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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACCCTACAGAACAGACTGTCATTGACAACTTCATGGTTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcagaattgttgtggatgttgtgttatgttgtagcgctgcatgacactgcactcatttaatagtgctaactgctatctgactataattttttgaaattcag

Basic information

species Oryza sativa
transcript LOC_Os03g14450.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14450.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S1_527V6.1 (Physcomitrella patens), 5'ss of exon 5
GACCCTACAGAACAGACTGTCATTGACAACTTCATGGTTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgta-----ctgcagaattgttgtggatgttg-tgttatgttgtagcgctgcatgacactgcactcatttaata------gtgctaactgctatctgactataattttttgaaattcag---------------------------------------------------
||||||||||| || ||||  ||||||||||||||||||||  |||| || || ||| | ||||||||||| ||||||||||| |||||      ||   |  ||| |       ||| ||     ||   | |    || ||   |   ||    |||       ||||| |    || ||||| || |    |    |   ||                                                   
GACCCTACAGATCAAACTGGAATTGACAACTTCATGGTTCATGAACTTGACGGTACCCAGAACGAGTGGGGGTGGTGCAAGCAGAAGgtgtcaatctctggccttgctcaaatcattggtgcagaatttgggagactgataacctggaggtctagaaatcagggatgtgcttaggaatagctgacgatcaggaatatgtaacgagcacggcttgtggctctatggtctgacaagtatcttacactgtattatgcag

upper sequence: LOC_Os03g14450.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S1_526V6.1 (Physcomitrella patens), 5'ss of exon 5
GACCCTACAGAACAGACTGTCATTGACAACTTCATGGTTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcagaattgttgtggatgttgtgttatgttgtagcgctgcatgacactgcactcatttaatagtgctaactgctatctgactataattttttgaaattcag-----------------------------------------------
||||| ||| | || ||||  || |||||||||||||||||  |||| || || ||| ||||||||||||| ||||||||||| ||||||    | |  ||   |      ||  |||   |  ||   |   ||      || | || |   || | | | ||  ||| |   || ||     | ||    |                                               
GACCCCACAAACCAAACTGCAATCGACAACTTCATGGTTCACGAACTTGACGGTACCCAAAACGAGTGGGGATGGTGCAAGCAGAAGgtatca-atatctgggcttctcaatgcatta--gtacagaatttggtggag--acattgatctttcaggggttattgaaatcagga-atgatcggcagcaagcatggcgtttggcctcatggtctgactagttccttgtactggattgtgcag

upper sequence: LOC_Os03g14450.1 (Oryza sativa), 5'ss of exon 5
lower sequence: EFJ32861 (Selaginella moellendorffii), 5'ss of exon 5
GACCCTACAGAACAGACTGTCATTGACAACTTCATGGTTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcagaattgttgtggatgttgtgttatgttgtagcgctgcatgacactgcactcatttaatagtgctaactgctatctgactataattttttgaaattcag
|| || || || || ||||  ||||||||||||||||||||  | || ||||||||  ||||| | ||||||||||||||||| |||||| |  | || | |            | | | || | | |||   | |  ||    || |||  | || |||                                 
GATCCGACCGATCAAACTGGTATTGACAACTTCATGGTTCACGAGCTCGATGGAACACAAAACAAATGGGGCTGGTGCAAGCAGAAGgtagtaaaaaacttt------------gcttttttctcgagctcgctcatcctcttttcgtttctttgttctag--------------------------------

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|88426468|gb|CI576710.1|CI576710
EST:     TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAG                         CTTGGTGCTAATGCTA
genomic: TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcaga ... tgaaattcagCTTGGTGCTAATGCTA
EST: gi|58661980|gb|CK050660.1|CK050660
EST:     TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAG                         CTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
genomic: TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcaga ... tgaaattcagCTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
EST: gi|5701699|gb|AU063506.2|AU063506
EST:     TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAG                         CTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
genomic: TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcaga ... tgaaattcagCTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
EST: gi|13895987|gb|AU182323.1|AU182323
EST:     TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAG                         CTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
genomic: TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcaga ... tgaaattcagCTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
EST: gi|117233450|gb|CT848145.1|CT848145
EST:     TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAG                         CTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
genomic: TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcaga ... tgaaattcagCTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
EST: gi|88427267|gb|CI586815.1|CI586815
EST:     TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAG                         CTTGGTGCTAATGCTATCCT
genomic: TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcaga ... tgaaattcagCTTGGTGCTAATGCTATCCT
EST: gi|5607353|gb|AU076025.1|AU076025
EST:     TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAG                         CTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
genomic: TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcaga ... tgaaattcagCTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
EST: gi|27553945|gb|CA997845.1|CA997845
EST:     TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAG                         CTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
genomic: TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcaga ... tgaaattcagCTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
EST: gi|29678593|gb|CB674868.1|CB674868
EST:     TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAG                         CTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
genomic: TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcaga ... tgaaattcagCTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
EST: gi|88443516|gb|CI596983.1|CI596983
EST:     TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAG                         CTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCC
genomic: TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcaga ... tgaaattcagCTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCC
EST: gi|88300608|gb|CI587412.1|CI587412
EST:     TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAG                         CTTGGTGCTAATGCTA
genomic: TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcaga ... tgaaattcagCTTGGTGCTAATGCTA
EST: gi|88393823|gb|CI621318.1|CI621318
EST:     TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAG                         CTTGGTGCTAATGCTA
genomic: TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcaga ... tgaaattcagCTTGGTGCTAATGCTA
EST: gi|58600258|gb|CK010786.1|CK010786
EST:     TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAG                         CTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
genomic: TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcaga ... tgaaattcagCTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
EST: gi|4880550|gb|AU064849.1|AU064849
EST:     TCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAAG                         TTTGGTGCTAATGCTAATCCTGGNTGTCTCACTTGCTCTATGCAAAGCCG
genomic: TCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAA-Ggtactgcaga ... tgaaattcagCTTGGTGCTAATGCTA-TCCTGGCTGTCTCACTTGCTCTATGCAAAGCCG
EST: gi|88421393|gb|CI569238.1|CI569238
EST:     TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAG                         CTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGGCGGA
genomic: TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcaga ... tgaaattcagCTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
EST: gi|88424448|gb|CI608034.1|CI608034
EST:     TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAG                         CTTGGTGCTAATGCTATC
genomic: TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcaga ... tgaaattcagCTTGGTGCTAATGCTATC
EST: gi|88424498|gb|CI608084.1|CI608084
EST:     TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAG                         CTTGGTGCTAATGCTATCCT
genomic: TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcaga ... tgaaattcagCTTGGTGCTAATGCTATCCT
EST: gi|27553947|gb|CA997847.1|CA997847
EST:     TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAG                         CTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
genomic: TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcaga ... tgaaattcagCTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
EST: gi|32947868|gb|BP184440.1|BP184440
EST:     TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAG                         CTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
genomic: TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcaga ... tgaaattcagCTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
EST: gi|58658595|gb|CK047275.1|CK047275
EST:     TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCACGCAAAAG                         CTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
genomic: TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcaga ... tgaaattcagCTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
EST: gi|428929|gb|D25085.1|D25085
EST:     TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAG                         NTTGGTGCTAATGCTATCCTGGCT
genomic: TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcaga ... tgaaattcagCTTGGTGCTAATGCTATCCTGGCT
EST: gi|568321|gb|D39165.1|D39165
EST:     GCAACTTGGATGGAACCCAAAAACGAGTTGGGCTTGGTGCAACGCAAAAG                         CTTGGTGCTAATGCTAATCCTGG
genomic: GCAACT-GGATGGAACC-AAAAACGAGTGGGGCT-GGTGCAA-GCAAAAGgtactgcaga ... tgaaattcagCTTGGTGCTAATGCTA-TCCTGG
EST: gi|88390958|gb|CI592866.1|CI592866
EST:     TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAG                         CTTGGTGCTAATGCT
genomic: TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcaga ... tgaaattcagCTTGGTGCTAATGCT
EST: gi|38565671|gb|CK085124.1|CK085124
EST:     TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAG                         CTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA
genomic: TTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcaga ... tgaaattcagCTTGGTGCTAATGCTATCCTGGCTGTCTCACTTGCTCTATGCAAAGCCGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACCCTACAGAACAGACTGTCATTGACAACTTCATGGTTCAGCAACTGGATGGAACCAAAAACGAGTGGGGCTGGTGCAAGCAAAAGgtactgcagaattgttgtggatgttgtgttatgttgtagcgctgcatgacactgcactcatttaatagtgctaactgctatctgactataattttttgaaattcag

- - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA