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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactatacttgcttctctcttgcagtggcacttccttccttaatttgttcctctgaatttctcactgaagctcttgttgaacttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT

Basic information

species Oryza sativa
transcript LOC_Os11g01439.1
intron # 1
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|88726871|gb|CI750526.1|CI750526
EST:     AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAG                         ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
genomic: AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAGgtactatact ... acttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
EST: gi|58611460|gb|CK039172.1|CK039172
EST:     AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAG                         ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
genomic: AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAGgtactatact ... acttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
EST: gi|88372838|gb|CI640289.1|CI640289
EST:     AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAG                         ATGGCCAAGCAAGGAAAGGAAAGGATAAAACTCGCTACTCTGAACAT
genomic: AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAGgtactatact ... acttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
EST: gi|88421042|gb|CI566883.1|CI566883
EST:     AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAG                         ATGGCCAAGCAAGGAAAGGAAAGGATAAAACTCGCTAATCTGAACAT
genomic: AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAGgtactatact ... acttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
EST: gi|88452974|gb|CI574521.1|CI574521
EST:     AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAG                         ATGGCCAAGCAAGGAAAGGAAAGGATAAAACTCGCTACTCTGAACAT
genomic: AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAGgtactatact ... acttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
EST: gi|29630414|gb|CB635423.1|CB635423
EST:     AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAG                         ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
genomic: AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAGgtactatact ... acttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
EST: gi|29629416|gb|CB634425.1|CB634425
EST:     AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAG                         ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
genomic: AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAGgtactatact ... acttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
EST: gi|88407871|gb|CI588900.1|CI588900
EST:     AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAG                         ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
genomic: AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAGgtactatact ... acttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
EST: gi|29625751|gb|CB630762.1|CB630762
EST:     AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAG                         ATGGCCAAGCAAGGAAAGGAAAGGATAAAACTCGCTACTCTGAACAT
genomic: AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAGgtactatact ... acttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
EST: gi|29665531|gb|CB661806.1|CB661806
EST:     AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAG                         ATGGCCAAGCAAGGAAAGGAAAGGATAAAACTCGCTACTCTGAACAT
genomic: AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAGgtactatact ... acttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
EST: gi|29632487|gb|CB637496.1|CB637496
EST:     AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAG                         ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
genomic: AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAGgtactatact ... acttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
EST: gi|88404492|gb|CI580928.1|CI580928
EST:     AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAG                         ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
genomic: AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAGgtactatact ... acttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
EST: gi|88386552|gb|CI575330.1|CI575330
EST:     GCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACCAGTGGCAACAGAG                         ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
genomic: GCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAA-CAGTGGCAACAGAGgtactatact ... acttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
EST: gi|88300355|gb|CI584774.1|CI584774
EST:     AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAG                         ATGGCCAAGCAAGGAAAGGAAAGGATAAAACTCGCTACTCTGAACAT
genomic: AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAGgtactatact ... acttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
EST: gi|88387409|gb|CI582927.1|CI582927
EST:     AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAG                         ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
genomic: AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAGgtactatact ... acttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
EST: gi|88401879|gb|CI591206.1|CI591206
EST:     AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAG                         ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
genomic: AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAGgtactatact ... acttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
EST: gi|88311624|gb|CI574841.1|CI574841
EST:     AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAG                         ATGGCCAAGCAAGGAAAGGAAAGGATAAAACTCGCTACTCTGAACAT
genomic: AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAGgtactatact ... acttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
EST: gi|29682182|gb|CB678457.1|CB678457
EST:     AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAG                         ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
genomic: AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAGgtactatact ... acttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
EST: gi|88452934|gb|CI574481.1|CI574481
EST:     AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAG                         ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
genomic: AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAGgtactatact ... acttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
EST: gi|88393142|gb|CI616626.1|CI616626
EST:     AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAG                         ATGGCCAAGCAAGGAAAGGAAAGGATAAAACTCGCTACTCTGAACAT
genomic: AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAGgtactatact ... acttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
EST: gi|58612670|gb|CK040382.1|CK040382
EST:     AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAG                         ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
genomic: AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAGgtactatact ... acttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
EST: gi|88428502|gb|CI564970.1|CI564970
EST:     AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAG                         ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
genomic: AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAGgtactatact ... acttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
EST: gi|702324|gb|D48615.1|D48615
EST:     AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAG                         ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
genomic: AGCCTCCGTCGCAGCTTTAACTCTTAAGAGAGCCAACAGTGGCAACAGAGgtactatact ... acttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccttaatttgttcctctgaatttctcactgaagctcttgttgaacttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT
                       ttctcac  putative branch site (score: 2)
     taatttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactatacttgcttctctcttgcagtggcacttccttccttaatttgttcctctgaatttctcactgaagctcttgttgaacttcaacagATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA