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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAGAATATCTGCAGCTTGATCAGTTCCAAAACTGAGATATATCTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcgatcgctttgctttaatttgcactatttaatttgtccatgccactgacagattcctcctcttggcagcag

Basic information

species Oryza sativa
transcript LOC_Os01g38229.2
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|29635968|gb|CB640977.1|CB640977
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGCAG                       
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACC-G--GCAGgtatactcga ... ttggcagc
EST: gi|2427665|gb|C72128.1|C72128
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAG                         TTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGCCGA
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ttggcagcagTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGCCGA
EST: gi|33676380|gb|CF304619.1|CF304619
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGCAG                       
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACC-G--GCAGgtatactcga ... ttggcagc
EST: gi|33676436|gb|CF304675.1|CF304675
EST:     AAAACTTTAGCTGGGCACGCACTACCGGCAGCAG                       
genomic: AAAACTTTAGCTGGGCACGCACTACC-G--GCAGgtatactcga ... ttggcagc
EST: gi|88367669|gb|CI568441.1|CI568441
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGCAG                       
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACC-G--GCAGgtatactcga ... ttggcagc
EST: gi|88405610|gb|CI588816.1|CI588816
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGCAG                       
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACC-G--GCAGgtatactcga ... ttggcagc
EST: gi|88401684|gb|CI588625.1|CI588625
EST:     CTGCAGCTTGATCAGTTCCAAAAATTTAGCTGGGCACGCACTACCGGCAGCAG                       
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACC-G--GCAGgtatactcga ... ttggcagc
EST: gi|88744080|gb|CI767440.1|CI767440
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGCAG                       
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACC-G--GCAGgtatactcga ... ttggcagc
EST: gi|88410785|gb|CI578591.1|CI578591
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGCAG                       
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACC-G--GCAGgtatactcga ... ttggcagc
EST: gi|88745808|gb|CI769168.1|CI769168
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGCAG                       
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACC-G--GCAGgtatactcga ... ttggcagc
EST: gi|88735124|gb|CI758632.1|CI758632
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGCAG                       
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACC-G--GCAGgtatactcga ... ttggcagc
EST: gi|88370128|gb|CI585133.1|CI585133
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGCAG                       
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACC-G--GCAGgtatactcga ... ttggcagc
EST: gi|88741944|gb|CI764449.1|CI764449
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGCAG                       
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACC-G--GCAGgtatactcga ... ttggcagc
EST: gi|88735330|gb|CI758838.1|CI758838
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGCAG                       
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACC-G--GCAGgtatactcga ... ttggcagc
EST: gi|88444063|gb|CI594436.1|CI594436
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAG                         TTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGCCGA
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ttggcagcagTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGCCGA
EST: gi|88762537|gb|CI772093.1|CI772093
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGCAG                       
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACC-G--GCAGgtatactcga ... ttggcagc
EST: gi|88386177|gb|CI570812.1|CI570812
EST:     CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGCAG                       
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACC-G--GCAGgtatactcga ... ttggcagc
EST: gi|88417649|gb|CI581672.1|CI581672
EST:     CTGCAGCTTGATCAGTT-CAAAACTTTAGCTGGGCACGCACTACCGGCAG                         TTCAAGGACAAACCAATTTGAAGGGGGCTAGCGCCAGCACAGGCATGCCGA
genomic: CTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ttggcagcagTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGCCGA

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: 7

AGAGAATATCTGCAGCTTGATCAGTTCCAAAACTGAGATATATCTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcga ... ttggcagcagTTCAAGGACAAACCAATTTGAAGGCGGCTAGCGCCAGCACAGGCATGCCGATCTCGCATGAGCTGGGCGAGCCTGACGAAAGCTTCTACAATCTATGGAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAGAATATCTGCAGCTTGATCAGTTCCAAAACTGAGATATATCTGCAGCTTGATCAGTTCCAAAACTTTAGCTGGGCACGCACTACCGGCAGgtatactcgatcgctttgctttaatttgcactatttaatttgtccatgccactgacagattcctcctcttggcagcag

- - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - -  GCAGCT