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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctattttcacaatcattaagtaaaataaccgtgggtaattcttgttattgattgttgtgtttgttctgcagCTCTTTGTGATTGAAGGAGACTTCATTCACCTTCGGGAAGGAGCACAGCAGATCATTTCAGCTACTACAGCTGCCGCCAAAATTGCCGCTGTTGCATCTT

Basic information

species Oryza sativa
transcript LOC_Os08g43060.3
intron # 13
splice site 3'
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|58678770|gb|CK067457.1|CK067457
EST:     GTGGCTAGCCATCCAGAG                         CTCTTTGTGATTGAAGGAGACTTCATTCACCTTCGGGAAGGAGCCACAGCA
genomic: GTGGCTAGCCATCCAGAGgtctattttc ... tgttctgcagCTCTTTGTGATTGAAGGAGACTTCATTCACCTTCGGGAAGGAG-CACAGCA
EST: gi|58673892|gb|CK062578.1|CK062578
EST:     ATAAGAAGCACTATGGGAAGCTAGATGATTTTGTGGCTAGCCATCCAGAG                         CTCTTTGTGATTGAAGGAGACTTCATTCACCTTCGGGAAGGAGCACAGCAG
genomic: ATAAGAAGCACTATGGGAAGCTAGATGATTTTGTGGCTAGCCATCCAGAGgtctattttc ... tgttctgcagCTCTTTGTGATTGAAGGAGACTTCATTCACCTTCGGGAAGGAGCACAGCAG
EST: gi|58682206|gb|CK070893.1|CK070893
EST:     ATAAGAAGCACTATGGGAAGCTAGATGATTTTGTGGCTAGCCATCCAGAG                         CTCTTTGTGATTGAAGGAGACTTCATTCACCTTCGGGAAGGAGCACAGCAG
genomic: ATAAGAAGCACTATGGGAAGCTAGATGATTTTGTGGCTAGCCATCCAGAGgtctattttc ... tgttctgcagCTCTTTGTGATTGAAGGAGACTTCATTCACCTTCGGGAAGGAGCACAGCAG
EST: gi|38482621|gb|CF966575.1|CF966575
EST:     ATAAGAAGCACTATGGGAAGCTAGATGATTTTGTGGCTAGCCATCCAGAG                         CTCTTTGTGATTGAAGGAGACTTCATTCACCTTCGGGAAGGAGCACAGCAG
genomic: ATAAGAAGCACTATGGGAAGCTAGATGATTTTGTGGCTAGCCATCCAGAGgtctattttc ... tgttctgcagCTCTTTGTGATTGAAGGAGACTTCATTCACCTTCGGGAAGGAGCACAGCAG
EST: gi|29638766|gb|CB643775.1|CB643775
EST:     ATAAGAAGCACTATGGGAAGCTAGATGATTTTGTGGCTAGCCATCCAGAG                         CTCTTTGTGATTGAAGGAGACTTCATTCACCTTCGGGAAGGAGCACAGCAG
genomic: ATAAGAAGCACTATGGGAAGCTAGATGATTTTGTGGCTAGCCATCCAGAGgtctattttc ... tgttctgcagCTCTTTGTGATTGAAGGAGACTTCATTCACCTTCGGGAAGGAGCACAGCAG
EST: gi|29644584|gb|CB649591.1|CB649591
EST:     ATAAGAAGCACTATGGGAAGCTAGATGATTTTGTGGCTAGCCATCCAGAG                         CTCTTTGTGATTGAAGGAGACTTCATTCACCTTCGGGAAGGAGCACAGCAG
genomic: ATAAGAAGCACTATGGGAAGCTAGATGATTTTGTGGCTAGCCATCCAGAGgtctattttc ... tgttctgcagCTCTTTGTGATTGAAGGAGACTTCATTCACCTTCGGGAAGGAGCACAGCAG
EST: gi|66913811|gb|CX100659.1|CX100659
EST:     ATAAGAAGCACTATGGGAAGCTAGATGATTTTGTGGCTAGCCATCCAGAG                         CTCTTTGTGATTGAAGGAGACTTCATTCACCTTCGGGAAGGAGCACAGCAG
genomic: ATAAGAAGCACTATGGGAAGCTAGATGATTTTGTGGCTAGCCATCCAGAGgtctattttc ... tgttctgcagCTCTTTGTGATTGAAGGAGACTTCATTCACCTTCGGGAAGGAGCACAGCAG
EST: gi|86829541|gb|CI286736.1|CI286736
EST:     ATAAGAAGCACTATGGGAAGCTAGATGATTTTGTGGCTAGCCATCCAGAG                         CTCTTTGTGATTGAAGGAGACTTCATTCACCTTCGGGAAGGAGCACAGCAG
genomic: ATAAGAAGCACTATGGGAAGCTAGATGATTTTGTGGCTAGCCATCCAGAGgtctattttc ... tgttctgcagCTCTTTGTGATTGAAGGAGACTTCATTCACCTTCGGGAAGGAGCACAGCAG
EST: gi|58655744|gb|CK044424.1|CK044424
EST:     ATAAGAAGCACTATGGGAAGCTAGATGATTTTGTGGCTAGCCATCCAGAG                         CTCTTTGTGATTGAAGGAGACTTCATTCACCTTCGGGAAGGAGCACAGCAG
genomic: ATAAGAAGCACTATGGGAAGCTAGATGATTTTGTGGCTAGCCATCCAGAGgtctattttc ... tgttctgcagCTCTTTGTGATTGAAGGAGACTTCATTCACCTTCGGGAAGGAGCACAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagtaaaataaccgtgggtaattcttgttattgattgttgtgtttgttctgcagCTCTTTGTGATTGAAGGAGACTTCATTCACCTTCGGGAAGGAGCACAGCAGATCATTTCAGCTACTACAGCTGCCGCCAAAATTGCCGCTGTTGCATCTT
                                           tttgttct  CT-rich tract
                   taattcttgttatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctattttcacaatcattaagtaaaataaccgtgggtaattcttgttattgattgttgtgtttgttctgcagCTCTTTGTGATTGAAGGAGACTTCATTCACCTTCGGGAAGGAGCACAGCAGATCATTTCAGCTACTACAGCTGCCGCCAAAATTGCCGCTGTTGCATCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT