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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAATGCAGAGTACAGCGCGGTGAAGAACCTACCAACAGATCAGGGCCGAGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAGgtaaaatatggtgcccttttattttgtataattgcatcttttgttttccgtaggtaaaatctcatggtattcttgaacaattacagtattacgcaaatgc...

Basic information

species Oryza sativa
transcript LOC_Os03g21990.1
intron # 4
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|58662654|gb|CK051340.1|CK051340
EST:     AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAG                         GAACACAAGATGTCAAAGATGCTGATAACAAAAGCAGCAGTACTGCTATTG
genomic: AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAGgtaaaatatg ... atcttttcagGAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
EST: gi|29636115|gb|CB641124.1|CB641124
EST:     AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAG                         GAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCACTACTGCTATTG
genomic: AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAGgtaaaatatg ... atcttttcagGAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
EST: gi|88373248|gb|CI614584.1|CI614584
EST:     AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAG                         GAACACAAGATGTCAAA
genomic: AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAGgtaaaatatg ... atcttttcagGAACACAAGATGTCAAA
EST: gi|44679480|gb|CR292914.1|CR292914
EST:     AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAG                         GAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
genomic: AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAGgtaaaatatg ... atcttttcagGAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
EST: gi|29643708|gb|CB648715.1|CB648715
EST:     AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAG                         GAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
genomic: AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAGgtaaaatatg ... atcttttcagGAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
EST: gi|58658761|gb|CK047441.1|CK047441
EST:     AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAG                         GAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
genomic: AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAGgtaaaatatg ... atcttttcagGAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
EST: gi|58593917|gb|CF992225.1|CF992225
EST:     AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAG                         GAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
genomic: AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAGgtaaaatatg ... atcttttcagGAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
EST: gi|58593323|gb|CF991631.1|CF991631
EST:     AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAG                         GAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
genomic: AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAGgtaaaatatg ... atcttttcagGAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
EST: gi|29679952|gb|CB676227.1|CB676227
EST:     AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAG                         GAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
genomic: AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAGgtaaaatatg ... atcttttcagGAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
EST: gi|27577849|gb|CB000544.1|CB000544
EST:     AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAG                         GAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
genomic: AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAGgtaaaatatg ... atcttttcagGAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
EST: gi|58689854|gb|CK078541.1|CK078541
EST:     AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAG                         GAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
genomic: AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAGgtaaaatatg ... atcttttcagGAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
EST: gi|88432601|gb|CI567640.1|CI567640
EST:     AGGACAGGTCAAGAGTGCTGCGGCAACTTCAACTGCATTGGCGCTTCCAG                         GAACACA-GATGTCAAAGATGCTGATA
genomic: AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAGgtaaaatatg ... atcttttcagGAACACAAGATGTCAAAGATGCTGATA
EST: gi|58671592|gb|CK060278.1|CK060278
EST:     AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAG                         GAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
genomic: AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAGgtaaaatatg ... atcttttcagGAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
EST: gi|58694088|gb|CK082775.1|CK082775
EST:     AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAG                         GAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
genomic: AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAGgtaaaatatg ... atcttttcagGAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
EST: gi|117225886|gb|CT848635.1|CT848635
EST:     AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAG                         GAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
genomic: AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAGgtaaaatatg ... atcttttcagGAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
EST: gi|58664642|gb|CK053328.1|CK053328
EST:     AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAG                         GAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
genomic: AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAGgtaaaatatg ... atcttttcagGAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
EST: gi|33653589|gb|CF276203.1|CF276203
EST:     AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAG                         -A--------TGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
genomic: AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAGgtaaaatatg ... atcttttcagGAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
EST: gi|58613176|gb|CK040888.1|CK040888
EST:     AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAG                         GAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG
genomic: AGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAGgtaaaatatg ... atcttttcagGAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTG

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), 73 (downstream exon)
Score: 19

GTGAATGCAGAGTACAGCGCGGTGAAGAACCTACCAACAGATCAGGGCCGAGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAGgtaaaatatg ... atcttttcagGAACACAAGATGTCAAAGATGCTGATAACAAAGGCAGCAGTACTGCTATTGTTCCTGCACCACATATGCTCCCCAAAGCACC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAATGCAGAGTACAGCGCGGTGAAGAACCTACCAACAGATCAGGGCCGAGGACAGGTCAAGAGTGCTGCGGCACCTTCAACTGCATTGGCGCTTCCAGgtaaaatatggtgcccttttattttgtataattgcatcttttgttttccgtaggtaaaatctcatggtattcttgaacaattacagtattacgcaaatgc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC