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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagccatttcatcacgttcctgatgtttctaggagacttatactactaatatataatatttgtagttgacagttttatgtgcaatgcagtgcttgatgttctcttgtactcttatgccattacgcagGGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG

Basic information

species Oryza sativa
transcript LOC_Os01g16170.1
intron # 2
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|29663778|gb|CB660053.1|CB660053
EST:     AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGG                         GGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
genomic: AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGGgtgagccatt ... cattacgcagGGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
EST: gi|29677835|gb|CB674110.1|CB674110
EST:     AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGG                         GGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
genomic: AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGGgtgagccatt ... cattacgcagGGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
EST: gi|29639705|gb|CB644714.1|CB644714
EST:     AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGG                         GGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
genomic: AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGGgtgagccatt ... cattacgcagGGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
EST: gi|29679456|gb|CB675731.1|CB675731
EST:     AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGG                         GGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
genomic: AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGGgtgagccatt ... cattacgcagGGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
EST: gi|29630352|gb|CB635361.1|CB635361
EST:     AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGG                         GGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
genomic: AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGGgtgagccatt ... cattacgcagGGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
EST: gi|29629095|gb|CB634106.1|CB634106
EST:     AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGG                         GGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
genomic: AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGGgtgagccatt ... cattacgcagGGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
EST: gi|29616200|gb|CB621212.1|CB621212
EST:     AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGG                         GGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
genomic: AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGGgtgagccatt ... cattacgcagGGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
EST: gi|29672767|gb|CB669042.1|CB669042
EST:     AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGG                         GGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
genomic: AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGGgtgagccatt ... cattacgcagGGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
EST: gi|29677585|gb|CB673860.1|CB673860
EST:     AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGG                         GGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
genomic: AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGGgtgagccatt ... cattacgcagGGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
EST: gi|58587497|gb|CF985805.1|CF985805
EST:     AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGG                         GGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
genomic: AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGGgtgagccatt ... cattacgcagGGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
EST: gi|29681319|gb|CB677594.1|CB677594
EST:     AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGG                         GGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
genomic: AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGGgtgagccatt ... cattacgcagGGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
EST: gi|58657684|gb|CK046364.1|CK046364
EST:     AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGG                         GGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
genomic: AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGGgtgagccatt ... cattacgcagGGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
EST: gi|29624849|gb|CB629860.1|CB629860
EST:     AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGA                         GGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
genomic: AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGGgtgagccatt ... cattacgcagGGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
EST: gi|29663859|gb|CB660134.1|CB660134
EST:     AAGTCAACAGAAGGCCTCTCCCTTGCTTTTCTAATGACATGGATTGTTGG                         GGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
genomic: AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGGgtgagccatt ... cattacgcagGGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
EST: gi|29641024|gb|CB646031.1|CB646031
EST:     AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGG                         GGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
genomic: AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGGgtgagccatt ... cattacgcagGGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
EST: gi|29678251|gb|CB674526.1|CB674526
EST:     AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGG                         GGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
genomic: AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGGgtgagccatt ... cattacgcagGGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
EST: gi|29664792|gb|CB661067.1|CB661067
EST:     AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGG                         GGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
genomic: AAGTCAACAGAAGGCCTTTCCCTTGCTTTTCTAATGACATGGATTGTTGGgtgagccatt ... cattacgcagGGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatgtgcaatgcagtgcttgatgttctcttgtactcttatgccattacgcagGGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG
                  gcttgat  putative branch site (score: 5)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagccatttcatcacgttcctgatgtttctaggagacttatactactaatatataatatttgtagttgacagttttatgtgcaatgcagtgcttgatgttctcttgtactcttatgccattacgcagGGACTTTTTTAACCTTATTGGCTGCTTCTTGGAACCTGAGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT