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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttttggatcaattggcactacttgttgcttgctatctgggggaagggattcaccatagcttgctgacggattgcccttttctattttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATCCAACGACCATGTTGCTGTAAATGAGGATGACGGGGAGAGTTATTTTTTG

Basic information

species Oryza sativa
transcript LOC_Os06g01630.6
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g01630.5 (Oryza sativa), 3'ss of exon 19
lower sequence: AT1G54220.2 (Arabidopsis thaliana), 3'ss of exon 18
gtacgttttggatcaattggcactacttgttgcttgctatc-tgggggaagggattcaccatagcttgctgacggattgcccttttctattttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATCCAACGACCATGTTGCTGTAAATGAGGATGACGGGGAGAGTTATTTTTTG
                   | | | |   |   |    ||| | |    |   ||||| |||   |||  ||    |     | ||||  || ||| ||||||||||||| || |||||| |||| || || ||||| ||||||||||| || |   | ||||| || |||| ||| |  |       | |         
-------------------gtaatccagttcattcatcatcattgattcattcattcatcatca-ttgtagaaatctaatattcttcttcttactg-cagGTGCCATTGGAGCTGAATGGTTGAAAGCATTTAAGGGATACATCGAGAACCCTAAATCTATGTTACTCTAAAAGAGAACCAACCACGCAATGGAAAAAAA

upper sequence: LOC_Os06g01630.5 (Oryza sativa), 3'ss of exon 19
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 19
gtacgttttggatcaattggcactacttgttgcttgctatctgggggaagggattcaccatagcttgc-----tgacggattgcccttttctattttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATCCAACGACCATGTTGCTGTAAATGAGGATGACGGGGAGAGTTATTTTTTG
||| ||      | ||   | |    |  |    ||  |   || |       | ||    |||||       | ||  |    |  |     ||| || |||||||| ||||||||||||||| |||||||||||||   ||| |||||||| |||    | |||||||||||  | |       |       | |    |  
gtaagtagctc-ttaacgagtatgtatattaagatgtgagtaggcgccttcattccaggccagcttttacatttaacacaaacactctcggcctttgcttgcagGTGCAATTGGTGCAGAATGGCTGAAGGCGTTCAAATCCTATATCGAGAACCCAGAATCAATGTTGCTGTAGGTCAAACAACAGCTTCCCATCACACGTCA
















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|88290045|gb|CI547682.1|CI547682
EST:     TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG                         GTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
genomic: TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
EST: gi|25803971|gb|CA759932.1|CA759932
EST:     TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG                         GTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
genomic: TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
EST: gi|29631523|gb|CB636532.1|CB636532
EST:     TGGTTCGTTTATGTCAGCAACATTTAGTTGCGACCACCGGGTCATTGACG                         GTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGTTACATCGAGAATC
genomic: TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
EST: gi|88256589|gb|CI358977.1|CI358977
EST:     TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG                         GTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
genomic: TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
EST: gi|88978612|gb|CI384953.1|CI384953
EST:     TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG                         GTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
genomic: TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
EST: gi|58585940|gb|CF984248.1|CF984248
EST:     TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG                         GTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
genomic: TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
EST: gi|24468761|gb|CA305710.1|CA305710
EST:     TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG                         GTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
genomic: TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
EST: gi|88247217|gb|CI247066.1|CI247066
EST:     TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG                         GTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
genomic: TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
EST: gi|86871900|gb|CI332072.1|CI332072
EST:     TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG                         GTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
genomic: TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
EST: gi|88251940|gb|CI350368.1|CI350368
EST:     TGGTTCGTTTATGTCAGCAACATTGAACTGCGACCACCGGGTCATTGACG                         GTGTCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
genomic: TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
EST: gi|89193198|gb|CI050496.1|CI050496
EST:     TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG                         GTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
genomic: TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
EST: gi|86863330|gb|CI344978.1|CI344978
EST:     GGTTCAGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG                         GTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
genomic: GGTTC-GTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
EST: gi|88222196|gb|CI222152.1|CI222152
EST:     TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG                         GTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
genomic: TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
EST: gi|87030828|gb|CI362042.1|CI362042
EST:     TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG                         GTGCCATTGGTGCAGAATGGATGAAGGCGTT-AAGGGCTACATCGAGAATC
genomic: TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
EST: gi|88257576|gb|CI360162.1|CI360162
EST:     TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG                         GTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
genomic: TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
EST: gi|86839043|gb|CI330409.1|CI330409
EST:     TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG                         GTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
genomic: TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
EST: gi|88222052|gb|CI222008.1|CI222008
EST:     TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG                         GTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
genomic: TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
EST: gi|88449787|gb|CI539162.1|CI539162
EST:     TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG                         GTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
genomic: TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
EST: gi|86862659|gb|CI345654.1|CI345654
EST:     TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG                         GTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
genomic: TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
EST: gi|89198662|gb|CI016747.1|CI016747
EST:     TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG                         GTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
genomic: TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
EST: gi|86825407|gb|CI360045.1|CI360045
EST:     TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG                         GTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
genomic: TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
EST: gi|88416802|gb|CI546081.1|CI546081
EST:     TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG                         GTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
genomic: TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
EST: gi|86835039|gb|CI346519.1|CI346519
EST:     TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACG                         GTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
genomic: TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
EST: gi|88268103|gb|CI378875.1|CI378875
EST:     TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACAGGGTCATTGACG                         GTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC
genomic: TGGTTCGTTTATGTCAGCAACATTGAGCTGCGACCACCGGGTCATTGACGgtacgttttg ... tttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggaagggattcaccatagcttgctgacggattgcccttttctattttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATCCAACGACCATGTTGCTGTAAATGAGGATGACGGGGAGAGTTATTTTTTG
                     tgctgac  putative branch site (score: 2)
                               ttgcccttttctattt  putative PPT
                                     ttttctatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttttggatcaattggcactacttgttgcttgctatctgggggaagggattcaccatagcttgctgacggattgcccttttctattttctggcagGTGCCATTGGTGCAGAATGGATGAAGGCGTTCAAGGGCTACATCGAGAATCCAACGACCATGTTGCTGTAAATGAGGATGACGGGGAGAGTTATTTTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG