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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCATGCACGGCCTCAGCGTGAGCTTCAGCGGCTTCAAGTACTCCATCGGGAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCGgtatctgaacattctacgcttcagtttcggatttctgaccaacgcaaggttcagagtttcgtgacacggcattggtgtgcag

Basic information

species Oryza sativa
transcript LOC_Os02g44860.1
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|88207597|gb|CI207446.1|CI207446
EST:     GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCG                         GATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
genomic: GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCGgtatctgaac ... tggtgtgcagGATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
EST: gi|86540666|gb|CI180872.1|CI180872
EST:     GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCG                         GATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
genomic: GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCGgtatctgaac ... tggtgtgcagGATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
EST: gi|87031196|gb|CI259776.1|CI259776
EST:     GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCG                         GATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
genomic: GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCGgtatctgaac ... tggtgtgcagGATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
EST: gi|86543711|gb|CI183917.1|CI183917
EST:     CCCCTACGACTCG                         GATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
genomic: CCCCAACGACTCGgtatctgaac ... tggtgtgcagGATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
EST: gi|88205419|gb|CI205268.1|CI205268
EST:     GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCG                         GATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
genomic: GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCGgtatctgaac ... tggtgtgcagGATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
EST: gi|86510030|gb|CI152663.1|CI152663
EST:     GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCG                         GATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
genomic: GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCGgtatctgaac ... tggtgtgcagGATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
EST: gi|86257456|gb|CI004273.1|CI004273
EST:     GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCTACGACTCG                         GAGTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
genomic: GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCGgtatctgaac ... tggtgtgcagGATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
EST: gi|88227293|gb|CI228406.1|CI228406
EST:     GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCG                         GATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
genomic: GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCGgtatctgaac ... tggtgtgcagGATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
EST: gi|88850514|gb|CI093195.1|CI093195
EST:     GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCG                         GATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
genomic: GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCGgtatctgaac ... tggtgtgcagGATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
EST: gi|58683450|gb|CK072137.1|CK072137
EST:     GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCG                         GATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
genomic: GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCGgtatctgaac ... tggtgtgcagGATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
EST: gi|88265973|gb|CI376875.1|CI376875
EST:     CATCATGAACCATCCCCAACGACTCG                         GATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCCGCAAGTTCAACGGCG
genomic: CATCATGAAGCATCCCCAACGACTCGgtatctgaac ... tggtgtgcagGATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
EST: gi|86505296|gb|CI147929.1|CI147929
EST:     GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCG                         GATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
genomic: GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCGgtatctgaac ... tggtgtgcagGATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
EST: gi|88214836|gb|CI212874.1|CI212874
EST:     CGTGGGGCAAAGCATCATGAAGCATCCCCAACGACTCG                         GATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
genomic: CGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCGgtatctgaac ... tggtgtgcagGATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
EST: gi|88221119|gb|CI221075.1|CI221075
EST:     CATGAAGCATCCCCAACGACTCG                         GATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
genomic: CATGAAGCATCCCCAACGACTCGgtatctgaac ... tggtgtgcagGATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
EST: gi|58588140|gb|CF986448.1|CF986448
EST:     GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGAATCG                         GATTCCAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
genomic: GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCGgtatctgaac ... tggtgtgcagGATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
EST: gi|86505244|gb|CI147877.1|CI147877
EST:     GAAGCATCCCCAACGACTCG                         GATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
genomic: GAAGCATCCCCAACGACTCGgtatctgaac ... tggtgtgcagGATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
EST: gi|88987975|gb|CI018029.1|CI018029
EST:     GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCG                         GATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
genomic: GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCGgtatctgaac ... tggtgtgcagGATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
EST: gi|86483191|gb|CI125824.1|CI125824
EST:     GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCG                         GATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
genomic: GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCGgtatctgaac ... tggtgtgcagGATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
EST: gi|88995519|gb|CI022842.1|CI022842
EST:     CCCCAACGACTCG                         GATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
genomic: CCCCAACGACTCGgtatctgaac ... tggtgtgcagGATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
EST: gi|86501401|gb|CI144034.1|CI144034
EST:     GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCG                         GATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
genomic: GAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCGgtatctgaac ... tggtgtgcagGATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
EST: gi|88971613|gb|CI388858.1|CI388858
EST:     CATCCCCAACGACTCG                         GATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
genomic: CATCCCCAACGACTCGgtatctgaac ... tggtgtgcagGATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
EST: gi|86425450|gb|CI070547.1|CI070547
EST:     CGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCG                         GATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG
genomic: CGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCGgtatctgaac ... tggtgtgcagGATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCG

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: 25 (upstream exon), 56 (downstream exon)
Score: 2

GCCATGCACGGCCTCAGCGTGAGCTTCAGCGGCTTCAAGTACTCCATCGGGAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCGgtatctgaac ... tggtgtgcagGATTCAAGGAGGTCACGACGGCTTGCTGCGGCTCCGGCAAGTTCAACGGCGAGTCCGGGTGCACGCCGAACGCCACGCTGTGCGACAACCGGCACGACTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCATGCACGGCCTCAGCGTGAGCTTCAGCGGCTTCAAGTACTCCATCGGGAGCTCCCATGCCGTGGTGCAAAGCATCATGAAGCATCCCCAACGACTCGgtatctgaacattctacgcttcagtttcggatttctgaccaacgcaaggttcagagtttcgtgacacggcattggtgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC