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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGACGCTGGTCCGGCAGGCCGTCACCAACGCCTTCGCCAACGACTCCGGCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGAgtatgtttcctcttctttctcttttcctttccaagtttagttttagtttttattcaaattaactagatcgtcagagaaagcggaagaagaattccgtggt...

Basic information

species Oryza sativa
transcript LOC_Os01g22336.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g22336.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G107228_T01 (Zea mays), 5'ss of exon 1
CGAGACGCTGGTCCGGCAGGCCGTCACCAACGCCTTCGCCAACGACTCCGGCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGAgtatgtttcctct--tctttctcttttcctttccaagt--ttagttttagtttttattcaaattaactagatcgtcagagaaagcggaagaa-gaattccgtggt
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CGAGTCCCTGGTCCGCCAGGCGGTGGCCAGCGCGTTCGCCAACGACTCCGGCATCGCCGCCGGCCTCATCCGCCTCCTTTTCCACGACTGCTTCGTCAGGgtacgtatacatggatctgtttgggttccttctctgctacttatactaagagcatctccaa--caacgtgacctataaatgctttataattttaaaataagt---
















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|88332745|gb|CI660263.1|CI660263
EST:     GCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGA                         GGTTGCGACGCGTCGGTGCTGCTGACGTCGCCCAACAACACGGCGGAGCGC
genomic: GCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGAgtatgtttcc ... tgggtgtcagGGTTGCGACGCGTCGGTGCTGCTGACGTCGCCCAACAACACGGCGGAGCGC
EST: gi|88589223|gb|CI707084.1|CI707084
EST:     GCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGA                         GGTTGCGACGCGTCGGTGCTGCTGACGTCGCCCAACAACACGGCGGAGCGC
genomic: GCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGAgtatgtttcc ... tgggtgtcagGGTTGCGACGCGTCGGTGCTGCTGACGTCGCCCAACAACACGGCGGAGCGC
EST: gi|88903925|gb|CI711627.1|CI711627
EST:     GCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGA                         GGTTGCGACGCGTCGGTGCTGCTGACGTCGCCCAACAACACGGCGGAGCGC
genomic: GCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGAgtatgtttcc ... tgggtgtcagGGTTGCGACGCGTCGGTGCTGCTGACGTCGCCCAACAACACGGCGGAGCGC
EST: gi|88589604|gb|CI705503.1|CI705503
EST:     GCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGA                         GGTTGCGACGCGTCGGTGCTGCTGACGTCGCCCAACAACACGGCGGAGCGC
genomic: GCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGAgtatgtttcc ... tgggtgtcagGGTTGCGACGCGTCGGTGCTGCTGACGTCGCCCAACAACACGGCGGAGCGC
EST: gi|88314926|gb|CI609985.1|CI609985
EST:     GCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGA                         GGTTGCGACGCGTCGGTGCTGCTGACGTCGCCCAACAACACGGCGGAGCGC
genomic: GCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGAgtatgtttcc ... tgggtgtcagGGTTGCGACGCGTCGGTGCTGCTGACGTCGCCCAACAACACGGCGGAGCGC
EST: gi|88903911|gb|CI711613.1|CI711613
EST:     GCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGA                         GGTTGCGACGCGTCGGTGCTGCTGACGTCGCCCAACAACACGGCGGAGCGC
genomic: GCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGAgtatgtttcc ... tgggtgtcagGGTTGCGACGCGTCGGTGCTGCTGACGTCGCCCAACAACACGGCGGAGCGC
EST: gi|88401143|gb|CI685128.1|CI685128
EST:     GCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGA                         GGTTGCGACGCGTCGGTGCTGCTGACGTCGCCCAACAACACGGCGGAGCGC
genomic: GCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGAgtatgtttcc ... tgggtgtcagGGTTGCGACGCGTCGGTGCTGCTGACGTCGCCCAACAACACGGCGGAGCGC
EST: gi|88592497|gb|CI710603.1|CI710603
EST:     GCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGA                         GGTTGCGACGCGTCGGTGCTGCTGACGTCGCCCAACAACACGGCGGAGCGC
genomic: GCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGAgtatgtttcc ... tgggtgtcagGGTTGCGACGCGTCGGTGCTGCTGACGTCGCCCAACAACACGGCGGAGCGC
EST: gi|88328424|gb|CI676629.1|CI676629
EST:     GCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGA                         GGTTGCGACGCGTCGGTGCTGCTGACGTCGCCCCAACAACACGGCGGAGCG
genomic: GCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGAgtatgtttcc ... tgggtgtcagGGTTGCGACGCGTCGGTGCTGCTGACGTCGCCC-AACAACACGGCGGAGCG
EST: gi|88326758|gb|CI675458.1|CI675458
EST:     GCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGA                         GGTTGCGACGCGTCGGTGCTGCTGACGTCGCCCAACAACACGGCGGAGCGC
genomic: GCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGAgtatgtttcc ... tgggtgtcagGGTTGCGACGCGTCGGTGCTGCTGACGTCGCCCAACAACACGGCGGAGCGC
EST: gi|66915397|gb|CX102245.1|CX102245
EST:     GCATCGCCGCCGGCCTCATACGACTCCATTTCCACGACTGCTTCGTCAGA                         GGTTGCGACGCGTCCGTGCTGCTGACGTCACCCAACAACACGGCGGAGCGC
genomic: GCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGAgtatgtttcc ... tgggtgtcagGGTTGCGACGCGTCGGTGCTGCTGACGTCGCCCAACAACACGGCGGAGCGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAGACGCTGGTCCGGCAGGCCGTCACCAACGCCTTCGCCAACGACTCCGGCATCGCCGCCGGCCTCATCCGCCTCCATTTCCACGACTGCTTCGTCAGAgtatgtttcctcttctttctcttttcctttccaagtttagttttagtttttattcaaattaactagatcgtcagagaaagcggaagaagaattccgtggt

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