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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaattcaacctatattaaagaaagaaaatattttagtaaattagtaaatatttattatttataaagcttttcacatgtatgcattaatcttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAGTTGCCTAGCGCTGACATCACTGTAGTTCTTTGCGGCAAACTTGGCTGTG

Basic information

species Oryza sativa
transcript LOC_Os02g35130.1
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|88742174|gb|CI765682.1|CI765682
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|88584807|gb|CI702386.1|CI702386
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|33380835|gb|CF196178.1|CF196178
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|88333408|gb|CI642445.1|CI642445
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|88592598|gb|CI710710.1|CI710710
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|88424310|gb|CI581865.1|CI581865
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGGGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|88381562|gb|CI682222.1|CI682222
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|88761356|gb|CI770912.1|CI770912
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|88329563|gb|CI648627.1|CI648627
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|88348617|gb|CI634212.1|CI634212
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|88734489|gb|CI757997.1|CI757997
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|88336951|gb|CI627031.1|CI627031
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|88733033|gb|CI756210.1|CI756210
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|88342052|gb|CI644389.1|CI644389
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|29678306|gb|CB674581.1|CB674581
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|88327626|gb|CI646819.1|CI646819
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|88744424|gb|CI767784.1|CI767784
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|88329955|gb|CI652342.1|CI652342
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|88761455|gb|CI771011.1|CI771011
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|88733176|gb|CI756353.1|CI756353
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|88344317|gb|CI655711.1|CI655711
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|88735635|gb|CI759143.1|CI759143
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|33675112|gb|CF303351.1|CF303351
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGTTGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|33684157|gb|CF312396.1|CF312396
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
EST: gi|88340780|gb|CI636940.1|CI636940
EST:     TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAA                         GTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG
genomic: TCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAG

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: 60 (upstream exon), 68 (downstream exon)
Score: 15

ACTTCTCGTCTTCCTCTCCTCTCTCTCGTTTCGATTCCCCCGCGAGAGATTCGATCCAACCAAACCCACCCGCTACCAGCGTCTTCTCCTTCGCGAGCAAgtaattctct ... ttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAGTTGCCTAGCGCTGACATCACTGTAGTTCTTTGCGGCAAACTTGGCTGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaatatttattatttataaagcttttcacatgtatgcattaatcttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAGTTGCCTAGCGCTGACATCACTGTAGTTCTTTGCGGCAAACTTGGCTGTG
                                     cattaat  putative branch site (score: 15)
                                           tcttct  CT-rich tract
     atttattatttataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaattcaacctatattaaagaaagaaaatattttagtaaattagtaaatatttattatttataaagcttttcacatgtatgcattaatcttctaaacagGTTTTTTGAGAGTTTGCAATGGGAGGAAGCGAATACGATGATGACTGGGAGTTGCCTAGCGCTGACATCACTGTAGTTCTTTGCGGCAAACTTGGCTGTG

- - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtatgc