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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgctccggtcttgtttgtttatgttttgtggggaggaatttttgtgtcgaattcttctttgctactacgcgattaatccgtcctttcttggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGAGTCCGCCGGGGAGGAAGGCCCCGGCCGGTGCGGGCGGGATCCGTCGGTG

Basic information

species Oryza sativa
transcript LOC_Os01g68630.1
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|88739553|gb|CI763061.1|CI763061
EST:     ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAG                         ATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
genomic: ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAGgtattctttg ... tggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
EST: gi|88363558|gb|CI618119.1|CI618119
EST:     ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAG                         ATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
genomic: ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAGgtattctttg ... tggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
EST: gi|88333218|gb|CI641061.1|CI641061
EST:     ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAG                         ATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
genomic: ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAGgtattctttg ... tggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
EST: gi|88827089|gb|CI777654.1|CI777654
EST:     ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAG                         ATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
genomic: ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAGgtattctttg ... tggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
EST: gi|88405667|gb|CI609566.1|CI609566
EST:     ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAG                         ATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
genomic: ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAGgtattctttg ... tggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
EST: gi|88415314|gb|CI586520.1|CI586520
EST:     ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAG                         ATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
genomic: ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAGgtattctttg ... tggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
EST: gi|58602230|gb|CK012758.1|CK012758
EST:     ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAG                         ATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
genomic: ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAGgtattctttg ... tggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
EST: gi|88370794|gb|CI592560.1|CI592560
EST:     ATCGATCCCTCGTGGCCTCATCCCCGCCGCCGCGCCACCTCGTCTCGAAG                         ATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
genomic: ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAGgtattctttg ... tggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
EST: gi|88424200|gb|CI581755.1|CI581755
EST:     ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAG                         ATTTCTTTGATGCGTGGTGGCAGTGGCGTTTTGGATCTTGGTGCCGCCATG
genomic: ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAGgtattctttg ... tggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCG-TTTGGATCTTGGTGCCGCCATG
EST: gi|88360260|gb|CI611979.1|CI611979
EST:     ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAG                         ATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
genomic: ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAGgtattctttg ... tggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
EST: gi|88745631|gb|CI768991.1|CI768991
EST:     ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAG                         ATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
genomic: ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAGgtattctttg ... tggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
EST: gi|88723905|gb|CI745602.1|CI745602
EST:     ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAG                         ATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
genomic: ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAGgtattctttg ... tggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
EST: gi|29616267|gb|CB621279.1|CB621279
EST:     ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAG                         ATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
genomic: ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAGgtattctttg ... tggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
EST: gi|58692183|gb|CK080870.1|CK080870
EST:     ATCGATCCCTCGTGGGCTCCTCCCCGCCGCCG-GCCACCTCGTCTCGAAG                         ATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
genomic: ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAGgtattctttg ... tggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
EST: gi|88744153|gb|CI767513.1|CI767513
EST:     ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAG                         ATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
genomic: ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAGgtattctttg ... tggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
EST: gi|88761819|gb|CI771375.1|CI771375
EST:     ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAG                         ATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
genomic: ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAGgtattctttg ... tggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
EST: gi|88431391|gb|CI576921.1|CI576921
EST:     ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAG                         ATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
genomic: ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAGgtattctttg ... tggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
EST: gi|88725216|gb|CI748475.1|CI748475
EST:     ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAG                         ATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
genomic: ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAGgtattctttg ... tggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
EST: gi|58655971|gb|CK044651.1|CK044651
EST:     ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAG                         ATTTCTTTGATGCGTGGTGGGGGTGGCGTTTGGATCTTGGTGCCGCCATGA
genomic: ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAGgtattctttg ... tggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
EST: gi|88826078|gb|CI776643.1|CI776643
EST:     ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAG                         ATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
genomic: ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAGgtattctttg ... tggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
EST: gi|88724504|gb|CI747763.1|CI747763
EST:     ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAG                         ATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA
genomic: ATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAGgtattctttg ... tggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGA

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: 17 (upstream exon), 59 (downstream exon)
Score: 1

CGTCCTCGCCACGCGCGAAGGCGGCGTCGATCGGTTCCCCCATTTTTCTCATCGATCCCTCGTGGCCTCCTCCCCGCCGCCGCGCCACCTCGTCTCGAAGgtattctttg ... tggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGAGTCCGCCGGGGAGGAAGGCCCCGGCCGGTGCGGGCGGGATCCGTCGGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtcgaattcttctttgctactacgcgattaatccgtcctttcttggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGAGTCCGCCGGGGAGGAAGGCCCCGGCCGGTGCGGGCGGGATCCGTCGGTG
                           gattaat  putative branch site (score: 1)
                                 tccgtcctttctt  CT-rich tract
                            attaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgctccggtcttgtttgtttatgttttgtggggaggaatttttgtgtcgaattcttctttgctactacgcgattaatccgtcctttcttggtttgcagATTTCTTTGATGCGTGGTGGCAGTGGCGTTTGGATCTTGGTGCCGCCATGAGTCCGCCGGGGAGGAAGGCCCCGGCCGGTGCGGGCGGGATCCGTCGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
-ctgctcc
- - - - - - -tgtttgt
- - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - tgtgtcg