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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttccatccacttttaccaaccaatcacaccttgtttcaattgccgcatgctaaacttttctctagactggctcaccattcaggaagcaaatctt...

Basic information

species Oryza sativa
transcript LOC_Os01g01700.1
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|87010441|gb|CI283516.1|CI283516
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|87028533|gb|CI265932.1|CI265932
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|86597337|gb|CI280474.1|CI280474
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|88486358|gb|CI423629.1|CI423629
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTTTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|88258657|gb|CI361243.1|CI361243
EST:     CACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGGTCAAGA
genomic: CACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|86530369|gb|CI170575.1|CI170575
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|86525235|gb|CI165441.1|CI165441
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|9865650|gb|AU101400.1|AU101400
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|89170244|gb|CI039521.1|CI039521
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|88239603|gb|CI240080.1|CI240080
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|89165245|gb|CI255302.1|CI255302
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|88264264|gb|CI368038.1|CI368038
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGTTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|88543062|gb|CI470432.1|CI470432
EST:     TGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: TGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|88979016|gb|CI025534.1|CI025534
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|86419648|gb|CI054449.1|CI054449
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|88559135|gb|CI489688.1|CI489688
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|88214117|gb|CI213966.1|CI213966
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|86854819|gb|CI260887.1|CI260887
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|88844742|gb|CI021317.1|CI021317
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|700261|gb|D46552.1|D46552
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTNAGGAGTGCACTGTCGCTTNGG                         GTGTCTGTAATCATGNTTTTNACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|88505015|gb|CI432521.1|CI432521
EST:     GCCACCAGTGAGGAGTGCACTTTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: GCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|88208384|gb|CI208233.1|CI208233
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|88506675|gb|CI434181.1|CI434181
EST:     CCA-GCGAAGCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|88432041|gb|CI562872.1|CI562872
EST:     CACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|88279001|gb|CI400001.1|CI400001
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|89170150|gb|CI039427.1|CI039427
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|86523241|gb|CI163447.1|CI163447
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|88202160|gb|CI202515.1|CI202515
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|86253813|gb|CI058540.1|CI058540
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|88961711|gb|CI096914.1|CI096914
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|86413387|gb|CI067792.1|CI067792
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|58599948|gb|CK010476.1|CK010476
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|86434462|gb|CI094805.1|CI094805
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|86828745|gb|CI280591.1|CI280591
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|86533593|gb|CI173799.1|CI173799
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
EST: gi|86828946|gb|CI280729.1|CI280729
EST:     CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG                         GTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA
genomic: CCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGA

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: 49 (upstream exon), 72 (downstream exon)
Score: 46

GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttcc ... tgtacaccagGTGTCTGTAATCATGCTTTTCACTTCCATTGCATCAGCAGGTGGCTCAAGACTCGCCAAGTGTGCCCGTTAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGGgtacgcttccatccacttttaccaaccaatcacaccttgtttcaattgccgcatgctaaacttttctctagactggctcaccattcaggaagcaaatctt

- - - - - - - - - - - - - - - - - - - GAGGAG