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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcctctcgatccaatccacctcaaatccccgccgccgctgccgccacctgaaaccatgtgaattttcgtgcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG

Basic information

species Oryza sativa
transcript LOC_Os03g61950.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g61950.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G351160_T01 (Zea mays), 3'ss of exon 1
---------------------------------gtaatcctctcgatccaatcc--acctcaaatccc-cgccgccgctgccgccacctga-aaccatgtgaattttcgtgcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG
                                 |    |  ||||||||  |||    ||  | || | | |  || ||    | |  | | ||||    || ||| ||      |||||||||||||| ||||| | ||| |||||||||||||||||||||||||| |||||||||||||||||||||||| | ||  |  ||||||||||||| |
gtatccatccagctcctcctcctcctcgccgccggcgccgcctcgatcccgtcctggactggagtctcaccctacccctctaacaaagtaacaacctcacgattttgcgatttcgtgcagCGGGCACACTGCGGTTATCATTGGCAAGTCCAAGGTGGTCGTCTTCGGAGGATTCGCCGACAAGCGCTTCCTCGCTGATGTTTCCGTCTACGACGTCG
















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|88389984|gb|CI590497.1|CI590497
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88423266|gb|CI576391.1|CI576391
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88468919|gb|CI696927.1|CI696927
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|117250064|gb|CT843884.1|CT843884
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88593275|gb|CI709438.1|CI709438
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88355627|gb|CI679350.1|CI679350
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88321948|gb|CI673096.1|CI673096
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88443548|gb|CI597015.1|CI597015
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88396872|gb|CI578021.1|CI578021
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88423265|gb|CI576390.1|CI576390
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88406641|gb|CI603835.1|CI603835
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|29686595|gb|CB682870.1|CB682870
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88361530|gb|CI605311.1|CI605311
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88587351|gb|CI705089.1|CI705089
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88352722|gb|CI678743.1|CI678743
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88397430|gb|CI684346.1|CI684346
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88581551|gb|CI698547.1|CI698547
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88585547|gb|CI703189.1|CI703189
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88316019|gb|CI618895.1|CI618895
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccccgccgccgctgccgccacctgaaaccatgtgaattttcgtgcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG
                                            tgcctct  CT-rich tract
                                  tgaatttt  TA-rich tract