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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAGgtttgtcattatcctggcgatgtagaaactcatttttttcattattagaacattgttattgaagcaatttgaataattgatctacag

Basic information

species Oryza sativa
transcript LOC_Os06g02550.2
intron # 15
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|29638209|gb|CB643218.1|CB643218
EST:     TTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAG                         TTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG
genomic: TTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAGgtttgtcatt ... tgatctacagTTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG
EST: gi|58685705|gb|CK074392.1|CK074392
EST:     TTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAG                         TTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG
genomic: TTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAGgtttgtcatt ... tgatctacagTTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG
EST: gi|88691087|gb|CI735166.1|CI735166
EST:     TTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAG                         TTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG
genomic: TTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAGgtttgtcatt ... tgatctacagTTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG
EST: gi|88691956|gb|CI735531.1|CI735531
EST:     TTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAG                         TTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG
genomic: TTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAGgtttgtcatt ... tgatctacagTTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG
EST: gi|218500572|gb|FG950928.1|FG950928
EST:     TTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAG                         TTGGGGCCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTG
genomic: TTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAGgtttgtcatt ... tgatctacagTTGGGGC-TAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTG
EST: gi|66916087|gb|CX102935.1|CX102935
EST:     TTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAG                         TTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG
genomic: TTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAGgtttgtcatt ... tgatctacagTTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG
EST: gi|58687727|gb|CK076414.1|CK076414
EST:     TTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAG                         TTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG
genomic: TTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAGgtttgtcatt ... tgatctacagTTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG
EST: gi|58593890|gb|CF992198.1|CF992198
EST:     AAAC-GATATGCAGCAACACCACCATCAG                         TTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGTGAGATATTCCGTG
genomic: AAACGGATATGCAGCAACACCACCATCAGgtttgtcatt ... tgatctacagTTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAG-GAGATATTCCGTG
EST: gi|29666198|gb|CB662473.1|CB662473
EST:     ATATGCAGCAACACCACCATCAG                         TTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG
genomic: ATATGCAGCAACACCACCATCAGgtttgtcatt ... tgatctacagTTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG
EST: gi|29626826|gb|CB631837.1|CB631837
EST:     TTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAG                         TTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG
genomic: TTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAGgtttgtcatt ... tgatctacagTTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG
EST: gi|29685601|gb|CB681876.1|CB681876
EST:     TTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAG                         TTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCT
genomic: TTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAGgtttgtcatt ... tgatctacagTTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCT
EST: gi|88689214|gb|CI732790.1|CI732790
EST:     TTCACTTCGATTCAGATCAANAAACGGATATGCAGCAACACCACCATCAG                         TTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG
genomic: TTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAGgtttgtcatt ... tgatctacagTTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG
EST: gi|29626870|gb|CB631881.1|CB631881
EST:     ATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAG                         TTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG
genomic: ATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAGgtttgtcatt ... tgatctacagTTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG
EST: gi|88691942|gb|CI735517.1|CI735517
EST:     TTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAG                         TTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG
genomic: TTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAGgtttgtcatt ... tgatctacagTTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG
EST: gi|88688550|gb|CI732126.1|CI732126
EST:     TTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAG                         TTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG
genomic: TTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAGgtttgtcatt ... tgatctacagTTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGG

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: 70 (upstream exon), 75 (downstream exon)
Score: 104

CCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAGgtttgtcatt ... tgatctacagTTGGGGCTAAAGGAGCTGTGGATCAGAAGAATGCTAGGAGATATTCCGTGGGGCCCTTATCTAATGGGAGACCAGCCGTTAATTACTCATACTTGAGCGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCATGCTTCTACATCCCCCCTTCACTTCGATTCAGATCAACAAACGGATATGCAGCAACACCACCATCAGgtttgtcattatcctggcgatgtagaaactcatttttttcattattagaacattgttattgaagcaatttgaataattgatctacag

- - - - - - - - - - - - - - - -  AGATCA