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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctccaaattagtgtctaaaaaacatatttatcactagtcccgaactactgatctttttttttaactatatctgcccactcactgctatgtgaactcagGTTGCTGGACACAAAGACCTTCTGGAGGGAGATCCTTACTTGAGGCAGAGACTGCGTATCCGTGATTCCTACATCACAGCGCTGAATGTTTGCCAAGCTT

Basic information

species Oryza sativa
transcript LOC_Os01g55350.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G110714_T02 (Zea mays), 3'ss of exon 10
--------atctccaaattagtgtctaaaaaacatatttatcactagtcccgaactactgatctttttttttaactatatctgcccactcactgctatgtgaactcagGTTGCTGGACACAAAGACCTTCTGGAGGGAGATCCTTACTTGAGGCAGAGACTGCGTATCCGTGATTCCTACATCACAGCGCTGAATGTTTGCCAAGCTT
        || |   ||  |   |        | | |  |   |  ||    |   |||  | || | | | |   |      |  ||   |||      |   |||||| ||||| ||||| |||||||||||||| || || ||| ||| |||||| ||||| |||||||| || |||| ||| |||||||| |||||||| || |
gtgatgtgatttgtcaaagatcttgctgcgtccgtttggactgcgtgtgtgtagagactattattgtgtgtgagacactgagactgac---ctggcgaaagttttcagGTCGCTGGGCACAAGGACCTTCTGGAGGGCGACCCGTACCTGAAGCAGAGGCTGCGCATCCGTGACTCGTACACCACGGCGCTGAACGTTTGCCAGGCCT

upper sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT3G14940.1 (Arabidopsis thaliana), 3'ss of exon 10
atctccaaattagtgtctaaaaaacatatttatcactagtcccgaactactgatctttttttttaactatatctgcccactcactgctatgtgaactcagGTTGCTGGACACAAAGACCTTCTGGAGGGAGATCCTTACTTGAGGCAGAGACTGCGTATCCGTGATTCCTACATCACAGCGCTGAATGTTTGCCAAGCTT
        || |      ||||||||   |  ||  |  | |  |  |  ||   || || ||  | ||   ||   |   |  || |         |||  ||||||||| ||||||||||| || ||||||||||||||||  ||||||||  |  | ||||| || ||||| ||  | || || ||||||||||| |
------gtataacataacaaaaaacagggtcctc--tgtttcatatttgttgggtttgttcttgcaataacactaaacttgcgttgttg--------cagACTGCTGGACATAAAGACCTTCTTGAAGGAGATCCTTACTTGAAACAGAGACTAAGGCTACGTGACTCTTACATTACGACCCTCAACGTTTGCCAAGCCT

upper sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT1G53310.2 (Arabidopsis thaliana), 3'ss of exon 10
atctccaaattagtgtctaaaaaacatatttatcactagtcccgaactactgatctttttttttaactatatctgcccactcactgctatgtgaactcagGTTGCTGGACACAAAGACCTTCTGGAGGGAGATCCTTACTTGAGGCAGAGACTGCGTATCCGTGATTCCTACATCACAGCGCTGAATGTTTGCCAAGCTT
                   ||||||| |    ||   | | |     |  |  | || || |     | | ||||      |  |||| | ||    |||   |||||||||||||| ||||| || || |||||||||||||  ||||||||| |  | |||||||| ||||| ||| | || ||||| || |||||||
-----------------gtaaaaacagagccttcttgacttctttcttcttattattattgtaaggttttgtctgaatgg-ctttgctgtttg----cagACCGCTGGACACAAAGATCTTCTTGAAGGTGATCCTTACTTGAAACAGAGACTGAGACTTCGTGATTCTTACATTACAACTCTCAATGTCTGTCAAGCTT

upper sequence: LOC_Os01g55350.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 9
atctccaaa---ttagtgtctaaaaaacatatttatcactagtcccgaactactgatctttttttttaactatatctgcccactcactgctatgtgaactcagGTTGCTGGACACAAAGACCTTCTGGAGGGAGATCCTTACTTGAGGCAGAGACTGCGTATCCGTGATTCCTACATCACAGCGCTGAATGTTTGCCAAGCTT
  ||  | |   | ||   || ||     |     |||  ||      |  | ||||   ||   | |  |  | ||      |   | || |||      || ||||||||||||| |||||||| || || ||||| ||||||| ||| ||||| ||  | ||||| |||||||||||| | || ||||| |||||||| |
--ctgaagaatttcagaacctgaattgtttccaactcatgagagtttcaa-aatgatagattgagtaacttccaacttgtttttttttcctctgtattggtagATTGCTGGACACAAGGACCTTCTTGAAGGGGATCCCTACTTGAAGCAAAGACTCCGCCTGCGTGACTCCTACATCACAACCCTAAATGTCTGCCAAGCAT

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|86535214|gb|CI175420.1|CI175420
EST:     GAAGAAACAAAGCAACTTCTTCTACAG                         GTTGCTGGACACAAAGACCTTCTGGAGGGAGATCCTTACTTGAGGCAGAGA
genomic: GAAGAAACAAAGCAACTTCTTCTACAGgtgattttct ... gtgaactcagGTTGCTGGACACAAAGACCTTCTGGAGGGAGATCCTTACTTGAGGCAGAGA
EST: gi|86479975|gb|CI122608.1|CI122608
EST:     GTGCTCGTCTTAGAGCAAACTATGAAGAAACAAAGCAACTTCTTCTACAG                         GTTGCTGGACACAAAGACCTTCTGGAGGGAGATCCTTACTTGAGGCAGAGA
genomic: GTGCTCGTCTTAGAGCAAACTATGAAGAAACAAAGCAACTTCTTCTACAGgtgattttct ... gtgaactcagGTTGCTGGACACAAAGACCTTCTGGAGGGAGATCCTTACTTGAGGCAGAGA
EST: gi|27920888|gb|CB096696.1|CB096696
EST:     GTGCTCGTCTTAGAGCAAACTATGAAGAAACAAAGCAACTTCTTCTACAG                         GTTGCTGGACACAAAGACCTTCTGGAGGGAGATCCTTACTTGAGGCAGAGA
genomic: GTGCTCGTCTTAGAGCAAACTATGAAGAAACAAAGCAACTTCTTCTACAGgtgattttct ... gtgaactcagGTTGCTGGACACAAAGACCTTCTGGAGGGAGATCCTTACTTGAGGCAGAGA
EST: gi|25807072|gb|CA763039.1|CA763039
EST:     GTGCTCGTCTTAGAGCAAACTATGAGGAAACAAAGCAACTTCTTCTACAG                         GTTGCTGGACACAAAGACCTTCTGGAGGGAGATCCTTACTTGAGGCAGAGA
genomic: GTGCTCGTCTTAGAGCAAACTATGAAGAAACAAAGCAACTTCTTCTACAGgtgattttct ... gtgaactcagGTTGCTGGACACAAAGACCTTCTGGAGGGAGATCCTTACTTGAGGCAGAGA
EST: gi|25807073|gb|CA763040.1|CA763040
EST:     GTGCTCGTCTTAGAGCAAACTATGAAGAAACAAAGCAACTTCTTCTACAG                         GTTGCTGGACACAAAGACCTTCTGGAGGGAGATCCTTACTTGAGGCAGAGA
genomic: GTGCTCGTCTTAGAGCAAACTATGAAGAAACAAAGCAACTTCTTCTACAGgtgattttct ... gtgaactcagGTTGCTGGACACAAAGACCTTCTGGAGGGAGATCCTTACTTGAGGCAGAGA
EST: gi|87032721|gb|CI270356.1|CI270356
EST:     GTGCTCGTCTTAGAGCAAACTATGAAGAAACAAAGCAACTTCTTCTACAG                         GTTGCTGGACACAAAGACCTTCTGGAGGGAGATCCTTACTTGAGGCAGAGA
genomic: GTGCTCGTCTTAGAGCAAACTATGAAGAAACAAAGCAACTTCTTCTACAGgtgattttct ... gtgaactcagGTTGCTGGACACAAAGACCTTCTGGAGGGAGATCCTTACTTGAGGCAGAGA
EST: gi|88217700|gb|CI217549.1|CI217549
EST:     AGAGCTAACTATGAAGAAACAAAGCAACTTCTTCTACAG                         GTTGCTGGACACAAAGACCTTCTGGAGGGAGATCCTTACTTGAGGCAGAGA
genomic: AGAGCAAACTATGAAGAAACAAAGCAACTTCTTCTACAGgtgattttct ... gtgaactcagGTTGCTGGACACAAAGACCTTCTGGAGGGAGATCCTTACTTGAGGCAGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actactgatctttttttttaactatatctgcccactcactgctatgtgaactcagGTTGCTGGACACAAAGACCTTCTGGAGGGAGATCCTTACTTGAGGCAGAGACTGCGTATCCGTGATTCCTACATCACAGCGCTGAATGTTTGCCAAGCTT
                                cactcac  putative branch site (score: 2)
     tgatctttttttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctccaaattagtgtctaaaaaacatatttatcactagtcccgaactactgatctttttttttaactatatctgcccactcactgctatgtgaactcagGTTGCTGGACACAAAGACCTTCTGGAGGGAGATCCTTACTTGAGGCAGAGACTGCGTATCCGTGATTCCTACATCACAGCGCTGAATGTTTGCCAAGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - -taaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cactgct