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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGAACTTGAAAAAATTGCAGTTGTTCATCTACTGCAGCACAGGTCTATCATCTCACTGATAGGGAATGTACAGAGATCGTCATTGATTCTTGAGAAGgttattatctcttagccaccgaaaactctggttggacatattgttgatgaacacgattacttgcaatcctgtatgctagggtgtacttttatttttgcagggcattgactggtttgttttttgcatctaatcatttacatttgttgctgtacgccag

Basic information

species Oryza sativa
transcript LOC_Os03g63330.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63330.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G024686_T01 (Zea mays), 5'ss of exon 11
TGAAGAACTTGAAAAAATTGCAGTTGTTCATCTACTGCAGCACAGGTCTATCATCTCACTGATAGGGAATGTACAGAGATCGTCATTGATTCTTGAGAAGgttattatctcttagccaccgaaaactctggttggacatattgttgatgaacacgattacttgcaatcctgtatgctagggtgtacttttatttttgcagggcattgactggtttgttttttgcatctaatcatttacatt-tgttgctgtacgccag
|||||| ||| ||||| |||||||||||||||| ||||| |  || || ||||||||||||||||||||||||||| ||||||||||||||||||| ||||| ||    | | |         |  | |     ||||| ||||                ||   | | |  ||||||||  || ||||||||||   ||   || |||  |      |         |||   | ||  | | |||||| | |||||
TGAAGAGCTTAAAAAATTTGCAGTTGTTCATCTGCTGCAACGTAGATCGATCATCTCACTGATAGGGAATGTACAGCGATCGTCATTGATTCTTGAAAAGgtcatagcttttca--tgatactacttgtaacatgacatcttgtga--------------ttctgaactttcatgctaggtcgtgcttttatttt---agataatggacatgagaacatg--------aatggctgaccctgttttgctgcatgccag
















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|29614037|gb|CB619050.1|CB619050
EST:     TCATCTCACTGATAGGGAATGTACAGAGATCGTCATTGATTCTTGAGAAG                         GCTTTCAATGTTCTACGGAGAAATGGCGTTAACGTCCAGATGATCTCACAA
genomic: TCATCTCACTGATAGGGAATGTACAGAGATCGTCATTGATTCTTGAGAAGgttattatct ... tgtacgccagGCTTTCAATGTTCTACGGAGAAATGGCGTTAACGTCCAGATGATCTCACAA
EST: gi|89175548|gb|CI042569.1|CI042569
EST:     TCATCTCACTGATAGGGAATGTACAGAGATCGTCATTGATTCTTGAGAAG                         GCTTTCAATGTTCTACGGAGAAATGGCGTTAACGTCCAGATGATCTCACAA
genomic: TCATCTCACTGATAGGGAATGTACAGAGATCGTCATTGATTCTTGAGAAGgttattatct ... tgtacgccagGCTTTCAATGTTCTACGGAGAAATGGCGTTAACGTCCAGATGATCTCACAA
EST: gi|29613803|gb|CB618816.1|CB618816
EST:     TCATCTCACTGATAGGGAATGTACAGAGATCGTCATTGATTCTTGAGAAG                         GCTTTCAATGTTCTACGGAGAAATGGCGTTAACGTCCAGATGATCTCACAA
genomic: TCATCTCACTGATAGGGAATGTACAGAGATCGTCATTGATTCTTGAGAAGgttattatct ... tgtacgccagGCTTTCAATGTTCTACGGAGAAATGGCGTTAACGTCCAGATGATCTCACAA
EST: gi|33802989|gb|CF327365.1|CF327365
EST:     TCATCTCACTGATAGGGAATGCACAGAGATCGTCATTGATTCTTGAGAAG                         GCTTTCAATGTTCTACGGAGAAATGGCGTTAACGTCCAGATGATCTCACAA
genomic: TCATCTCACTGATAGGGAATGTACAGAGATCGTCATTGATTCTTGAGAAGgttattatct ... tgtacgccagGCTTTCAATGTTCTACGGAGAAATGGCGTTAACGTCCAGATGATCTCACAA
EST: gi|33802987|gb|CF327364.1|CF327364
EST:     TCATCTCACTGATAGGGAATGCACAGAGATCGTCATTGATTCTTGAGAAG                         GCTTTCAATGTTCTACGGAGAAATGGCGTTAACGTCCAGATGATCTCACAA
genomic: TCATCTCACTGATAGGGAATGTACAGAGATCGTCATTGATTCTTGAGAAGgttattatct ... tgtacgccagGCTTTCAATGTTCTACGGAGAAATGGCGTTAACGTCCAGATGATCTCACAA
EST: gi|88244538|gb|CI243660.1|CI243660
EST:     TGATTCTTGAGAAG                         GCTTTCAATGTTGTACGGAGAAATGGCGTTAACGTCCAGATGATCTCACAA
genomic: TGATTCTTGAGAAGgttattatct ... tgtacgccagGCTTTCAATGTTCTACGGAGAAATGGCGTTAACGTCCAGATGATCTCACAA
EST: gi|29618752|gb|CB623764.1|CB623764
EST:     TCATCTCACTGATAGGGAATGTACAGAGATCGTCATTGATTCTTGAGAAG                         GCTTTCAATGTTCTACGGAGAAATGGCGTTAACGTCCAGATGATCTCACAA
genomic: TCATCTCACTGATAGGGAATGTACAGAGATCGTCATTGATTCTTGAGAAGgttattatct ... tgtacgccagGCTTTCAATGTTCTACGGAGAAATGGCGTTAACGTCCAGATGATCTCACAA
EST: gi|89172744|gb|CI022623.1|CI022623
EST:     TCATCTCACTGATAGGGAATGTACAGAGATCGTCATTGATTCTTGAGAAG                         GCTTTCAATGTTCTACGGAGAAATGGCGTTAACGTCCAGATGATCTCACAA
genomic: TCATCTCACTGATAGGGAATGTACAGAGATCGTCATTGATTCTTGAGAAGgttattatct ... tgtacgccagGCTTTCAATGTTCTACGGAGAAATGGCGTTAACGTCCAGATGATCTCACAA
EST: gi|29683344|gb|CB679619.1|CB679619
EST:     TCATCTCACTGATAGGGAATGTACAGAGATCGTCATTGATTCTTGAGAAG                         GCTTTCAATGTTCTACGGAGAAATGGCGTTAACGTCCAGATGATCTCACAA
genomic: TCATCTCACTGATAGGGAATGTACAGAGATCGTCATTGATTCTTGAGAAGgttattatct ... tgtacgccagGCTTTCAATGTTCTACGGAGAAATGGCGTTAACGTCCAGATGATCTCACAA
EST: gi|86504684|gb|CI147317.1|CI147317
EST:     TCGTCATTGATTCTTGAGAAG                         GCTTTCAATGTTCTACGGAGAAATGGCGTTAACGTCCAGATGATCTCACAA
genomic: TCGTCATTGATTCTTGAGAAGgttattatct ... tgtacgccagGCTTTCAATGTTCTACGGAGAAATGGCGTTAACGTCCAGATGATCTCACAA

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: 64 (upstream exon), 63 (downstream exon)
Score: 31

TGAAGAACTTGAAAAAATTGCAGTTGTTCATCTACTGCAGCACAGGTCTATCATCTCACTGATAGGGAATGTACAGAGATCGTCATTGATTCTTGAGAAGgttattatct ... tgtacgccagGCTTTCAATGTTCTACGGAGAAATGGCGTTAACGTCCAGATGATCTCACAAGGGGCATCCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGAACTTGAAAAAATTGCAGTTGTTCATCTACTGCAGCACAGGTCTATCATCTCACTGATAGGGAATGTACAGAGATCGTCATTGATTCTTGAGAAGgttattatctcttagccaccgaaaactctggttggacatattgttgatgaacacgattacttgcaatcctgtatgctagggtgtacttttatttttgcagggcattgactggtttgttttttgcatctaatcatttacatttgttgctgtacgccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC