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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTCCTGCCGCAGGTGAAGGGTTTGCTCCGGCCGGACTTCTCCGTCGCCGCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAGgtgagcgtcctcccccactcccctgctctgtttcccttccccttttgttttgagagagatgattagtgatttatttggcattgggtgaacaactcggcct...

Basic information

species Oryza sativa
transcript LOC_Os01g62420.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62420.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G146206_T02 (Zea mays), 5'ss of exon 3
TGTTCCTGCCGCAGGTGAAGGGTTTGCTCCGGCCGGACTTCTCCGTCGCCGCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAGgtgagcgtc-ctcccccactcc--cctgctctgtttcccttccccttttgttttgagagagatgattagtgatttatttggcattgggtgaacaactcggcct
           ||||| |||||  |||| |||| ||||||| ||||||| |||||||| ||||||||||||||||||||||||||||| |||||||||||||   | || |||     ||    ||||   ||||||            |||       |  | |||  ||  |   |     | ||  ||  |    ||  |
-----------CAGGTCAAGGGGCTGCTGCGGCTGGACTTCGCCGTCGCAGCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttctctcttttgctttgacctgtcatgtttcagcgtggtagaagttcaagcgcatctaattt-tgtctcggtc--tctcggaggagtatagtggtat

upper sequence: LOC_Os01g62420.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G146206_T04 (Zea mays), 5'ss of exon 3
TGTTCCTGCCGCAGGTGAAGGGTTTGCTCCGGCCGGACTTCTCCGTCGCCGCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAGgtgagcgtc-ctcccccactcc--cctgctctgtttcccttccccttttgttttgagagagatgattagtgatttatttggcattgggtgaacaactcggcct
| || |||| |||||| |||||  |||| |||| ||||||| ||||||| |||||||| ||||||||||||||||||||||||||||| |||||||||||||   | || |||     ||    ||||   ||||||            |||       |  | |||  ||  |   |     | ||  ||  |    ||  |
TTTTTCTGCAGCAGGTCAAGGGGCTGCTGCGGCTGGACTTCGCCGTCGCAGCGCAGAACTGCTGGGTGCGCAAGGGCGGCGCCTTCACCGGCGAGATCAGgttttcttctctcttttgctttgacctgtcatgtttcagcgtggtagaagttcaagcgcatctaattt-tgtctcggtc--tctcggaggagtatagtggtat
















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|2312292|gb|C28447.1|C28447
EST:     GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGC-TTCACTGGCGAGATCAG                         TGCCGAGATGTTGGTGA-CCTNCAGGTGCCTTGGGTGATTCTGGGACACTC
genomic: GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAGgtgagcgtcc ... atatttgcagTGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTC
EST: gi|58682138|gb|CK070825.1|CK070825
EST:     GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAG                         TGCCGAGATGTNGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTC
genomic: GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAGgtgagcgtcc ... atatttgcagTGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTC
EST: gi|25800835|gb|CA756796.1|CA756796
EST:     GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAG                         TGCCGAGATGTTGGTGAACCTGC
genomic: GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAGgtgagcgtcc ... atatttgcagTGCCGAGATGTTGGTGAACCTGC
EST: gi|88391559|gb|CI600748.1|CI600748
EST:     GAGCACAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGACATCAG                         TGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTC
genomic: GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAGgtgagcgtcc ... atatttgcagTGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTC
EST: gi|88722774|gb|CI746284.1|CI746284
EST:     GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAG                         TGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACAC
genomic: GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAGgtgagcgtcc ... atatttgcagTGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACAC
EST: gi|33686817|gb|CF315056.1|CF315056
EST:     GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAG                         TGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCCGGGACACTC
genomic: GCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAGgtgagcgtcc ... atatttgcagTGCCGAGATGTTGGTGAACCTGCAGGTGCCTTGGGTGATTCTGGGACACTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTCCTGCCGCAGGTGAAGGGTTTGCTCCGGCCGGACTTCTCCGTCGCCGCGCAGAATTGCTGGGTGCGCAAGGGCGGCGCCTTCACTGGCGAGATCAGgtgagcgtcctcccccactcccctgctctgtttcccttccccttttgttttgagagagatgattagtgatttatttggcattgggtgaacaactcggcct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA