Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTAGCTCATTGGTGCTACAATGATGGTGAAGTGCCAGTTGTTGCCATATATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagcagaacttttccaaagctaaacatttttactactattttgatatttttattccacttatcttagatgatgatttagccttttaatcaactgttag

Basic information

species Oryza sativa
transcript LOC_Os01g55690.1
intron # 2
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|88327006|gb|CI676122.1|CI676122
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|116875081|gb|EC365589.1|EC365589
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|116875186|gb|EC365694.1|EC365694
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|116875215|gb|EC365723.1|EC365723
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|116875058|gb|EC365566.1|EC365566
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|88382708|gb|CI682597.1|CI682597
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|116875467|gb|EC365975.1|EC365975
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|116875195|gb|EC365703.1|EC365703
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|116875160|gb|EC365668.1|EC365668
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|116875209|gb|EC365717.1|EC365717
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|116875074|gb|EC365582.1|EC365582
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAGGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|116875041|gb|EC365549.1|EC365549
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|88410738|gb|CI687079.1|CI687079
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|116875225|gb|EC365733.1|EC365733
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|116875073|gb|EC365581.1|EC365581
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|116875413|gb|EC365921.1|EC365921
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|116875134|gb|EC365642.1|EC365642
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|116875445|gb|EC365953.1|EC365953
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATATCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|88579128|gb|CI688101.1|CI688101
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|116875057|gb|EC365565.1|EC365565
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|116875187|gb|EC365695.1|EC365695
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|88379084|gb|CI681917.1|CI681917
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAAC
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAAC
EST: gi|88325338|gb|CI675133.1|CI675133
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GACTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAGGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|88584207|gb|CI701743.1|CI701743
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|88463472|gb|CI695936.1|CI695936
EST:     GGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAT
genomic: GGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|116875637|gb|EC366145.1|EC366145
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|88585857|gb|CI701525.1|CI701525
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|218487483|gb|FG950699.1|FG950699
EST:     TGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCTTGAG
genomic: TGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|88378933|gb|CI681756.1|CI681756
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAG
EST: gi|88586956|gb|CI704679.1|CI704679
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|88589688|gb|CI708487.1|CI708487
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GACTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAGGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|88578391|gb|CI687317.1|CI687317
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|116875133|gb|EC365641.1|EC365641
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGTTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|2798964|gb|AA752258.1|AA752258
EST:     ATGTCACTGATCT-AACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTNNAAATAAGAGAANCCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|116875048|gb|EC365556.1|EC365556
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTGGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|88432975|gb|CI690833.1|CI690833
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|218479300|gb|FG957923.1|FG957923
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|116875607|gb|EC366115.1|EC366115
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
EST: gi|116875052|gb|EC365560.1|EC365560
EST:     ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGG                         GATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG
genomic: ATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAG

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: 75 (upstream exon), 75 (downstream exon)
Score: 6817

TGTAGCTCATTGGTGCTACAATGATGGTGAAGTGCCAGTTGTTGCCATATATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagc ... caactgttagGATTTCTTGTTAGCTGGAAATAAGAGAAACCCTCAAGCATACAGGCGTGAGGTTGAGGAGCGGTCACAGAACATATTTAGTGGCTTTAGCACTGAACTAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTAGCTCATTGGTGCTACAATGATGGTGAAGTGCCAGTTGTTGCCATATATGTCACTGATCTCAACAACGGTGCTAATCAACTTGACCCTAGGCAAAGGgtaattaagcagaacttttccaaagctaaacatttttactactattttgatatttttattccacttatcttagatgatgatttagccttttaatcaactgttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG