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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTAGTGTCCCTGAAGGAAAGAAGAGGGACAGGAGAAATGACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatgcttttttcatgaatactatctactattgttgttgtagtaggaggcttcaagggctaatgtgggctgtttgtatcag

Basic information

species Oryza sativa
transcript LOC_Os11g01890.1
intron # 5
splice site 5'
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|29662883|gb|CB659158.1|CB659158
EST:     ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAG                         ACCAAAAGGGATGATGCGACCCCTGTGATCCAAAGAGAGGAGTGGGCAAAG
genomic: ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
EST: gi|86839053|gb|CI330414.1|CI330414
EST:     ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAG                         ACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
genomic: ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
EST: gi|88833861|gb|CI077342.1|CI077342
EST:     TGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATCGACAAG                         ACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
genomic: TGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
EST: gi|88834115|gb|CI077596.1|CI077596
EST:     ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATCGACAAG                         ACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
genomic: ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
EST: gi|88465820|gb|CI524770.1|CI524770
EST:     TGGAGGGGAATCATTCAGAATAATTGACAAG                         ACCAAAAGGGATGATGCGACCACTNTGATCCAAAGAGAGGAGTGGGCAAAG
genomic: TGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
EST: gi|86542640|gb|CI182846.1|CI182846
EST:     ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATT-----G                         A-C--AAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
genomic: ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
EST: gi|33653426|gb|CF276040.1|CF276040
EST:     ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAG                         ACCAAAAGGGATGATGCGACCNACTGTGATCCAAAGAGAGGAGTGGGCAAA
genomic: ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACC-ACTGTGATCCAAAGAGAGGAGTGGGCAAA
EST: gi|88224094|gb|CI223943.1|CI223943
EST:     ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAG                         ACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
genomic: ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
EST: gi|87025956|gb|CI257114.1|CI257114
EST:     ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATCGACAAG                         ACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
genomic: ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
EST: gi|86526172|gb|CI166378.1|CI166378
EST:     TCAGAATAATTGACAAG                         ACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
genomic: TCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
EST: gi|88218129|gb|CI217978.1|CI217978
EST:     ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAG                         ACCAAAAGGGATGATGCGACCACTATGATCCAAAGAGAGGAGTGGGCAAAG
genomic: ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
EST: gi|88221121|gb|CI221077.1|CI221077
EST:     CTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAG                         ACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
genomic: CTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
EST: gi|89170131|gb|CI039408.1|CI039408
EST:     ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATCGACAAG                         ACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
genomic: ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
EST: gi|29662875|gb|CB659150.1|CB659150
EST:     ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAG                         ACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
genomic: ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
EST: gi|88256611|gb|CI358999.1|CI358999
EST:     ACTTCCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAG                         ACCCAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
genomic: ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
EST: gi|87025963|gb|CI257121.1|CI257121
EST:     ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATCGACAAG                         ACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
genomic: ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
EST: gi|86896801|gb|CI317335.1|CI317335
EST:     CTTTCTACTCATACGAGATGGAGGGGGAATCATTCAGAATAATTGACAAG                         ACCAAAAGGGATTATGCGACCACTGTGATCCAAAGAGAGGGAGTGGGCAAA
genomic: CTTGCTACTCATACGAGATGGA-GGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGA-GGAGTGGGCAAA
EST: gi|58603685|gb|CK014213.1|CK014213
EST:     ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAG                         ACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
genomic: ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
EST: gi|88228264|gb|CI227744.1|CI227744
EST:     ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATCGACAAG                         ACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGTGTGGGCAAAG
genomic: ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
EST: gi|86436668|gb|CI118390.1|CI118390
EST:     ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAG                         ACCTAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
genomic: ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
EST: gi|86539535|gb|CI179741.1|CI179741
EST:     ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAG                         ACCAAAAGGGATGATGCGACCACTATGATCCAAAGAGAGGAGTGGGCAAAG
genomic: ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
EST: gi|86432201|gb|CI085812.1|CI085812
EST:     ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATCGACAAG                         ACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
genomic: ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
EST: gi|86855486|gb|CI267015.1|CI267015
EST:     ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATCGACAAG                         ACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
genomic: ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
EST: gi|88852689|gb|CI008882.1|CI008882
EST:     ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAG                         ACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG
genomic: ACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAG

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: 71 (upstream exon), 72 (downstream exon)
Score: 18

GTTAGTGTCCCTGAAGGAAAGAAGAGGGACAGGAGAAATGACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatg ... tttgtatcagACCAAAAGGGATGATGCGACCACTGTGATCCAAAGAGAGGAGTGGGCAAAGTCGAGGCAAGATGTGGAGAAGCACTTTAGGAAGCTCCGCGACTTTGACT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTAGTGTCCCTGAAGGAAAGAAGAGGGACAGGAGAAATGACTTGCTACTCATACGAGATGGAGGGGAATCATTCAGAATAATTGACAAGgtactatatgcttttttcatgaatactatctactattgttgttgtagtaggaggcttcaagggctaatgtgggctgtttgtatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG