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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatactgcagcatatagtacatgcatgttattcagcagcgtgcgagtacagagcatgtgtgctccacataataattaagtgtactaattaactaactcttggttcatgttacatgtacgcttgctctgttgacaaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGGCGGCGAGCGACGTCGTGAAGCTCTACAAGTCCAAGGGGATCGACTCCAT

Basic information

species Oryza sativa
transcript LOC_Os01g71350.1
intron # 1
splice site 3'
intron type U2

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|87006151|gb|CI291347.1|CI291347
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88419634|gb|CI686852.1|CI686852
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88591471|gb|CI707508.1|CI707508
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88331193|gb|CI639604.1|CI639604
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88574200|gb|CI665969.1|CI665969
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88578099|gb|CI674731.1|CI674731
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88572328|gb|CI663899.1|CI663899
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88344189|gb|CI654993.1|CI654993
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGNATTTCCTGGAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGNGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88587583|gb|CI705340.1|CI705340
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88740407|gb|CI763915.1|CI763915
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88467129|gb|CI696488.1|CI696488
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88340847|gb|CI637007.1|CI637007
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGNGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|87017752|gb|CI289885.1|CI289885
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88588189|gb|CI705990.1|CI705990
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88338149|gb|CI677141.1|CI677141
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88743521|gb|CI767029.1|CI767029
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88591024|gb|CI707930.1|CI707930
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88763280|gb|CI772741.1|CI772741
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88325259|gb|CI675053.1|CI675053
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88585410|gb|CI703040.1|CI703040
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88313424|gb|CI671538.1|CI671538
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|117223363|gb|CT848626.1|CT848626
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88330997|gb|CI638405.1|CI638405
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88737933|gb|CI761072.1|CI761072
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88738424|gb|CI761932.1|CI761932
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTANGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88335260|gb|CI650225.1|CI650225
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88578006|gb|CI674631.1|CI674631
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88583785|gb|CI701292.1|CI701292
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|86847693|gb|CI288781.1|CI288781
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
EST: gi|88735707|gb|CI759215.1|CI759215
EST:     ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAG                         CGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG
genomic: ATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 70 (upstream exon), 26 (downstream exon)
Score: 3

ACTTGCAGCAGCTGCAAAATAAGCGAAGATGACTACGCAAGGATTTGCTCCCGTGCTTGCAGTAGCATTGCTCCTTGCAGCATTTCCTGCAGgtatactgca ... aaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGGCGGCGAGCGACGTCGTGAAGCTCTACAAGTCCAAGGGGATCGACTCCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taactaactcttggttcatgttacatgtacgcttgctctgttgacaaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGGCGGCGAGCGACGTCGTGAAGCTCTACAAGTCCAAGGGGATCGACTCCAT
                                           acaaattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatactgcagcatatagtacatgcatgttattcagcagcgtgcgagtacagagcatgtgtgctccacataataattaagtgtactaattaactaactcttggttcatgttacatgtacgcttgctctgttgacaaattaacagCGGTTCAGTCCATTGGCGTGTGCTACGGCGTGATCGGCAACAACCTGCCGGCGGCGAGCGACGTCGTGAAGCTCTACAAGTCCAAGGGGATCGACTCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC