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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCATGTACGATGACATCGCGCACAACCCGGAGAATCCGAGGCCTGGTGTCATCATCAACCATCCCCAGGGTGGCGATGTCTATGCTGGGGTCCCGAAGgtaaccgtgcatgttcattcttcaggagaattattgatgctagctataatttcttcggttacctttctaaagaaatgttacagtgtgacgataagatttt...

Basic information

species Oryza sativa
transcript LOC_Os01g37910.1
intron # 2
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|58610712|gb|CK038424.1|CK038424
EST:     TCATCATCAACCATCCCCAGGGTGGCGATGTCTATGCGGGGGTCCCGAAG                         GATTACACTGGGAAGGAGGTTAATGTCAAAAACTTGTTTGCTGTTCTGCTC
genomic: TCATCATCAACCATCCCCAGGGTGGCGATGTCTATGCTGGGGTCCCGAAGgtaaccgtgc ... ttcactgtagGATTACACTGGGAAGGAGGTTAATGTCAAAAACTTGTTTGCTGTTCTGCTC
EST: gi|33799061|gb|CF325390.1|CF325390
EST:     TCATCATCAACCATCCCCAGGGTGGCGATGTCTATGCTGGGGTCCCGAAG                         GATTACACTGGGAAGGAGGTTAATGTCAAAAACTTGTTTGCTGTTCTGCTC
genomic: TCATCATCAACCATCCCCAGGGTGGCGATGTCTATGCTGGGGTCCCGAAGgtaaccgtgc ... ttcactgtagGATTACACTGGGAAGGAGGTTAATGTCAAAAACTTGTTTGCTGTTCTGCTC
EST: gi|58689661|gb|CK078348.1|CK078348
EST:     TCATCATCAACCATCCCCAGTGTGGCGATGTCTATGCTGGGGTCCCGAAG                         GATTACACTGGGAAGGAGGTTAATGTCAAAAACTTGTTTGCTGTTCTGCTC
genomic: TCATCATCAACCATCCCCAGGGTGGCGATGTCTATGCTGGGGTCCCGAAGgtaaccgtgc ... ttcactgtagGATTACACTGGGAAGGAGGTTAATGTCAAAAACTTGTTTGCTGTTCTGCTC
EST: gi|58688754|gb|CK077441.1|CK077441
EST:     TCATCATCAACCATCCCCAGGGTGGCGATGTCTATGCTGGGGTCCCGAAG                         GATTACACTGGGAAGGAGGTTAATGTCAAAAACTTGTTTGCTGTTCTGCTC
genomic: TCATCATCAACCATCCCCAGGGTGGCGATGTCTATGCTGGGGTCCCGAAGgtaaccgtgc ... ttcactgtagGATTACACTGGGAAGGAGGTTAATGTCAAAAACTTGTTTGCTGTTCTGCTC
EST: gi|58607687|gb|CK035720.1|CK035720
EST:     TCGTCATCAACCATCCCCAGGGTGGCGATGTCTATGCTGGGGTCCCGAAG                         GATTACACTGGGAAGGAGGTTAATGTCAAAAACTTGTTTGCTGTTCTGCTC
genomic: TCATCATCAACCATCCCCAGGGTGGCGATGTCTATGCTGGGGTCCCGAAGgtaaccgtgc ... ttcactgtagGATTACACTGGGAAGGAGGTTAATGTCAAAAACTTGTTTGCTGTTCTGCTC
EST: gi|58691139|gb|CK079826.1|CK079826
EST:     TCATCATCAACCATCCCCA-GGTGGCGATGTCTATGCTGGGGTCCCGAAG                         GATTACACTGGGAAGGAGGTTAATGTCAAAAACTTGTTTGCTGTTCTGCTC
genomic: TCATCATCAACCATCCCCAGGGTGGCGATGTCTATGCTGGGGTCCCGAAGgtaaccgtgc ... ttcactgtagGATTACACTGGGAAGGAGGTTAATGTCAAAAACTTGTTTGCTGTTCTGCTC
EST: gi|58692937|gb|CK081624.1|CK081624
EST:     TCATCATCAACCATCCCCAGGGTGGCGATGTCTATGCTGGGGTCCCGAAG                         GATTACACTGGGAAGGAGGTTAATGTCAAAAACTTGTTTGCTGTTCTGCTC
genomic: TCATCATCAACCATCCCCAGGGTGGCGATGTCTATGCTGGGGTCCCGAAGgtaaccgtgc ... ttcactgtagGATTACACTGGGAAGGAGGTTAATGTCAAAAACTTGTTTGCTGTTCTGCTC
EST: gi|58688098|gb|CK076785.1|CK076785
EST:     TCATCATCAACCATCCCCAGTGTGGCGATGTCTATGCTGGGGTCCCGAAG                         GATTACACTGGGAAGGAGGTTAATGTCAAAAACTTGTTTGCTGTTCTGCTC
genomic: TCATCATCAACCATCCCCAGGGTGGCGATGTCTATGCTGGGGTCCCGAAGgtaaccgtgc ... ttcactgtagGATTACACTGGGAAGGAGGTTAATGTCAAAAACTTGTTTGCTGTTCTGCTC
EST: gi|58691202|gb|CK079889.1|CK079889
EST:     TCATCATCAACCATCCCCAGGNTGGCGATGTCTATGCTGGGGTCCCGAAG                         GATTACACTGGGAAGGAGGTTAATGTCAAAAACTTGTTTGCTGTTCTGCTC
genomic: TCATCATCAACCATCCCCAGGGTGGCGATGTCTATGCTGGGGTCCCGAAGgtaaccgtgc ... ttcactgtagGATTACACTGGGAAGGAGGTTAATGTCAAAAACTTGTTTGCTGTTCTGCTC
EST: gi|58692544|gb|CK081231.1|CK081231
EST:     TCATCATCAACCATCCCCAGGGTGGCGATGTCTATGCTGGGGTCCCGAAG                         GATTACACTGGGAAGGAGGTTAATGTCAAAAACTTGTTTGCTGTTCTGCTC
genomic: TCATCATCAACCATCCCCAGGGTGGCGATGTCTATGCTGGGGTCCCGAAGgtaaccgtgc ... ttcactgtagGATTACACTGGGAAGGAGGTTAATGTCAAAAACTTGTTTGCTGTTCTGCTC

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: 71 (upstream exon), 75 (downstream exon)
Score: 161

CTTCATGTACGATGACATCGCGCACAACCCGGAGAATCCGAGGCCTGGTGTCATCATCAACCATCCCCAGGGTGGCGATGTCTATGCTGGGGTCCCGAAGgtaaccgtgc ... ttcactgtagGATTACACTGGGAAGGAGGTTAATGTCAAAAACTTGTTTGCTGTTCTGCTCGGTAACAAAACTGCTGTCAAAGGTGGGAGTGGCAAAGTCCTGGACAGTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCATGTACGATGACATCGCGCACAACCCGGAGAATCCGAGGCCTGGTGTCATCATCAACCATCCCCAGGGTGGCGATGTCTATGCTGGGGTCCCGAAGgtaaccgtgcatgttcattcttcaggagaattattgatgctagctataatttcttcggttacctttctaaagaaatgttacagtgtgacgataagatttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG