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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGCGCGGCTCTGCGAGGCGGGGTTCTTCACCGATTACGCCAACCCCGCCACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACATgtgagacccccttccttgtctctgaatctcagatttttgggggttgattgcttgaactcacgcctgatgtacgcgcgcggattcagtagtggtaacccca...

Basic information

species Oryza sativa
transcript LOC_Os01g54960.1
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|218492722|gb|FG955669.1|FG955669
EST:     ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACAT                         TGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
genomic: ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACATgtgagacccc ... ttatcttcagTGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
EST: gi|33813299|gb|CF332536.1|CF332536
EST:     ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACAT                         TGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
genomic: ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACATgtgagacccc ... ttatcttcagTGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
EST: gi|88337647|gb|CI632149.1|CI632149
EST:     ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACAT                         TGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
genomic: ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACATgtgagacccc ... ttatcttcagTGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
EST: gi|88345501|gb|CI629762.1|CI629762
EST:     ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACAT                         TGCAGGGCTTCACGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
genomic: ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACATgtgagacccc ... ttatcttcagTGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
EST: gi|218486024|gb|FG960390.1|FG960390
EST:     ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACAT                         TGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
genomic: ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACATgtgagacccc ... ttatcttcagTGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
EST: gi|58588527|gb|CF986835.1|CF986835
EST:     ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACAT                         TGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
genomic: ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACATgtgagacccc ... ttatcttcagTGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
EST: gi|25797852|gb|CA753813.1|CA753813
EST:     ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACAT                         TGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
genomic: ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACATgtgagacccc ... ttatcttcagTGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
EST: gi|66913285|gb|CX100133.1|CX100133
EST:     ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACAT                         TGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
genomic: ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACATgtgagacccc ... ttatcttcagTGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
EST: gi|88581174|gb|CI698148.1|CI698148
EST:     ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACAT                         TGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
genomic: ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACATgtgagacccc ... ttatcttcagTGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
EST: gi|88371819|gb|CI680929.1|CI680929
EST:     ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACAT                         TGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
genomic: ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACATgtgagacccc ... ttatcttcagTGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
EST: gi|88421270|gb|CI569115.1|CI569115
EST:     ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACAT                         TGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCACAATTGCTCA
genomic: ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACATgtgagacccc ... ttatcttcagTGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
EST: gi|58689578|gb|CK078265.1|CK078265
EST:     ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACAT                         TGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
genomic: ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACATgtgagacccc ... ttatcttcagTGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
EST: gi|44674636|gb|CR288070.1|CR288070
EST:     ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACAT                         TGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
genomic: ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACATgtgagacccc ... ttatcttcagTGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
EST: gi|88422118|gb|CI688914.1|CI688914
EST:     ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACAT                         TGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
genomic: ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACATgtgagacccc ... ttatcttcagTGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
EST: gi|33816772|gb|CF334220.1|CF334220
EST:     ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACA-                         T----GGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
genomic: ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACATgtgagacccc ... ttatcttcagTGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
EST: gi|58688025|gb|CK076712.1|CK076712
EST:     ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACAT                         TGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
genomic: ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACATgtgagacccc ... ttatcttcagTGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
EST: gi|88350573|gb|CI630091.1|CI630091
EST:     CTACGCGGATCTGCATCGGCCGGAGCGCGGAGCGGTGCGCCGAGAAACAT                         TGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
genomic: CTACGCGGATCTGCATCGGCCGGAG-GCGGAGCGGTGCGCCGAGAAACATgtgagacccc ... ttatcttcagTGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
EST: gi|88337789|gb|CI632291.1|CI632291
EST:     ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACAT                         TGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGGTCA
genomic: ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACATgtgagacccc ... ttatcttcagTGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
EST: gi|88348488|gb|CI629977.1|CI629977
EST:     ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACAT                         TGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
genomic: ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACATgtgagacccc ... ttatcttcagTGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
EST: gi|218494237|gb|FG952757.1|FG952757
EST:     ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACAT                         TGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
genomic: ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACATgtgagacccc ... ttatcttcagTGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
EST: gi|88766293|gb|CI775383.1|CI775383
EST:     ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACAT                         TGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA
genomic: ACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACATgtgagacccc ... ttatcttcagTGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCA

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: 73 (upstream exon), 63 (downstream exon)
Score: 5

CCGCGCGGCTCTGCGAGGCGGGGTTCTTCACCGATTACGCCAACCCCGCCACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACATgtgagacccc ... ttatcttcagTGCAGGGCTTCAAGTTGCATCATCCAATTTGGGCCGATGCAAAATTGCTCATGTTAAAAGTGGAGATGCTGATGGTTACCCAACGACTGAAGATTTGTCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGCGCGGCTCTGCGAGGCGGGGTTCTTCACCGATTACGCCAACCCCGCCACTACGCGGATCTGCATCGGCCGGAGGCGGAGCGGTGCGCCGAGAAACATgtgagacccccttccttgtctctgaatctcagatttttgggggttgattgcttgaactcacgcctgatgtacgcgcgcggattcagtagtggtaacccca

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