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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattctctcctcccaaatgtagatgccaagtttatttattttgtgcaggctactccctctgattgatattcatttggtgctgtgatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACCATGGAGACTATCCTTACCCAGCTCAAGAAGGAGATGGCAACCCCGCAGA

Basic information

species Oryza sativa
transcript LOC_Os09g12570.1
intron # 3
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|88463486|gb|CI695950.1|CI695950
EST:     GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCG                         GTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGC
genomic: GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGC
EST: gi|88976079|gb|CI024322.1|CI024322
EST:     GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCG                         GTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
genomic: GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
EST: gi|86897150|gb|CI294270.1|CI294270
EST:     GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCG                         GTTGACTCGAGGAAGTTTGGTGTTCTAGCAA
genomic: GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAA
EST: gi|86508960|gb|CI151593.1|CI151593
EST:     GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCG                         GTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
genomic: GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
EST: gi|22305081|gb|BQ906303.1|BQ906303
EST:     GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCG                         GTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
genomic: GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
EST: gi|15851620|gb|BI799896.1|BI799896
EST:     GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCG                         GTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
genomic: GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
EST: gi|88401056|gb|CI685038.1|CI685038
EST:     GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCG                         GTTGACTCGAGGAAGTTTGGTGTTCTA
genomic: GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTA
EST: gi|86256646|gb|CI061409.1|CI061409
EST:     CAATATGTCGTGTGTTAATCATGAGACTGGAGCG                         GTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
genomic: CAATATGTCGTGTGTTAATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
EST: gi|86599346|gb|CI251304.1|CI251304
EST:     GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCG                         GTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
genomic: GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
EST: gi|2280993|gb|C25488.1|C25488
EST:     GTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTTGGAGCG                         GTTGACTCGAGGAAGTTTTGGTGTTCTAGCAAACTTGGCAGCGCGAGTAC
genomic: GTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACT-GGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTT-GGTGTTCTAGCAAACT-GGCAGCGCGAGTAC
EST: gi|33659068|gb|CF281681.1|CF281681
EST:     GTTTCATTCAAGAATCAATATGTNCGTGTGTTAATCATGAGACTGGAGCG                         GTTGACTCGAGGAAGTNTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACAC
genomic: GTTTCATTCAAGAATCAATATGT-CGTGTGTTAATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGT-TTGGTGTTCTAGCAAACTGGCAGCGCGAGTACAC
EST: gi|88361792|gb|CI681952.1|CI681952
EST:     GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCG                         GTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
genomic: GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
EST: gi|55439495|gb|CV733057.1|CV733057
EST:     AATCAATATGTCGTGTGTTAATCATGAGACTGGAGCG                         GTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
genomic: AATCAATATGTCGTGTGTTAATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
EST: gi|88217406|gb|CI217255.1|CI217255
EST:     GTGTGTTAATCATGAGACTGGAGCG                         GTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
genomic: GTGTGTTAATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
EST: gi|10930784|gb|AU161058.1|AU161058
EST:     GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTTGAGCG                         GTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTTGCAGCGCGAGTACACC
genomic: GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
EST: gi|88210947|gb|CI212587.1|CI212587
EST:     GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCG                         GTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
genomic: GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
EST: gi|88349347|gb|CI678329.1|CI678329
EST:     GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCG                         GTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
genomic: GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
EST: gi|55439494|gb|CV733056.1|CV733056
EST:     GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCG                         GTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
genomic: GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
EST: gi|15856105|gb|BI808917.1|BI808917
EST:     TTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGACCG                         GTTGACTCGAGGAA-TTTGGTGTTCTA-CAAACT-GCAGCGCGAGTACACC
genomic: TTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
EST: gi|29644928|gb|CB649935.1|CB649935
EST:     GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCG                         GTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
genomic: GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
EST: gi|88243671|gb|CI242793.1|CI242793
EST:     GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCG                         GTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
genomic: GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
EST: gi|55410535|gb|CV722911.1|CV722911
EST:     GAGACTGGAGCG                         GTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
genomic: GAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
EST: gi|38472011|gb|CF956142.1|CF956142
EST:     AATCATGAGACTGGAGCG                         GTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
genomic: AATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
EST: gi|88741058|gb|CI764566.1|CI764566
EST:     GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCG                         GTTGACTCGAGGAAGTTTGGTGTTCT
genomic: GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCT
EST: gi|27548074|gb|CA767449.2|CA767449
EST:     GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCG                         GTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC
genomic: GGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACC

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: 74 (upstream exon), 69 (downstream exon)
Score: 70

GCTGAAGCTGTTCTGTGACAAGGACTACCCAGAGAAGCCACCATCTGTCCGGTTTCATTCAAGAATCAATATGTCGTGTGTTAATCATGAGACTGGAGCGgtattctctc ... gatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACCATGGAGACTATCCTTACCCAGCTCAAGAAGGAGATGGCAACCCCGCAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtgcaggctactccctctgattgatattcatttggtgctgtgatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACCATGGAGACTATCCTTACCCAGCTCAAGAAGGAGATGGCAACCCCGCAGA
                      gattgat  putative branch site (score: 70)
                       attgatattcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattctctcctcccaaatgtagatgccaagtttatttattttgtgcaggctactccctctgattgatattcatttggtgctgtgatcctatagGTTGACTCGAGGAAGTTTGGTGTTCTAGCAAACTGGCAGCGCGAGTACACCATGGAGACTATCCTTACCCAGCTCAAGAAGGAGATGGCAACCCCGCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG