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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAATTATGGAAAGAAAGATCCAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAGgtttgccttgactctatatgctttatatgtttcttcatggggtttaccttattgtcaaaagaatcttactctcttgtaaattatgatttctatagcggat...

Basic information

species Oryza sativa
transcript LOC_Os05g46580.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g46580.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G168681_T01 (Zea mays), 5'ss of exon 11
GAAAATTATGGAAAGAAAGATCCAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAGgtttgccttg----actctatatgct-ttatatgtttcttcatggggtttaccttattgtcaaaagaatcttactctcttgtaaattatgatttctatagcggat
||||||||||| |||||||||||||||||||||||||||||||||| |||||||| ||||||  |||||||||| || ||      || ||  |||    | | ||||| |   | |    ||     |||   |   || |  ||| |     | || |||   |  |||      
GAAAATTATGGCAAGAAAGATCCAGCCTGTGTGGCAAAAGTGAAGAACCTCTACAAAGAACTTGACCTAGAGgtctgtctctctctaccctggatgaagctttctgtttatctgtagatcgtaatcacttgctcatgtaaacccactat---aaacataatgcagtaaatactaa--
















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|86427859|gb|CI072956.1|CI072956
EST:     CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAG                         GCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT
genomic: CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAGgtttgccttg ... tcattcttagGCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT
EST: gi|88536591|gb|CI466359.1|CI466359
EST:     CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAG                         GCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT
genomic: CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAGgtttgccttg ... tcattcttagGCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT
EST: gi|89168374|gb|CI109578.1|CI109578
EST:     CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAG                         GCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT
genomic: CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAGgtttgccttg ... tcattcttagGCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT
EST: gi|88384763|gb|CI556641.1|CI556641
EST:     CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAG                         GCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT
genomic: CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAGgtttgccttg ... tcattcttagGCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT
EST: gi|58685871|gb|CK074558.1|CK074558
EST:     CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAG                         GCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT
genomic: CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAGgtttgccttg ... tcattcttagGCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT
EST: gi|58678948|gb|CK067635.1|CK067635
EST:     CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAG                         GCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT
genomic: CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAGgtttgccttg ... tcattcttagGCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT
EST: gi|88366302|gb|CI551134.1|CI551134
EST:     CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAG                         GCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT
genomic: CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAGgtttgccttg ... tcattcttagGCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT
EST: gi|86434011|gb|CI094354.1|CI094354
EST:     CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAG                         GCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT
genomic: CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAGgtttgccttg ... tcattcttagGCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT
EST: gi|88247621|gb|CI247470.1|CI247470
EST:     CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAG                         GCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT
genomic: CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAGgtttgccttg ... tcattcttagGCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT
EST: gi|163928447|gb|EG711347.1|EG711347
EST:     CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAG                         GCGGTCTTTCTGGACTATGAGAA
genomic: CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAGgtttgccttg ... tcattcttagGCGGTCTTTCTGGACTATGAGAA
EST: gi|88247405|gb|CI247254.1|CI247254
EST:     CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAG                         GCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT
genomic: CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAGgtttgccttg ... tcattcttagGCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT
EST: gi|88968869|gb|CI098954.1|CI098954
EST:     CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAG                         GCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT
genomic: CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAGgtttgccttg ... tcattcttagGCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT
EST: gi|58674478|gb|CK063165.1|CK063165
EST:     CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAG                         GCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT
genomic: CAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAGgtttgccttg ... tcattcttagGCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGAT

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: 25 (upstream exon), 74 (downstream exon)
Score: 26

GAAAATTATGGAAAGAAAGATCCAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAGgtttgccttg ... tcattcttagGCGGTCTTTCTGGACTATGAGAACGAGAGTTACAAGAAGTTGATTGCGGATATAGAAGCCCAGCCAAGCATAGCTGTTCAGAATGTTCTGAAGTCCTTCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAATTATGGAAAGAAAGATCCAGCCTGTGTGGCAAAAGTGAAGAGCCTCTACAGAGAACTAAACCTAGAGgtttgccttgactctatatgctttatatgtttcttcatggggtttaccttattgtcaaaagaatcttactctcttgtaaattatgatttctatagcggat

- - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagaa