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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGATCTAGAATCAAGTGGAACTTTACCAAATTTCTTATTGATAAGAATGGCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctctctctctctctctagcctctcgcttactcgctctatatgcacatacacaattttgatatatctgtttaaaatgtacag

Basic information

species Oryza sativa
transcript LOC_Os03g24380.1
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|30228288|gb|CB966179.1|CB966179
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTTGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|86527805|gb|CI168011.1|CI168011
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|88450244|gb|CI542005.1|CI542005
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|18386081|gb|BM419280.1|BM419280
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|29639181|gb|CB644190.1|CB644190
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|14714308|gb|AU198231.1|AU198231
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|8527832|gb|AU092647.1|AU092647
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|88969143|gb|CI382692.1|CI382692
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|25807079|gb|CA763033.1|CA763033
EST:     GCAAAGTCATTAACAGATACTTGACTGCGACCAGTCCCTTGTTTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTTGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|33680364|gb|CF308603.1|CF308603
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|7378306|gb|AU088577.1|AU088577
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCCGCTCCGAGGATTAGATCCCGTACCCTCCCCCAT
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGG-CGCT-CGAGGATTAGATCTCGTACCCTCCCCCAT
EST: gi|88448866|gb|CI557938.1|CI557938
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|88296846|gb|CI540198.1|CI540198
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|88471220|gb|CI408491.1|CI408491
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|88296988|gb|CI542700.1|CI542700
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGGCTCGAGGAGTAGATCTCGTACCCTCCCCCATC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGC-GCTCGAGGATTAGATCTCGTACCCTCCCCCATC
EST: gi|88507237|gb|CI434743.1|CI434743
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|30227513|gb|CB965405.1|CB965405
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTTGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|86868821|gb|CI334193.1|CI334193
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|88517887|gb|CI444776.1|CI444776
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|8528179|gb|AU092994.1|AU092994
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|3762605|gb|AU029357.1|AU029357
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|88291772|gb|CI539943.1|CI539943
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|8528215|gb|AU093030.1|AU093030
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|88438224|gb|CI538583.1|CI538583
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|88295754|gb|CI532715.1|CI532715
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|29639182|gb|CB644191.1|CB644191
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|88408928|gb|CI554250.1|CI554250
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|88376727|gb|CI538031.1|CI538031
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|88447126|gb|CI531369.1|CI531369
EST:     CTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: CTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
EST: gi|88457806|gb|CI539602.1|CI539602
EST:     GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAG                         AAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC
genomic: GCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCC

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: 72 (upstream exon), 70 (downstream exon)
Score: 35

TGGATCTAGAATCAAGTGGAACTTTACCAAATTTCTTATTGATAAGAATGGCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctct ... aaatgtacagAAAGACATCCTGAAGGCGCTCGAGGATTAGATCTCGTACCCTCCCCCATCCTTCATTTGCAGAAGTAGGCAAAGTATCTGGTTGTAATATCTAGACCTAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGATCTAGAATCAAGTGGAACTTTACCAAATTTCTTATTGATAAGAATGGCAAAGTCATTAACAGATACTCGACTGCGACCAGTCCCTTGTCTTTTGAGgtctctctctctctctctctctagcctctcgcttactcgctctatatgcacatacacaattttgatatatctgtttaaaatgtacag

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