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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttcctttgtgtacttgaagccctttattctcccacaagaacacgaacagttaaaatcaaaccattacacggcacttataatctgatactatactagaactgttactgaagttcttttccttctttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAATGTACCAGAGAACGATGTAAAGAGGATGCGTGTGCATTCGTAGGGGCCTG

Basic information

species Oryza sativa
transcript LOC_Os04g35570.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g35570.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G003565_T02 (Zea mays), 3'ss of exon 11
-------------------gtgagttcctttgtgtacttgaagccctttattctcccacaagaacacgaac-agttaaaatcaaac-----cattacacggcacttataatctgatactatactagaactgt-tactgaagttcttttccttctttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAATGTACCAGAGAACGATGTAAAGAGGATGCGTGTGCATTCGTAGGGGCCTG
                   | | ||    |        ||||||   |    ||   ||   | ||| |   ||||| |  || ||     | |   |   |||| | |  | || |  | |  | | | || |  ||||  |  || || | ||   ||| |||| |  ||  |||| | ||||||||||||||||||||| || ||||| || || || |||||||| || ||||||||||| ||||| |||| |  |   |
gtgagttcgatcagttgacgcgcgtgttgtctgaactctgaagcgaatcg--cttaaactgcagcactagttagttacacacacacgcgcgcgtacgagaacactgacagacagagaaaaaagaaaatccgtgtgatgaa--ttcttgccgtgttcgtctgcagGTCCGTAAAGCAGGCGGAGGCACGGCACGAGGCAACGGCGCCGACGCGAACGTGCCGGAGAACGACGTGAAGAGGATGCGCGTGCAGTCGTCGTAGTAGG
















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|88436332|gb|CI519251.1|CI519251
EST:     AAAGATATGCCATTNTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|88958142|gb|CI095661.1|CI095661
EST:     AGGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|88964024|gb|CI032941.1|CI032941
EST:     CGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCCAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: CGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|15856310|gb|BI809122.1|BI809122
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCC-AATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|86415370|gb|CI069773.1|CI069773
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|16754351|gb|BM038730.1|BM038730
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|88248942|gb|CI248791.1|CI248791
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|88961319|gb|CI096706.1|CI096706
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCTAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|88828239|gb|CI000348.1|CI000348
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|89166050|gb|CI103140.1|CI103140
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|89164549|gb|CI101637.1|CI101637
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|88263438|gb|CI367212.1|CI367212
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCAGGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|86540621|gb|CI180827.1|CI180827
EST:     ATCAGAAAGATATGCCATTGTTCCTGATGATAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: ATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|86872164|gb|CI333325.1|CI333325
EST:     AAGTCTGGGTCTCCCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|88907919|gb|CI090515.1|CI090515
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|89169126|gb|CI038633.1|CI038633
EST:     CCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: CCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|88457049|gb|CI529250.1|CI529250
EST:     CATTGTTCCTNATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: CATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|86506853|gb|CI149486.1|CI149486
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|86251782|gb|CI018974.1|CI018974
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|58611154|gb|CK038866.1|CK038866
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAGAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|88967445|gb|CI002565.1|CI002565
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|86892443|gb|CI332348.1|CI332348
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|88987585|gb|CI034496.1|CI034496
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|88955925|gb|CI092213.1|CI092213
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|86484671|gb|CI127304.1|CI127304
EST:     ATCAGAAAGATATGCCATTGTTTCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: ATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|86484298|gb|CI126931.1|CI126931
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|38478796|gb|CF962929.1|CF962929
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|88958358|gb|CI095876.1|CI095876
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|89181199|gb|CI045282.1|CI045282
EST:     AAGTCTGGGTCTCGCCATCAGGAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|88959294|gb|CI092989.1|CI092989
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCTAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|86251095|gb|CI055228.1|CI055228
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|89166860|gb|CI104146.1|CI104146
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|86412988|gb|CI067393.1|CI067393
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAAT
EST: gi|88252026|gb|CI350454.1|CI350454
EST:     AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTNTTCCTGATGAAAAA                         GTTCCAAATTCAGGTGAAGGCACGGCAGCGAGGCAACGGGGCGGACGCAAA
genomic: AAGTCTGGGTCTCGCCATCAGAAAGATATGCCATTGTTCCTGATGAAAAAgtgagttcct ... ttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCA-CGAGGCAACGGGGCGGACGCAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatctgatactatactagaactgttactgaagttcttttccttctttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAATGTACCAGAGAACGATGTAAAGAGGATGCGTGTGCATTCGTAGGGGCCTG
 atctgat  putative branch site (score: 4)
                                ttcttttccttcttta  putative PPT
      atactata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttcctttgtgtacttgaagccctttattctcccacaagaacacgaacagttaaaatcaaaccattacacggcacttataatctgatactatactagaactgttactgaagttcttttccttctttacctgtagGTTCCAAATTCAGGTGAAGGCACGGCACGAGGCAACGGGGCGGACGCAAATGTACCAGAGAACGATGTAAAGAGGATGCGTGTGCATTCGTAGGGGCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG