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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatagagacgagatggagagagagagagagagagagagagagcgagctacactagccgtggtcactgcgtgaatttgtgattgattgtctctcaaccattgggcttagtcttttttttcttttttttgggtgcgagtagGTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAGGA

Basic information

species Oryza sativa
transcript LOC_Os01g13190.1
intron # 1
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|32948183|gb|BP184755.1|BP184755
EST:     CCCGCATCGACTTCTCCTCCATTTTCGGCACG                         GTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
genomic: CCCGCATCGACTTCTCCTCCATTTTCGGCACGgtgagataga ... gtgcgagtagGTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
EST: gi|29680232|gb|CB676507.1|CB676507
EST:     GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACG                         GTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
genomic: GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACGgtgagataga ... gtgcgagtagGTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
EST: gi|88449248|gb|CI582120.1|CI582120
EST:     GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACG                         GTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
genomic: GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACGgtgagataga ... gtgcgagtagGTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
EST: gi|88724368|gb|CI747627.1|CI747627
EST:     GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACG                         GTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
genomic: GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACGgtgagataga ... gtgcgagtagGTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
EST: gi|88387313|gb|CI580658.1|CI580658
EST:     GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACG                         GTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
genomic: GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACGgtgagataga ... gtgcgagtagGTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
EST: gi|88339460|gb|CI635438.1|CI635438
EST:     GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACG                         GTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
genomic: GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACGgtgagataga ... gtgcgagtagGTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
EST: gi|117232645|gb|CT842234.1|CT842234
EST:     GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACG                         GTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
genomic: GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACGgtgagataga ... gtgcgagtagGTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
EST: gi|88298841|gb|CI566038.1|CI566038
EST:     GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACG                         GTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
genomic: GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACGgtgagataga ... gtgcgagtagGTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
EST: gi|58673757|gb|CK062443.1|CK062443
EST:     GCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACG                         GTCAA--CGA-TGTTGAAGCCGTGCGCATGCGAGGCGATGCTGCGGTCAAG
genomic: GCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACGgtgagataga ... gtgcgagtagGTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
EST: gi|88392984|gb|CI614866.1|CI614866
EST:     GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACG                         GTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
genomic: GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACGgtgagataga ... gtgcgagtagGTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
EST: gi|29683233|gb|CB679508.1|CB679508
EST:     GCGCGCCCCCGCATCCTCTTCTCCTCCATTTTCGGCACG                         GTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
genomic: GCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACGgtgagataga ... gtgcgagtagGTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
EST: gi|29662201|gb|CB658476.1|CB658476
EST:     GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACG                         GTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
genomic: GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACGgtgagataga ... gtgcgagtagGTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
EST: gi|86906628|gb|CI291123.1|CI291123
EST:     GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACG                         GTCAATCCGATTGTTGAAGACGTGCGCATGC
genomic: GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACGgtgagataga ... gtgcgagtagGTCAATCCGATTGTTGAAGACGTGCGCATGC
EST: gi|88388089|gb|CI590365.1|CI590365
EST:     GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACG                         GTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
genomic: GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACGgtgagataga ... gtgcgagtagGTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
EST: gi|88721621|gb|CI744920.1|CI744920
EST:     GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACG                         GTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG
genomic: GCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACGgtgagataga ... gtgcgagtagGTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAG

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: 32 (upstream exon), 53 (downstream exon)
Score: 8

CGCCGCCATGAAGTCGTACAGGCTGTCGGAGCTCAGCGACGCCGAGGTCGGCGGCCTCAAGGCGCGCCCCCGCATCGACTTCTCCTCCATTTTCGGCACGgtgagataga ... gtgcgagtagGTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtctctcaaccattgggcttagtcttttttttcttttttttgggtgcgagtagGTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAGGA
                        tcttttttttcttttt  CT-rich tract
                    ttagtcttttttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagatagagacgagatggagagagagagagagagagagagagagcgagctacactagccgtggtcactgcgtgaatttgtgattgattgtctctcaaccattgggcttagtcttttttttcttttttttgggtgcgagtagGTCAATCCGATTGTTGAAGACGTGCGCATGCGAGGCGATGCTGCGGTCAAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC