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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaaaatttgtaatttgtaaatgtatagtttacccatctgatcaaggccttattaacaaatatttttctaaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACCGATCCTTGATCAATCT

Basic information

species Oryza sativa
transcript LOC_Os09g07510.3
intron # 11
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|87041566|gb|CI196188.1|CI196188
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|58693179|gb|CK081866.1|CK081866
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|86487397|gb|CI130030.1|CI130030
EST:     TGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTCCTGCAGGCACTTATACC
genomic: TGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|88840225|gb|CI079679.1|CI079679
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTTAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|29667131|gb|CB663406.1|CB663406
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|38476835|gb|CF960968.1|CF960968
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACAT
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACAT
EST: gi|29658916|gb|CB655191.1|CB655191
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATATTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|88962171|gb|CI097324.1|CI097324
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|87038212|gb|CI192834.1|CI192834
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|87037905|gb|CI192527.1|CI192527
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|58598388|gb|CK008916.1|CK008916
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|87036423|gb|CI191045.1|CI191045
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|87041468|gb|CI196090.1|CI196090
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|87017349|gb|CI301385.1|CI301385
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAG
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAG
EST: gi|33654810|gb|CF277424.1|CF277424
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|88967779|gb|CI098021.1|CI098021
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|29642127|gb|CB647134.1|CB647134
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|29641703|gb|CB646710.1|CB646710
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|42592112|gb|CK738598.1|CK738598
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|29631456|gb|CB636465.1|CB636465
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|89181442|gb|CI112948.1|CI112948
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|88250842|gb|CI248693.1|CI248693
EST:     ATCACTTGTCAACAGCTGCTCCCCGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|89163971|gb|CI101059.1|CI101059
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|22307172|gb|BQ908394.1|BQ908394
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCNAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|89193364|gb|CI050662.1|CI050662
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|87041657|gb|CI196279.1|CI196279
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|89193243|gb|CI050541.1|CI050541
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|86899096|gb|CI296244.1|CI296244
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGT
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGT
EST: gi|86481308|gb|CI123941.1|CI123941
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|86903252|gb|CI313615.1|CI313615
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTTTGATTAATTCCTCAAAGGACAG                         AGGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATAC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagA-GTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATAC
EST: gi|7134620|gb|AU082588.1|AU082588
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|86497016|gb|CI139649.1|CI139649
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|88849706|gb|CI089812.1|CI089812
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|88837381|gb|CI078741.1|CI078741
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|87028909|gb|CI351212.1|CI351212
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|89183582|gb|CI046147.1|CI046147
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCCAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|58663458|gb|CK052144.1|CK052144
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
EST: gi|89175570|gb|CI042591.1|CI042591
EST:     ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAG                         AGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC
genomic: ATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACC

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), 75 (downstream exon)
Score: 86

TGACCATCCTGCAAGCTATTTCATTGCTGGCCCCTGTCATGGGTGCCGAAATCACTTGTCAACAGCTGCTCCCTGTTGTGATTAATTCCTCAAAGGACAGgtgaaaaatt ... taaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACCGATCCTTGATCAATCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatagtttacccatctgatcaaggccttattaacaaatatttttctaaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACCGATCCTTGATCAATCT
                                     tatttttct  CT-rich tract
                          ttattaacaaatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaaaatttgtaatttgtaaatgtatagtttacccatctgatcaaggccttattaacaaatatttttctaaatttcagAGTGCCAAACATCAAATTCAATGTTGCGAAGGTTCTGCAGGCACTTATACCGATCCTTGATCAATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG