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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttcacttcagagaatttacagatgtttctacaagtatcctacttaacacaattatactacgaacagctgttcgccagcatagctgatcacgggatacttacctattacaactttgtagttgagttaaccacagaagcaacagtcttacgattgctatacatggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGCAAAGTCCTCATCAGTGATTACTGTAGGAATCCTGGGAAACCATCAGAAG

Basic information

species Oryza sativa
transcript LOC_Os05g47540.4
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g47540.4 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G170400_T03 (Zea mays), 3'ss of exon 6
gtatgtttcacttcagagaatttacagatgtttctacaagtatcctacttaacacaattatactacgaacagctgttcgccagcatagctgatcacgggatacttacctattacaactttgtagttgagttaaccacagaagcaacagtctt-acgattgctatacatggttttac---agGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGCAAAGTCCTCATCAGTGATTACTGTAGGAATCCTGGGAAACCATCAGAAG
                                                                               |||  ||  |        ||    ||    || ||| ||   |  |  ||||| |  || || | | | || | ||   |||    | | ||||||    |||| || |||||| |||||||||| |||||||| ||||| || || || ||||||||||| ||||| || ||||||| ||||||||| |||||||||||||
-----------------------------------------------------------------------------atccaagatgtcgtcctttagg----ttgttgatgacatctgaatgttaaagttagcatcaaaatccatattcctgacagatgccccgctttgttttattatagGACAAGCCTGCTCTGTTCAGAAGCTTCTTCAAATGGCTAAAGCCCGGCGGCAAAGTCCTAATCAGCGACTACTGTAAGAATCCTGGAAAACCATCAGAAG

upper sequence: LOC_Os05g47540.4 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv01s0011g05220.t01 (Vitis vinifera), 3'ss of exon 7
gtatgtttcacttcagagaatttacagatgtttctacaagtatcctacttaacacaattatactacgaacagctgttcgccagcatagctgatcacgggatacttacctattacaactttgtagttgagttaaccacagaagcaacagtcttacgattgctatacatggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGCAAAGTCCTCATCAGTGATTACTGTAGGAATCCTGGGAAACCATCAGAAG
                                                                         || | | ||   |  | | |    |      |   | ||    ||||    |    ||  |  || |  |  |    | |      || |  |     || ||||| |||||||| || || |||  ||||||||||||| |||| ||||| || ||||| || || ||||||||||| |  |   | ||    ||||||   |
----------------------------------------------------------------------gagtgctagtcacggtttcggcttgaagttgcaatgattgtt----ctttcccttctctttttcttcatatcctgccacttgatagaaactgtgaaa---ctttcagGACAAACCTGCATTATTTAGATCTTTCTTCAAGTGGTTGAAGCCTGGAGGAAAAGTTCTAATTAGTGATTACTGCAAAAGATCAGGACCTCCATCACCTG
















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|58602312|gb|CK012840.1|CK012840
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
EST: gi|58597182|gb|CK007710.1|CK007710
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         TATAAACCTGCTT
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTT
EST: gi|29683444|gb|CB679719.1|CB679719
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
EST: gi|58674502|gb|CK063189.1|CK063189
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
EST: gi|58683338|gb|CK072025.1|CK072025
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
EST: gi|29684171|gb|CB680446.1|CB680446
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
EST: gi|38476504|gb|CF960637.1|CF960637
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
EST: gi|163927459|gb|EG709939.1|EG709939
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
EST: gi|58660916|gb|CK049596.1|CK049596
EST:     CAAATACATTTGATGTGGTCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
EST: gi|58680027|gb|CK068714.1|CK068714
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
EST: gi|86593866|gb|CI260095.1|CI260095
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
EST: gi|29687877|gb|CB684152.1|CB684152
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTTGTTC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTC
EST: gi|11544379|gb|BF475197.1|BF475197
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
EST: gi|8335582|gb|BE040460.1|BE040460
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTNTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGNGGGC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
EST: gi|58664248|gb|CK052934.1|CK052934
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
EST: gi|163926647|gb|EG713663.1|EG713663
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
EST: gi|87006597|gb|CI294980.1|CI294980
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
EST: gi|58675947|gb|CK064634.1|CK064634
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
EST: gi|38476652|gb|CF960785.1|CF960785
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
EST: gi|38475834|gb|CF959967.1|CF959967
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCGGGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGG
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACC-TGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGG
EST: gi|58681219|gb|CK069906.1|CK069906
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTNGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
EST: gi|29687878|gb|CB684153.1|CB684153
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
EST: gi|58677395|gb|CK066082.1|CK066082
EST:     AAATACATTTGATGTGATCTACAGCCTGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
genomic: AAATACATTTGATGTGATCTACAGCC-GTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
EST: gi|396941608|gb|HO188265.1|HO188265
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
EST: gi|38475419|gb|CF959552.1|CF959552
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
EST: gi|58672620|gb|CK061306.1|CK061306
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
EST: gi|58682135|gb|CK070822.1|CK070822
EST:     CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACAT                         GATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC
genomic: CAAATACATTTGATGTGATCTACAGCCGTGACACCATTCTTCACATACATgtatgtttca ... ggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttgagttaaccacagaagcaacagtcttacgattgctatacatggttttacagGATAAACCTGCTTTGTTCAGAAGTTTCTTCAAGTGGCTGAAACCTGGGGGCAAAGTCCTCATCAGTGATTACTGTAGGAATCCTGGGAAACCATCAGAAG
                         gtcttac  putative branch site (score: 3)
                                      tatacat  TA-rich tract