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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattcctttgctaattactttctttttgacgctacaaaataaaggtgattccttgtctcacagctggtaaacttttgcagCTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATAAGTCGACGGGGAAGAACTCCCACTGTAAAATGTAGACAAGCAGCTGCGA

Basic information

species Oryza sativa
transcript LOC_Os05g05200.1
intron # 18
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|88848612|gb|CI087134.1|CI087134
EST:     CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG                         CTTATGTTTTATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
genomic: CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAGgtgattcctt ... acttttgcagCTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
EST: gi|88542819|gb|CI472173.1|CI472173
EST:     CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG                         CTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
genomic: CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAGgtgattcctt ... acttttgcagCTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
EST: gi|88532803|gb|CI461436.1|CI461436
EST:     CCCTTCCTGTCCTTGCCTTCATATTTATGTCATTCTATGTGGGAGTTAAG                         CTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
genomic: CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAGgtgattcctt ... acttttgcagCTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
EST: gi|86527322|gb|CI167528.1|CI167528
EST:     CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG                         CTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
genomic: CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAGgtgattcctt ... acttttgcagCTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
EST: gi|88558171|gb|CI488639.1|CI488639
EST:     TTATCTCATTCTATGTGGGAGTTAAG                         CTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
genomic: TTATCTCATTCTATGTGGGAGTTAAGgtgattcctt ... acttttgcagCTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
EST: gi|88556119|gb|CI486428.1|CI486428
EST:     CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG                         CTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
genomic: CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAGgtgattcctt ... acttttgcagCTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
EST: gi|86822518|gb|CI358035.1|CI358035
EST:     CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG                         CTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
genomic: CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAGgtgattcctt ... acttttgcagCTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
EST: gi|86527366|gb|CI167572.1|CI167572
EST:     CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG                         CTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
genomic: CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAGgtgattcctt ... acttttgcagCTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
EST: gi|88521914|gb|CI449634.1|CI449634
EST:     CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG                         CTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
genomic: CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAGgtgattcctt ... acttttgcagCTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
EST: gi|88544168|gb|CI474240.1|CI474240
EST:     CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG                         CTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
genomic: CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAGgtgattcctt ... acttttgcagCTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
EST: gi|88531552|gb|CI460035.1|CI460035
EST:     CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG                         CTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
genomic: CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAGgtgattcctt ... acttttgcagCTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
EST: gi|86882287|gb|CI325746.1|CI325746
EST:     CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG                         CTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
genomic: CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAGgtgattcctt ... acttttgcagCTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
EST: gi|88321005|gb|CI530357.1|CI530357
EST:     CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG                         CTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
genomic: CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAGgtgattcctt ... acttttgcagCTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
EST: gi|88264213|gb|CI367987.1|CI367987
EST:     CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG                         CTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
genomic: CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAGgtgattcctt ... acttttgcagCTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
EST: gi|88546313|gb|CI475939.1|CI475939
EST:     CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAG                         CTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA
genomic: CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAGgtgattcctt ... acttttgcagCTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATA

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: 56 (upstream exon), 13 (downstream exon)
Score: 1

CCCTTCCTGTCCTTGCCTTCATATTTATCTCATTCTATGTGGGAGTTAAGgtgattcctt ... acttttgcagCTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATAAGTCGACGGGGAAGAACTCCCACTGTAAAATGTAGACAAGCAGCTGCGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgacgctacaaaataaaggtgattccttgtctcacagctggtaaacttttgcagCTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATAAGTCGACGGGGAAGAACTCCCACTGTAAAATGTAGACAAGCAGCTGCGA
                             gtctcac  putative branch site (score: 1)
                                              cttttgc  putative PPT
       tacaaaataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattcctttgctaattactttctttttgacgctacaaaataaaggtgattccttgtctcacagctggtaaacttttgcagCTTATGTTTCATATACGTGACGCACATGAGAATCAAGGGTGATAACTGATAAGTCGACGGGGAAGAACTCCCACTGTAAAATGTAGACAAGCAGCTGCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC