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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttctcaatcctcttgtttattctgtttttgataatctatatatctattgttttttcacacttaaattgacagCTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAAGAACCGGTGCCACTGGGGGCCTTGGAGGGTTGGGGTCAGCTGATCTGAGCAG

Basic information

species Oryza sativa
transcript LOC_Os10g39620.5
intron # 2
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|58665177|gb|CK053863.1|CK053863
EST:     AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATG                         CTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAAGAA
genomic: AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATGgtatgttctc ... aaattgacagCTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAAGAA
EST: gi|58661978|gb|CK050658.1|CK050658
EST:     AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATG                         CTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAAGAA
genomic: AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATGgtatgttctc ... aaattgacagCTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAAGAA
EST: gi|58681205|gb|CK069892.1|CK069892
EST:     AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATG                         CTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCT
genomic: AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATGgtatgttctc ... aaattgacagCTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCT
EST: gi|58691736|gb|CK080423.1|CK080423
EST:     AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATG                         CTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAAGAA
genomic: AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATGgtatgttctc ... aaattgacagCTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAAGAA
EST: gi|87006797|gb|CI285831.1|CI285831
EST:     AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATG                         CTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAAGAA
genomic: AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATGgtatgttctc ... aaattgacagCTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAAGAA
EST: gi|84117240|gb|CD151007.1|CD151007
EST:     AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATG                         CTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAA
genomic: AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATGgtatgttctc ... aaattgacagCTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAA
EST: gi|33812321|gb|CF332050.1|CF332050
EST:     AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATG                         CTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAAGAA
genomic: AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATGgtatgttctc ... aaattgacagCTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAAGAA
EST: gi|58676841|gb|CK065528.1|CK065528
EST:     AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATG                         CTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAAGAA
genomic: AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATGgtatgttctc ... aaattgacagCTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAAGAA
EST: gi|58597929|gb|CK008457.1|CK008457
EST:     AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATG                         CTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAAGAA
genomic: AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATGgtatgttctc ... aaattgacagCTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAAGAA
EST: gi|58681884|gb|CK070571.1|CK070571
EST:     AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATG                         CTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAAGAA
genomic: AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATGgtatgttctc ... aaattgacagCTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAAGAA
EST: gi|426183|gb|D22043.1|D22043
EST:     AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATG                         CTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAAGAA
genomic: AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATGgtatgttctc ... aaattgacagCTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAAGAA
EST: gi|88388915|gb|CI592803.1|CI592803
EST:     AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATG                         CTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAAGAA
genomic: AACCCCTGCTCCAAACACTAATCCACTTCCAAATCCTTGGAGCTCCAATGgtatgttctc ... aaattgacagCTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattctgtttttgataatctatatatctattgttttttcacacttaaattgacagCTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAAGAACCGGTGCCACTGGGGGCCTTGGAGGGTTGGGGTCAGCTGATCTGAGCAG
        ttttgat  putative branch site (score: 4)
       tttttgataatctata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttctcaatcctcttgtttattctgtttttgataatctatatatctattgttttttcacacttaaattgacagCTGGAGGTGCGCAAGGAGCAACACGGGCAGGTTCTACTGGCAATGCAAGAACCGGTGCCACTGGGGGCCTTGGAGGGTTGGGGTCAGCTGATCTGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG