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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGTCTCCTCCGCTCCGCTCGTTGCGCCGCCGCCAAGACGAGCAGGGGAGGGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTGgtgcgtcctctttctgattcatctctctctcccaccccaccgggacctggctggaacttgcttgcgttcgtgaaccctactagcttctcttctagatctc...

Basic information

species Oryza sativa
transcript LOC_Os10g41590.1
intron # 1
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|88336575|gb|CI656846.1|CI656846
EST:     GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTG                         ATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
genomic: GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTGgtgcgtcctc ... agaataacagATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
EST: gi|88424216|gb|CI581771.1|CI581771
EST:     GGCCGGGTGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTG                         ATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
genomic: GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTGgtgcgtcctc ... agaataacagATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
EST: gi|88728249|gb|CI751759.1|CI751759
EST:     GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTG                         ATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
genomic: GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTGgtgcgtcctc ... agaataacagATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
EST: gi|88296461|gb|CI669237.1|CI669237
EST:     GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTG                         ATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
genomic: GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTGgtgcgtcctc ... agaataacagATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
EST: gi|88454307|gb|CI569879.1|CI569879
EST:     GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTG                         ATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
genomic: GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTGgtgcgtcctc ... agaataacagATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
EST: gi|88317188|gb|CI626831.1|CI626831
EST:     GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTG                         ATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
genomic: GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTGgtgcgtcctc ... agaataacagATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
EST: gi|88309663|gb|CI656404.1|CI656404
EST:     GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTG                         ATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
genomic: GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTGgtgcgtcctc ... agaataacagATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
EST: gi|88407459|gb|CI586300.1|CI586300
EST:     GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTG                         ATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
genomic: GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTGgtgcgtcctc ... agaataacagATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
EST: gi|88403667|gb|CI575551.1|CI575551
EST:     GGCCGGGCGGCGATCTCCATCCGTCGAGCAGCGGAGGGGAGGGGATCCTG                         ATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
genomic: GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTGgtgcgtcctc ... agaataacagATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
EST: gi|88400700|gb|CI596121.1|CI596121
EST:     GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTG                         ATGGATGCCGCAGCCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGAAATT
genomic: GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTGgtgcgtcctc ... agaataacagATGGATGCCGCAG-CTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATT
EST: gi|88316061|gb|CI618937.1|CI618937
EST:     GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTG                         ATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGAAATTG
genomic: GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTGgtgcgtcctc ... agaataacagATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
EST: gi|88431474|gb|CI579591.1|CI579591
EST:     GCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGGAGGGGAGGGGATCCTG                         ATGGATGCCGAAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATGG
genomic: GCCGGGCGGCGATCTCCATCCGGCGAGCAGC-GGAGGGGAGGGGATCCTGgtgcgtcctc ... agaataacagATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
EST: gi|88729990|gb|CI753605.1|CI753605
EST:     GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTG                         ATGGATGCCGCAGCTCTTCACTATGAGAACCAGAAGCTGGTGCAGCAATTG
genomic: GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTGgtgcgtcctc ... agaataacagATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
EST: gi|58669159|gb|CK057845.1|CK057845
EST:     GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTG                         ATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
genomic: GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTGgtgcgtcctc ... agaataacagATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
EST: gi|88394940|gb|CI607667.1|CI607667
EST:     GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTG                         ATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
genomic: GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTGgtgcgtcctc ... agaataacagATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
EST: gi|88336123|gb|CI647317.1|CI647317
EST:     GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTG                         ATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG
genomic: GGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTGgtgcgtcctc ... agaataacagATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTG

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: 43 (upstream exon), 62 (downstream exon)
Score: 6

TCGTCTCCTCCGCTCCGCTCGTTGCGCCGCCGCCAAGACGAGCAGGGGAGGGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTGgtgcgtcctc ... agaataacagATGGATGCCGCAGCTCTTCAGTATGAGAACCAGAAGCTGGTGCAGCAATTGGAGGCACAGAAGTCCAAAATGCGTGCATTGGAAGGCAAGTTCAAGGAGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGTCTCCTCCGCTCCGCTCGTTGCGCCGCCGCCAAGACGAGCAGGGGAGGGCCGGGCGGCGATCTCCATCCGGCGAGCAGCGGAGGGGAGGGGATCCTGgtgcgtcctctttctgattcatctctctctcccaccccaccgggacctggctggaacttgcttgcgttcgtgaaccctactagcttctcttctagatctc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccacc