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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatacttcagtaattcactgcaattctttacctcattttgatagtcaataaaaatcattgaacatatatataccatttggcag

Basic information

species Oryza sativa
transcript LOC_Os03g02590.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g02590.3 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G029824_T03 (Zea mays), 5'ss of exon 4
AACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatacttcagtaattca----ctgcaattcttta----cctca---ttttgatagtcaataaaaatcattgaacatatatataccatttggcag
|||||||||   || |||||  |||  ||| ||||||| |||||||||||||| ||||| | ||||||||| |||||||||||||  ||||  ||    ||||    || ||  ||  ||    | |||   ||||  ||     | |   | | ||| |   |   | ||| |  ||||
AACAAGGAGGCGACGGACCGCGTTGCCAGGTTATCCCTGTACTGCTGGATGGCTTCTTCTGCCTGTGCAGGTCTAGTTGAGgtatgtatacaacacagtttcagtttcttcacatccatatatgcttcagggttttcctaagtggtgatggt-actgatcgcgtgcctgccactgtgcag
















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|218487592|gb|FG945521.1|FG945521
EST:     TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAG                         CTTGGAGAGCTTAAGAGGCTATC
genomic: TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATC
EST: gi|89187844|gb|CI009828.1|CI009828
EST:     TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAG                         CTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
genomic: TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
EST: gi|88836930|gb|CI008366.1|CI008366
EST:     CTTCAGTCTGTGCAGGGCTAGTTGAG                         CTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
genomic: CTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
EST: gi|218504458|gb|FG953020.1|FG953020
EST:     TAT-CCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAG                         CTTGGAGAGCTTAAGAGGCTATC-AAATCAATGAGGAAGCTGGCGAGAGAG
genomic: TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
EST: gi|33662420|gb|CF293387.1|CF293387
EST:     TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAG                         CTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
genomic: TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
EST: gi|218490956|gb|FG953067.1|FG953067
EST:     TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAG                         CTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
genomic: TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
EST: gi|313084054|gb|HO213837.1|HO213837
EST:     TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAG                         CTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
genomic: TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
EST: gi|89195811|gb|CI007230.1|CI007230
EST:     TGCTGGAT-GCCTCTTCAGTCTGTGCAGGGCTAGTTGAG                         CTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
genomic: TGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
EST: gi|86415722|gb|CI029733.1|CI029733
EST:     CTTCAGTCTGTGCAGGGCTAGTTGAG                         CTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
genomic: CTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
EST: gi|38480632|gb|CF964721.1|CF964721
EST:     TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAG                         CTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
genomic: TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
EST: gi|88981185|gb|CI026937.1|CI026937
EST:     CTTCAGTCTGTGCAGGGCTAGTTGAG                         CTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
genomic: CTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
EST: gi|86852434|gb|CI320359.1|CI320359
EST:     TCAGTCT-TCCAGGGCTAG-TGAG                         C-TGGAGAGC-TAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
genomic: TCAGTCTGTGCAGGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
EST: gi|84117673|gb|CD151440.1|CD151440
EST:     TATCCCTCTACTACTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAG                         CTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGA
genomic: TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGA
EST: gi|88965198|gb|CI009234.1|CI009234
EST:     TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAG                         CTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
genomic: TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
EST: gi|88995411|gb|CI036986.1|CI036986
EST:     TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAG                         CTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
genomic: TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
EST: gi|18386960|gb|BM420158.1|BM420158
EST:     TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAG                         CTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
genomic: TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
EST: gi|29687966|gb|CB684241.1|CB684241
EST:     TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAG                         CTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
genomic: TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
EST: gi|88216352|gb|CI216201.1|CI216201
EST:     TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAG                         CTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
genomic: TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
EST: gi|15858218|gb|BI811030.1|BI811030
EST:     GGGCTA-TTGAG                         CTTGGAGAGCTTAAGAGGCTATC-AAATCAATGAGGAAGCTGGCGAGAGA-
genomic: GGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
EST: gi|11863341|gb|AT003766.1|AT003766
EST:     GGATGGCCTCTNCAGTCTGNGCAGGGCTAGTTGAG                         CTTGGAGAGCTTAAGNGGCTATCAAAATCAATGAGNAAGCTGGCGAGAGAG
genomic: GGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
EST: gi|86829554|gb|CI286745.1|CI286745
EST:     TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAG                         CTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
genomic: TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
EST: gi|88217343|gb|CI217192.1|CI217192
EST:     CTCTTCAGTCTGTGCAGGGCTAGTTGAG                         CTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
genomic: CTCTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
EST: gi|25798400|gb|CA754361.1|CA754361
EST:     TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAG                         CTTGGAGAGCTTAAGAGGCTATCANAATCAATGAGGAAGCTGGCGAGAGAG
genomic: TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
EST: gi|58585983|gb|CF984291.1|CF984291
EST:     TATCCCGGTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAG                         CTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG
genomic: TATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatac ... catttggcagCTTGGAGAGCTTAAGAGGCTATCAAAATCAATGAGGAAGCTGGCGAGAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACAAGGAGCGCACAGACCGGATTGTAAGGATATCCCTCTACTGCTGGATGGCCTCTTCAGTCTGTGCAGGGCTAGTTGAGgtataaatacttcagtaattcactgcaattctttacctcattttgatagtcaataaaaatcattgaacatatatataccatttggcag

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