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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctggtataggtgttccatttctattcatccattttatctttatccgagttggaacattttgttgatatttttcttcgtttatttggaatggtggatgaagACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAAT

Basic information

species Oryza sativa
transcript LOC_Os10g37730.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g37730.3 (Oryza sativa), 3'ss of exon 2
lower sequence: AC194389.3_FGT001 (Zea mays), 3'ss of exon 2
------ctggtataggtgttccatttctattcatccattttatctttatccgagttggaacattttgttgatatttttcttcgtttatttggaatggtggatgaagACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAAT
        || |||||  ||  |||| | ||||| | |    | |||||| |  |   || | | |||||||   |   | |  || ||| || || ||||| ||||||||| ||||||| || || |||||||| |||||||||||||| ||||||||||| || || |||||||||
ctgcatgggggataggaattatatttttgttcattc-tacagtttttatctgtatca-aatagtctgttgat---tggttgcaattgttttga-tgatggatcaagACTGCGCTGATGCATGCTTGTCGGCATGGGCACTGGGAGGTGGTGCAGATGCTTCTTCTATTTAGATGCAAT
















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|13420680|gb|AU174770.1|AU174770
EST:     GAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAG                         ACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
genomic: GAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAGgtagatcttt ... gtggatgaagACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
EST: gi|29682101|gb|CB678376.1|CB678376
EST:     TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAG                         ACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
genomic: TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAGgtagatcttt ... gtggatgaagACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
EST: gi|29631918|gb|CB636927.1|CB636927
EST:     TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAG                         ACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCANATG
genomic: TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAGgtagatcttt ... gtggatgaagACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
EST: gi|88385475|gb|CI564135.1|CI564135
EST:     TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAG                         ACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
genomic: TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAGgtagatcttt ... gtggatgaagACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
EST: gi|29645490|gb|CB650497.1|CB650497
EST:     TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAG                         ACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
genomic: TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAGgtagatcttt ... gtggatgaagACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
EST: gi|88299379|gb|CI572331.1|CI572331
EST:     TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAG                         ACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
genomic: TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAGgtagatcttt ... gtggatgaagACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
EST: gi|88314988|gb|CI610047.1|CI610047
EST:     TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAG                         ACTGCGTTGATGCACGCATGCCGGCA
genomic: TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAGgtagatcttt ... gtggatgaagACTGCGTTGATGCACGCATGCCGGCA
EST: gi|29673129|gb|CB669404.1|CB669404
EST:     TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAG                         ACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
genomic: TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAGgtagatcttt ... gtggatgaagACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
EST: gi|29632141|gb|CB637150.1|CB637150
EST:     TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAG                         ACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
genomic: TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAGgtagatcttt ... gtggatgaagACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
EST: gi|88424663|gb|CI606462.1|CI606462
EST:     TGTTGCTGGAGAAGGGCGCGGATGTGAAAGTACGGAACTACTGCGGGCAG                         AATGCGTTGATGCACGCATGCCG
genomic: TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAGgtagatcttt ... gtggatgaagACTGCGTTGATGCACGCATGCCG
EST: gi|29641797|gb|CB646804.1|CB646804
EST:     TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAG                         ACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
genomic: TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAGgtagatcttt ... gtggatgaagACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
EST: gi|88426126|gb|CI574009.1|CI574009
EST:     TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAG                         ACTGCGTTGATGC
genomic: TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAGgtagatcttt ... gtggatgaagACTGCGTTGATGC
EST: gi|29628246|gb|CB633257.1|CB633257
EST:     TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAG                         ACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
genomic: TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAGgtagatcttt ... gtggatgaagACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
EST: gi|29673087|gb|CB669362.1|CB669362
EST:     TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAG                         ACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
genomic: TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAGgtagatcttt ... gtggatgaagACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
EST: gi|29644924|gb|CB649931.1|CB649931
EST:     TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAG                         ACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
genomic: TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAGgtagatcttt ... gtggatgaagACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
EST: gi|29631475|gb|CB636484.1|CB636484
EST:     TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAG                         ACTGCGTTGATGCACGCATGCCGGCAT
genomic: TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAGgtagatcttt ... gtggatgaagACTGCGTTGATGCACGCATGCCGGCAT
EST: gi|29615014|gb|CB620027.1|CB620027
EST:     TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAG                         ACTGCGTTCCTGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG
genomic: TGTTGCTGGAGAAGGGCGCGGATGTGAACGTACGGAACTACTGCGGGCAGgtagatcttt ... gtggatgaagACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagttggaacattttgttgatatttttcttcgtttatttggaatggtggatgaagACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAAT
              tgttgat  putative branch site (score: 4)
          attttgttgatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctggtataggtgttccatttctattcatccattttatctttatccgagttggaacattttgttgatatttttcttcgtttatttggaatggtggatgaagACTGCGTTGATGCACGCATGCCGGCATGGCCACTGGGAGGTGGTTCAGATGCTTCTGCTCTTCAGATGCAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG