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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttgaaatttattcagactactagtattgtgttgcaggggttttgctgattatgcttatgcatgaacatatcattcggattggactgcactaatctgcagAATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAGACCTGCTGATGATCAACAACAGATCATGGAGCTTCCCGATGAACAGAGT

Basic information

species Oryza sativa
transcript LOC_Os03g01750.6
intron # 13
splice site 3'
intron type U2

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|88690033|gb|CI734112.1|CI734112
EST:     GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAG                         AATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
genomic: GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAGgtaagttgaa ... taatctgcagAATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
EST: gi|29640153|gb|CB645162.1|CB645162
EST:     GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAG                         AATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
genomic: GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAGgtaagttgaa ... taatctgcagAATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
EST: gi|88689968|gb|CI734047.1|CI734047
EST:     GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAG                         AATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
genomic: GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAGgtaagttgaa ... taatctgcagAATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
EST: gi|88505802|gb|CI433308.1|CI433308
EST:     CAGTACGTTGAGCGATAGAG                         AATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
genomic: CAGTACGTTGAGCGATAGAGgtaagttgaa ... taatctgcagAATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
EST: gi|86823806|gb|CI258828.1|CI258828
EST:     GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAG                         AATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
genomic: GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAGgtaagttgaa ... taatctgcagAATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
EST: gi|88688614|gb|CI732190.1|CI732190
EST:     GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAG                         AATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
genomic: GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAGgtaagttgaa ... taatctgcagAATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
EST: gi|87007869|gb|CI296847.1|CI296847
EST:     GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAG                         AATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
genomic: GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAGgtaagttgaa ... taatctgcagAATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
EST: gi|88688572|gb|CI732148.1|CI732148
EST:     GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAG                         AATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
genomic: GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAGgtaagttgaa ... taatctgcagAATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
EST: gi|88689587|gb|CI733163.1|CI733163
EST:     GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAG                         AATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
genomic: GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAGgtaagttgaa ... taatctgcagAATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
EST: gi|88688617|gb|CI732193.1|CI732193
EST:     GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAG                         AATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
genomic: GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAGgtaagttgaa ... taatctgcagAATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
EST: gi|88963923|gb|CI031256.1|CI031256
EST:     GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAG                         AATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
genomic: GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAGgtaagttgaa ... taatctgcagAATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
EST: gi|27549021|gb|CA767031.2|CA767031
EST:     GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAG                         AATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
genomic: GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAGgtaagttgaa ... taatctgcagAATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
EST: gi|88689057|gb|CI732633.1|CI732633
EST:     GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAG                         AATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
genomic: GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAGgtaagttgaa ... taatctgcagAATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
EST: gi|88693785|gb|CI735362.1|CI735362
EST:     GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAG                         AATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG
genomic: GAAAGGCTGATGATTAGAGAGTACTTGGAACAGTACGTTGAGCGATAGAGgtaagttgaa ... taatctgcagAATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgattatgcttatgcatgaacatatcattcggattggactgcactaatctgcagAATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAGACCTGCTGATGATCAACAACAGATCATGGAGCTTCCCGATGAACAGAGT
                                          cactaat  putative branch site (score: 2)
                      atatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttgaaatttattcagactactagtattgtgttgcaggggttttgctgattatgcttatgcatgaacatatcattcggattggactgcactaatctgcagAATTGACATTGGATTATCGACTCGTTTTGGGCTCGCTGTGCAACAGGGAAGACCTGCTGATGATCAACAACAGATCATGGAGCTTCCCGATGAACAGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT