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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGCCACCACCACCTTCATATGAAGAAATTAACGGTGTTTTCATGAGGAATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAGgtacccaatcatcacttcaccacaatgcacaagtttgtagcttactactacagtacttctaataagttttgtctgttgagattttattgctgatttctatgcatggtcatctttttgacag

Basic information

species Oryza sativa
transcript LOC_Os10g36870.1
intron # 8
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|88274989|gb|CI395593.1|CI395593
EST:     ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAG                         GCCATCCAGTCTTATCGTGCTTAGAGTGAAACTGAGCTCAACCTGGCAGCT
genomic: ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAGgtacccaatc ... tttttgacagGCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
EST: gi|163923564|gb|EG713305.1|EG713305
EST:     ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAG                         GCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
genomic: ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAGgtacccaatc ... tttttgacagGCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
EST: gi|86433259|gb|CI093602.1|CI093602
EST:     ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAG                         GCCATCCAGTCTGATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
genomic: ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAGgtacccaatc ... tttttgacagGCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
EST: gi|88224342|gb|CI224191.1|CI224191
EST:     ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAG                         GCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
genomic: ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAGgtacccaatc ... tttttgacagGCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
EST: gi|89194036|gb|CI116473.1|CI116473
EST:     ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGGATTCTTCTTGGCTGAG                         GCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
genomic: ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAGgtacccaatc ... tttttgacagGCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
EST: gi|86503263|gb|CI145896.1|CI145896
EST:     ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAG                         GCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
genomic: ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAGgtacccaatc ... tttttgacagGCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
EST: gi|27546007|gb|CA764097.2|CA764097
EST:     ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAG                         GCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
genomic: ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAGgtacccaatc ... tttttgacagGCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
EST: gi|58686839|gb|CK075526.1|CK075526
EST:     ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAG                         GCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
genomic: ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAGgtacccaatc ... tttttgacagGCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
EST: gi|58677463|gb|CK066150.1|CK066150
EST:     ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAG                         GCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
genomic: ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAGgtacccaatc ... tttttgacagGCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
EST: gi|88971184|gb|CI387161.1|CI387161
EST:     TCTTGGCTGAG                         GCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
genomic: TCTTGGCTGAGgtacccaatc ... tttttgacagGCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
EST: gi|86826437|gb|CI364093.1|CI364093
EST:     ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAG                         GCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
genomic: ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAGgtacccaatc ... tttttgacagGCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
EST: gi|88955398|gb|CI091490.1|CI091490
EST:     ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAG                         GCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
genomic: ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAGgtacccaatc ... tttttgacagGCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
EST: gi|86494493|gb|CI137126.1|CI137126
EST:     ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAG                         GCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
genomic: ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAGgtacccaatc ... tttttgacagGCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
EST: gi|86887314|gb|CI313217.1|CI313217
EST:     ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAG                         GCCATCCAGTCTTATCGTGCTGAGAATGAAACTGAGCTCAACCTGGCAGCT
genomic: ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAGgtacccaatc ... tttttgacagGCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
EST: gi|86504689|gb|CI147322.1|CI147322
EST:     ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAG                         GCCATCCAGTCTTATCGTGCTGAGAGTGAAATTGAGCTCAACCTGGCAGCT
genomic: ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAGgtacccaatc ... tttttgacagGCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
EST: gi|86522594|gb|CI162800.1|CI162800
EST:     ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAG                         GCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
genomic: ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAGgtacccaatc ... tttttgacagGCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
EST: gi|88955405|gb|CI091497.1|CI091497
EST:     TGGAATTCTTCTTGGCTGAG                         GCCATCCAGTCTCATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
genomic: TGGAATTCTTCTTGGCTGAGgtacccaatc ... tttttgacagGCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
EST: gi|88226552|gb|CI226468.1|CI226468
EST:     ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAG                         GCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
genomic: ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAGgtacccaatc ... tttttgacagGCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
EST: gi|86493455|gb|CI136088.1|CI136088
EST:     ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAG                         GCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAACT
genomic: ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAGgtacccaatc ... tttttgacagGCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
EST: gi|88227434|gb|CI226914.1|CI226914
EST:     ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAG                         GCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
genomic: ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAGgtacccaatc ... tttttgacagGCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
EST: gi|87011472|gb|CI279381.1|CI279381
EST:     ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAG                         GCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
genomic: ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAGgtacccaatc ... tttttgacagGCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
EST: gi|88830101|gb|CI074773.1|CI074773
EST:     ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAG                         GCAATCCAGTCTGATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT
genomic: ATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAGgtacccaatc ... tttttgacagGCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCT

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: 70 (upstream exon), 50 (downstream exon)
Score: 13

TATGCCACCACCACCTTCATATGAAGAAATTAACGGTGTTTTCATGAGGAATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAGgtacccaatc ... tttttgacagGCCATCCAGTCTTATCGTGCTGAGAGTGAAACTGAGCTCAACCTGGCAGCTGGTGACTATATAGTTGTCCGGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATGCCACCACCACCTTCATATGAAGAAATTAACGGTGTTTTCATGAGGAATCCAACAGTCGCTGAATTGGTGGAAACTGTGGAATTCTTCTTGGCTGAGgtacccaatcatcacttcaccacaatgcacaagtttgtagcttactactacagtacttctaataagttttgtctgttgagattttattgctgatttctatgcatggtcatctttttgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA