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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccaaaaaaactgtaactgttctgaacacgtaagtgaatgtcattctctactagctcaaaacttgtgagtttaactgttcttttcaattgctgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATCAATTCAGCTCTTTCAGATGATGACGACATGCTCTCCGAGATCGAGAGCC

Basic information

species Oryza sativa
transcript LOC_Os11g01439.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01439.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G062738_T01 (Zea mays), 3'ss of exon 2
--ccaaaaaaactgtaactgttctgaacacg-taagtgaatgtcattctctactagctcaaaacttgtgagtttaactgttcttttcaattgctgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATCAATTCAGCTCTTTCA---------GATGATGACGACATGCTCTCCGAGATCGAGAGCC
      | |   | |  | ||||  |    | |||  |||  |  |  | || |||       | | ||  |   |||   || | ||| ||||||  | |||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| |  ||          || || || || ||||| |||||||         
gtatgtacatcttatgtcagttcaaagtttgctaaaagaaaattgtgttgtattagt----ggcctatg--tcatacttacctctccaactgctgt--tacagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATCAACTCAGCCCGCTCGCTAGGCGATGACGACGATGATATGCTTTCCGAGA---------
















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:     ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
genomic: ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACATgtaagtgcat ... tgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
EST: gi|58611460|gb|CK039172.1|CK039172
EST:     ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
genomic: ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACATgtaagtgcat ... tgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
EST: gi|88372838|gb|CI640289.1|CI640289
EST:     ATGGCCAAGCAAGGAAAGGAAAGGATAAAACTCGCTACTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
genomic: ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACATgtaagtgcat ... tgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
EST: gi|88421042|gb|CI566883.1|CI566883
EST:     ATGGCCAAGCAAGGAAAGGAAAGGATAAAACTCGCTAATCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAAT
genomic: ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACATgtaagtgcat ... tgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAAT
EST: gi|88452974|gb|CI574521.1|CI574521
EST:     ATGGCCAAGCAAGGAAAGGAAAGGATAAAACTCGCTACTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
genomic: ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACATgtaagtgcat ... tgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
EST: gi|29630414|gb|CB635423.1|CB635423
EST:     ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
genomic: ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACATgtaagtgcat ... tgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
EST: gi|29629416|gb|CB634425.1|CB634425
EST:     ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
genomic: ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACATgtaagtgcat ... tgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
EST: gi|88407871|gb|CI588900.1|CI588900
EST:     ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGGGGCATAATC
genomic: ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACATgtaagtgcat ... tgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
EST: gi|29625751|gb|CB630762.1|CB630762
EST:     ATGGCCAAGCAAGGAAAGGAAAGGATAAAACTCGCTACTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
genomic: ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACATgtaagtgcat ... tgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
EST: gi|29665531|gb|CB661806.1|CB661806
EST:     ATGGCCAAGCAAGGAAAGGAAAGGATAAAACTCGCTACTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
genomic: ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACATgtaagtgcat ... tgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
EST: gi|29632487|gb|CB637496.1|CB637496
EST:     ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
genomic: ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACATgtaagtgcat ... tgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
EST: gi|88404492|gb|CI580928.1|CI580928
EST:     ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
genomic: ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACATgtaagtgcat ... tgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
EST: gi|88386552|gb|CI575330.1|CI575330
EST:     ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
genomic: ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACATgtaagtgcat ... tgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
EST: gi|88300355|gb|CI584774.1|CI584774
EST:     ATGGCCAAGCAAGGAAAGGAAAGGATAAAACTCGCTACTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
genomic: ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACATgtaagtgcat ... tgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
EST: gi|88387409|gb|CI582927.1|CI582927
EST:     ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
genomic: ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACATgtaagtgcat ... tgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
EST: gi|88401879|gb|CI591206.1|CI591206
EST:     ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
genomic: ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACATgtaagtgcat ... tgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
EST: gi|88311624|gb|CI574841.1|CI574841
EST:     ATGGCCAAGCAAGGAAAGGAAAGGATAAAACTCGCTACTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
genomic: ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACATgtaagtgcat ... tgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
EST: gi|29682182|gb|CB678457.1|CB678457
EST:     ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
genomic: ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACATgtaagtgcat ... tgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
EST: gi|88452934|gb|CI574481.1|CI574481
EST:     ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
genomic: ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACATgtaagtgcat ... tgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
EST: gi|88393142|gb|CI616626.1|CI616626
EST:     ATGGCCAAGCAAGGAAAGGAAAGGATAAAACTCGCTACTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCCGGCATAAT
genomic: ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACATgtaagtgcat ... tgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGC-GGCATAAT
EST: gi|58612670|gb|CK040382.1|CK040382
EST:     ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
genomic: ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACATgtaagtgcat ... tgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
EST: gi|88428502|gb|CI564970.1|CI564970
EST:     ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
genomic: ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACATgtaagtgcat ... tgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
EST: gi|702324|gb|D48615.1|D48615
EST:     ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACAT                         GGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC
genomic: ATGGCCAAGCAAGGAAAGGAAAAGACAAAACTCGCTACTCTGAACATgtaagtgcat ... tgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctactagctcaaaacttgtgagtttaactgttcttttcaattgctgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATCAATTCAGCTCTTTCAGATGATGACGACATGCTCTCCGAGATCGAGAGCC
                      gtttaac  putative branch site (score: 3)
                                  ttttcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaaaaaaactgtaactgttctgaacacgtaagtgaatgtcattctctactagctcaaaacttgtgagtttaactgttcttttcaattgctgtggttcagGGGGAGAAAGAAGAAGAGAAGGAAGAGGTTAAAACAATCAGCGGCATAATCAATTCAGCTCTTTCAGATGATGACGACATGCTCTCCGAGATCGAGAGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC