Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGACAATGAGGAATTCTTCACTTCATATGATGAAGTTTTTGAGAGTTTTGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaaagtcttatcccttttccattgtttcaacaacacatattttggtgatgttacaaatccctgtactttgatgtgtag

Basic information

species Oryza sativa
transcript LOC_Os02g05330.1
intron # 3
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|88743061|gb|CI766569.1|CI766569
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTG
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTG
EST: gi|88728620|gb|CI752130.1|CI752130
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTT
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTT
EST: gi|29642250|gb|CB647257.1|CB647257
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|29666181|gb|CB662456.1|CB662456
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|88360157|gb|CI610271.1|CI610271
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|33685122|gb|CF313361.1|CF313361
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGGATTGTTCCCTTCTGC
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGG-ATTGTTCCCTTCTGC
EST: gi|29642449|gb|CB647456.1|CB647456
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|86894710|gb|CI308357.1|CI308357
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCGTCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|58672128|gb|CK060814.1|CK060814
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|55410405|gb|CV722781.1|CV722781
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|88402741|gb|CI613189.1|CI613189
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTG
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTG
EST: gi|58607105|gb|CK035138.1|CK035138
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|33655674|gb|CF278288.1|CF278288
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|58673254|gb|CK061940.1|CK061940
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|29666180|gb|CB662455.1|CB662455
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|58693161|gb|CK081848.1|CK081848
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|58692381|gb|CK081068.1|CK081068
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|88738783|gb|CI762291.1|CI762291
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATC
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATC
EST: gi|58600294|gb|CK010822.1|CK010822
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|58609408|gb|CK037441.1|CK037441
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|58668040|gb|CK056726.1|CK056726
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|58685951|gb|CK074638.1|CK074638
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|58661671|gb|CK050351.1|CK050351
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|58689524|gb|CK078211.1|CK078211
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|86884303|gb|CI311706.1|CI311706
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|58685755|gb|CK074442.1|CK074442
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|58696214|gb|CK084901.1|CK084901
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|29644972|gb|CB649979.1|CB649979
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|58602353|gb|CK012881.1|CK012881
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|33653523|gb|CF276137.1|CF276137
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|29684184|gb|CB680459.1|CB680459
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|88395055|gb|CI609371.1|CI609371
EST:     TGATGACATGGGCCTCCAAGAGAAC-TTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|86888514|gb|CI303796.1|CI303796
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAG
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAG
EST: gi|58660136|gb|CK048816.1|CK048816
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|86890857|gb|CI305795.1|CI305795
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|33795013|gb|CF323385.1|CF323385
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCA
EST: gi|88761507|gb|CI771063.1|CI771063
EST:     TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATG                         GTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGA
genomic: TGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGA

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: 64 (upstream exon), 74 (downstream exon)
Score: 50

GGTGACAATGAGGAATTCTTCACTTCATATGATGAAGTTTTTGAGAGTTTTGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaa ... tgatgtgtagGTTTTGAGAAGCCATCAGCTATTCAGCAAAGGGGGATTGTTCCCTTCTGCAAAGGGCTTGATGTGATTCAGCAGGCTCAATCTGGAACAGGAAAAACTGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGACAATGAGGAATTCTTCACTTCATATGATGAAGTTTTTGAGAGTTTTGATGACATGGGCCTCCAAGAGAACCTTCTCAGAGGCATCTATGCTTATGgtatacaaaaagtcttatcccttttccattgtttcaacaacacatattttggtgatgttacaaatccctgtactttgatgtgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA