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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatacctttgtagtatttcgttttagttaggtttctatttttgatttatccttttctttaatgtgctatcctgtttctttaacaagaaactcacttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTTAATCTCTTTCGAGAAGTCCCATCGGCATCATTTTCTTCAGTTAACAAAA

Basic information

species Oryza sativa
transcript LOC_Os08g06110.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g06110.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G474769_T02 (Zea mays), 3'ss of exon 2
gtacatacctttgtagtatttcgttttagttaggtttctatttttgatttatccttttcttta-atgtgctatcctgtttctttaacaagaaactcacttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTTAATCTCTTTCGAGAAGTCCCATCGGCATCATTTTCTTCAGTTAACAAAA
            ||| | || | |  || || | ||||        |  | |  |  ||| || | ||    |    || ||||||    ||||||| || ||| |||||| ||||||| |||||| | |||| ||||| ||||||||| ||||||||||||||||| || || | ||||||  ||||||||||||||||||||||||
------------gtaattttccctggtattttgctttcctaggaatacatgttatcctctgtataagtatctttaatttcctttaattgtaaactcatttgcatccagAAATTTCAAAGGAAGGAGTTGTCTGGAAAAGAAAGTTGCTCGGAAGTTCTTAATCTCTTCCGTGATGCCCCATCTCCATCATTTTCTTCAGTTAACAAAA

upper sequence: LOC_Os08g06110.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G014902_T01 (Zea mays), 3'ss of exon 9
gtacatacctttgtagtatttcgttttagttaggtttctatttttgatttatccttttctttaatgtgctatcctgtttctttaacaagaaactcacttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTTAATCTCTTTCGAGAAGTCCCATCGGCATCATTTTCTTCAGTTAACAAAA
||| ||  ||   | ||| || | |||  |  |     | ||        ||||| |   | | | |  |   ||  |||||| |     ||||||||| ||| |||||  ||||||| |||||| | ||||||||||||||| |||| ||||||||||||||||| || || | |||||| |||||||||||||||||||||||||
gtaaat-tctacctggtactttgctttcctaggacacatgtt--------atcctctgtataagtatctttaact--ttcttttattcttaactcacttgcatccagAATTTTCAAAGGAAGGAGTTGTCTGAAAAAGGAAGTCGCTCGGAAGTTCTTAATCTCTTCCGTGATGCCCCATCTGCATCATTTTCTTCAGTTAACAAAA
















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|29613821|gb|CB618834.1|CB618834
EST:     ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
genomic: ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
EST: gi|29674993|gb|CB671268.1|CB671268
EST:     ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
genomic: ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
EST: gi|13904796|gb|BF889434.1|BF889434
EST:     ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
genomic: ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
EST: gi|29629255|gb|CB634266.1|CB634266
EST:     ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAATTTGCTCCGAAGTTCTT
genomic: ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
EST: gi|58663892|gb|CK052578.1|CK052578
EST:     ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
genomic: ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
EST: gi|29676888|gb|CB673163.1|CB673163
EST:     ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
genomic: ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
EST: gi|29622092|gb|CB627103.1|CB627103
EST:     ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
genomic: ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
EST: gi|29624811|gb|CB629822.1|CB629822
EST:     ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
genomic: ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
EST: gi|29623819|gb|CB628830.1|CB628830
EST:     ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
genomic: ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
EST: gi|88307208|gb|CI640647.1|CI640647
EST:     ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
genomic: ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
EST: gi|14713755|gb|AU197723.1|AU197723
EST:     ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
genomic: ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
EST: gi|58672987|gb|CK061673.1|CK061673
EST:     ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
genomic: ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
EST: gi|29637151|gb|CB642160.1|CB642160
EST:     ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
genomic: ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
EST: gi|29612984|gb|CB617997.1|CB617997
EST:     ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
genomic: ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
EST: gi|29613167|gb|CB618180.1|CB618180
EST:     ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
genomic: ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
EST: gi|58663489|gb|CK052175.1|CK052175
EST:     ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
genomic: ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
EST: gi|29615308|gb|CB620320.1|CB620320
EST:     ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
genomic: ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
EST: gi|58604509|gb|CK015037.1|CK015037
EST:     GCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
genomic: GCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
EST: gi|58605207|gb|CK033240.1|CK033240
EST:     ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTG
genomic: ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTG
EST: gi|58669379|gb|CK058065.1|CK058065
EST:     ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
genomic: ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
EST: gi|29630692|gb|CB635701.1|CB635701
EST:     ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
genomic: ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
EST: gi|29613863|gb|CB618876.1|CB618876
EST:     ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
genomic: ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
EST: gi|29677549|gb|CB673824.1|CB673824
EST:     CACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
genomic: CACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
EST: gi|29677851|gb|CB674126.1|CB674126
EST:     ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
genomic: ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
EST: gi|29628510|gb|CB633521.1|CB633521
EST:     ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAG                         AAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT
genomic: ATATGACGAACAATAGCACTGCACAAATGGCAGGTGATGCAGCTCTTGAGgtacatacct ... ttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttttctttaatgtgctatcctgtttctttaacaagaaactcacttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTTAATCTCTTTCGAGAAGTCCCATCGGCATCATTTTCTTCAGTTAACAAAA
                                          cacttac  putative branch site (score: 2)
                                        ctcactt  CT-rich tract
                        tttctttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatacctttgtagtatttcgttttagttaggtttctatttttgatttatccttttctttaatgtgctatcctgtttctttaacaagaaactcacttacattcagAAACTTCAAAGAAAGGAGATATCTGAAAAAGGAAGTTGCTCCGAAGTTCTTAATCTCTTTCGAGAAGTCCCATCGGCATCATTTTCTTCAGTTAACAAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT