: CTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
EST: gi|218478287|gb|FG959067.1|FG959067
EST:     ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTGTTGGACAATCGATTCCGAGCTACCAGT
genomic: ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
EST: gi|218482816|gb|FG952976.1|FG952976
EST:     ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTCTTGGACAATCG
genomic: ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCG
EST: gi|29663427|gb|CB659702.1|CB659702
EST:     ATGGAAAGGACCATGTGTGTG-ATCTCTGCGCAATAGACTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
genomic: ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
EST: gi|218482252|gb|FG960526.1|FG960526
EST:     ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTCTTGGACAATCGA
genomic: ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGA
EST: gi|2317303|gb|C22357.1|C22357
EST:     GGAAAGGACCATGTGTGTGAATCTCTGGCGCAATAGACTGCAGAATGGAG                         GCAACTGTTGGCATATTATTTACTCTTGGGACAATCGATTCCGAGCTACC
genomic: GGAAAGGACCATGTGTGTGAATCTCTG-CGCAATAGACTGCAGAATG-AGgtatatgcaa ... cattttctagGCAACTGTTG-CATATTATTTACTCTTGG-ACAATCGATTCCGAGCTACC
EST: gi|218484843|gb|FG952392.1|FG952392
EST:     ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
genomic: ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
EST: gi|29614996|gb|CB620009.1|CB620009
EST:     AAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
genomic: AAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
EST: gi|29672731|gb|CB669006.1|CB669006
EST:     CAATAGACTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
genomic: CAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
EST: gi|29616520|gb|CB621532.1|CB621532
EST:     ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAG                         GCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT
genomic: ATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGT

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), 75 (downstream exon)
Score: 147

ATTGATGAAGATACCCTTCAAGATGTCGTAAACTTGGGTTATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaa ... cattttctagGCAACTGTTGCATATTATTTACTCTTGGACAATCGATTCCGAGCTACCAGTGGCTATTTGGGAGCAGACTATCAAGAATCTTTG




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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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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGATGAAGATACCCTTCAAGATGTCGTAAACTTGGGTTATGGAAAGGACCATGTGTGTGAATCTCTGCGCAATAGACTGCAGAATGAGgtatatgcaaacaaatgaactgttcatcctttttaatgatcacattgctgattttagaccattttctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG