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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgccacatcatgctactttcgtgcatgccattctactgcttactccatttcaaaataagttaaccttctatgagatgtgatattaacttattttggaggagagtaagtactaggttatccagtggctctatagtctaatcgaaattattttctaatgtaatttgcagATCCTGGATCACGAAGACAACGCCATGATCAGGCCACTCACGCTGCTTCCATGAACAAGACTGCACACTGTACGTGGTGGTTGATGCATGAGGAGATCAA

Basic information

species Oryza sativa
transcript LOC_Os01g03630.1
intron # 1
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|88514142|gb|CI441648.1|CI441648
EST:     CCCTTCGACGCCACGGGCGGCGCCGGGATACGTCTATCACTGCCAC                         ATCCTGGATCACGAAGACAACGCCATGATCAGGCCACTCACGCTGCTTCCA
genomic: CCCTTCGACGCCAC-GGCGGCGCCGGGATACGTCTATCACTGCCACgtaagcgcca ... taatttgcagATCCTGGATCACGAAGACAACGCCATGATCAGGCCACTCACGCTGCTTCCA
EST: gi|88233609|gb|CI233458.1|CI233458
EST:     CCTACCCCTTCGACGCCACGGCGGCGCCGGGATACGTCTATCACTGCCAC                         ATCCTGGATCACGAAGACAACGCCATGATCAGGCCACTCACGCTGCTTCCA
genomic: CCTACCCCTTCGACGCCACGGCGGCGCCGGGATACGTCTATCACTGCCACgtaagcgcca ... taatttgcagATCCTGGATCACGAAGACAACGCCATGATCAGGCCACTCACGCTGCTTCCA
EST: gi|88233560|gb|CI233409.1|CI233409
EST:     CCTACCCCTTCGACGCCACGGCGGCGCCGGGATACGTCTATCACTGCCAC                         ATCCTGGATCACGAAGACAACGCCATGATCAGGCCACTCACGCTGCTTCCA
genomic: CCTACCCCTTCGACGCCACGGCGGCGCCGGGATACGTCTATCACTGCCACgtaagcgcca ... taatttgcagATCCTGGATCACGAAGACAACGCCATGATCAGGCCACTCACGCTGCTTCCA
EST: gi|88234168|gb|CI234017.1|CI234017
EST:     CCTACCCCTTCGACGCCACGGCGGCGCCGGGATACGTCTATCACTGCCAC                         ATCCTGGATCACGAAGACAACGCCATGATCAGGCCACTCACGCTGCTTCCA
genomic: CCTACCCCTTCGACGCCACGGCGGCGCCGGGATACGTCTATCACTGCCACgtaagcgcca ... taatttgcagATCCTGGATCACGAAGACAACGCCATGATCAGGCCACTCACGCTGCTTCCA
EST: gi|89194486|gb|CI116923.1|CI116923
EST:     CCTACCCCTTCGACGCCACGGCGGCGCCGGGATACGTCTATCACTGCCAC                         ATCCTGGATCACGAAGACAACGCCATGATCAGGCCACTCACGCTGCTTCCA
genomic: CCTACCCCTTCGACGCCACGGCGGCGCCGGGATACGTCTATCACTGCCACgtaagcgcca ... taatttgcagATCCTGGATCACGAAGACAACGCCATGATCAGGCCACTCACGCTGCTTCCA
EST: gi|88502233|gb|CI429739.1|CI429739
EST:     CCTACCCCTTGGACGCCACGGCGGCGCCGGGATACGTCTATCACTGCCAC                         ATCCTGGATCACGAAGACAACGCCATGATCAGGCCACTCACGCTGCTTCCA
genomic: CCTACCCCTTCGACGCCACGGCGGCGCCGGGATACGTCTATCACTGCCACgtaagcgcca ... taatttgcagATCCTGGATCACGAAGACAACGCCATGATCAGGCCACTCACGCTGCTTCCA
EST: gi|88235135|gb|CI236337.1|CI236337
EST:     CCTACCCCTTCGACGCCACGGCGGCGCCGGGATACGTCTATCACTGCCAC                         ATCCTGGATCACGAAGACAACGCCATGATCAGGCCACTCACGCTGCTTCCA
genomic: CCTACCCCTTCGACGCCACGGCGGCGCCGGGATACGTCTATCACTGCCACgtaagcgcca ... taatttgcagATCCTGGATCACGAAGACAACGCCATGATCAGGCCACTCACGCTGCTTCCA
EST: gi|88197761|gb|CI197611.1|CI197611
EST:     CCTACCCCTTCGACGCCACGGCGGCGCCGGGATACGTCTATCACTGCCAC                         ATCCTGGATCACGAAGACAACGCCATGATCAGGCCACTCACGCTGCTTCCA
genomic: CCTACCCCTTCGACGCCACGGCGGCGCCGGGATACGTCTATCACTGCCACgtaagcgcca ... taatttgcagATCCTGGATCACGAAGACAACGCCATGATCAGGCCACTCACGCTGCTTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttatccagtggctctatagtctaatcgaaattattttctaatgtaatttgcagATCCTGGATCACGAAGACAACGCCATGATCAGGCCACTCACGCTGCTTCCATGAACAAGACTGCACACTGTACGTGGTGGTTGATGCATGAGGAGATCAA
                                     ttctaat  putative branch site (score: 2)
                       taatcgaaattatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcgccacatcatgctactttcgtgcatgccattctactgcttactccatttcaaaataagttaaccttctatgagatgtgatattaacttattttggaggagagtaagtactaggttatccagtggctctatagtctaatcgaaattattttctaatgtaatttgcagATCCTGGATCACGAAGACAACGCCATGATCAGGCCACTCACGCTGCTTCCATGAACAAGACTGCACACTGTACGTGGTGGTTGATGCATGAGGAGATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA