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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaatcctttttattttcctctctctttttctcttttattcaacatcaagcggcactgtgcagttggtagcctcaagggctggttattttcaggt...

Basic information

species Oryza sativa
transcript LOC_Os11g03470.4
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g03470.4 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G151977_T01 (Zea mays), 5'ss of exon 11
GTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgta-tgctaatcctttttattttcctctctctttttctcttttattcaacatcaagcggcactgtgcagttggtagcctcaagggctggttattttcaggt
|||||| || |||||| |||| ||||| ||  | ||||| ||||| || ||||| |||||||||||||||||| || ||  | | ||| | ||  | | ||| | |   |||  ||   | |     |  | | | |||     |   | | | ||||       ||||  
GTGCCAGGTAGGCCTTAAAGAGCTCCCAAAGGATTCTGCGCTGGGTAGATTGAGGGGAAGTGACAATGTGgtaatgttacccttctttctattattttttctctcttcatttggttatccctggtttgagattttacagaaaaaaaatt-atgtgctg----ccatcag--
















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|88257730|gb|CI360316.1|CI360316
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|29685332|gb|CB681607.1|CB681607
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|89163490|gb|CI100380.1|CI100380
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|88291219|gb|CI527609.1|CI527609
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|86879665|gb|CI327232.1|CI327232
EST:     AACTCCCG-AAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGGGTATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGG
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGA-GATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGG
EST: gi|88460564|gb|CI532037.1|CI532037
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|86535227|gb|CI175433.1|CI175433
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|88964320|gb|CI045513.1|CI045513
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|86601034|gb|CI356791.1|CI356791
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|88966008|gb|CI006763.1|CI006763
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|89163605|gb|CI100495.1|CI100495
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|86491794|gb|CI134427.1|CI134427
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|86604043|gb|CI114817.1|CI114817
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|86491655|gb|CI134288.1|CI134288
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|88463800|gb|CI527127.1|CI527127
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|86480044|gb|CI122677.1|CI122677
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
EST: gi|89195888|gb|CI007307.1|CI007307
EST:     AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTG                         GTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC
genomic: AACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaat ... tcttgggcagGTGGAGATATACAGCAGATGCTACGAGAGCGCCCCTCTGGTGATTCAGGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCCAAGTGGGCCTTGAAGAACTCCCGAAAAACTCTGCACTGGGAAGGTTGAGAGGAAGTGACAATGTGgtatgctaatcctttttattttcctctctctttttctcttttattcaacatcaagcggcactgtgcagttggtagcctcaagggctggttattttcaggt

- - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctctct