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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAGgtgacattttcctttcttaacacttggcatataatacaatccacaccattcctttgaattatgagctcttacttgatgtatgttttctgtatttag

Basic information

species Oryza sativa
transcript LOC_Os12g01430.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01430.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G109133_T01 (Zea mays), 5'ss of exon 1
GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAGgtgacat---tttcctttcttaacacttggcatataatacaatccacaccattcctttga--attatgagctcttacttgatgtatgttttctgtatttag
    ||  | ||||| |||||||| |||||||||| |||||||||| | ||||||||||||||||| |||||||| || ||||||||||||| || |    || ||||| | |  | || | |   | |  | ||||      ||     |  | |||||| | ||    || |||  ||  |||| |||||
----TTTTTCGCTGGGAAGAAGGTTATGCAGATAGGGTTGGGGCGTCCGCCTGCTGATGAAGCTAAGACAGGCCTCCACAAACTTTCCAAGgcgagagctattccctttttcagaatttagtaggcattgtattccagtttcctcagaccatcagtatgaggttttgaccgaagtaacttcgctgtgtttag

upper sequence: LOC_Os12g01430.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G155437_T01 (Zea mays), 5'ss of exon 3
GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAGgtgacat---tttcctttcttaacacttggcatataatacaatccacaccattcctttga--attatgagctcttacttgatgtatgttttctgtatttag
|||||| || ||||| |||||||| |||||||||||| ||||||||||| |||||||||||||||| |||||||| || |||||||| |||| || |    || ||||| | |  | || | |     |  | ||||      ||     |  | |||||| | ||    || |||  ||  |||| |||||
GATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCAGCTGCTGATGAAGCTAAGACAGGCCTCCACAAACTTTCAAAGgcgagagctgttccctttttcagaatttagtaggcgctgtattccagtttcctcagaccatcagtatgaggttttgaccgaagtaacttcgctgtgtttag

upper sequence: LOC_Os12g01430.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G477632_T01 (Zea mays), 5'ss of exon 2
---------GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAGgtgacat---tttcctttcttaacacttggcatataatacaatccacaccattcctttga--attatgagctcttacttgatgtatgttttctgtatttag
         |||||| || ||||| |||||||| ||||||||||||||||||||| | ||||||||||||||| | |||||||| || ||||||||||||| || |    || ||||| |  | | || | |     |  | ||||      ||     |  | |||||| | ||    || |||  ||  |||| |||||
CTGTTCCAGGATATTTCTCGCTGGGAAGAAGGTTATGCAGATAGCGTTGGGGCGTCCGCCTGCTGATGAAGCTGAGACAGGCCTCCACAAACTTTCCAAGgcgagagctgttccctttttcgaaatttagtaggcgctgtattccagtttcctcagaccatcagtatgaggttttgaccgaagtaacttcgctgtgtttag

upper sequence: LOC_Os12g01430.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G467086_T01 (Zea mays), 5'ss of exon 3
GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAGgtgacattt-tcctttcttaacacttggcatataatacaatccacaccattcctttgaattatgagctcttacttgatgtatgttttctgtatttag
||| || || |||||||||||||| |||||||||||| |||||||||| |||||||||||||||||||||||||| || |||||||||||||||| |  | | | || | |  | || | |   | | || |||   |||||       | |||||  | ||  |  | |||  ||  | || |||||
GATTTTTCTCGCTGGAAAGAAGGTTATGCAGATAGCGCTGGGGCGTTCGCCTGCTGATGAAGCTAAAACAGGCCTCCACAAACTTTCCAAGgtgagacctgttccttttcagaatttagtaggcactgcattcc---ccatt-------aatatgacgttttgatgaaagtaacttcgccgtgtttag

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|33798312|gb|CF325013.1|CF325013
EST:     GGCGTTCATCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAG                         TTCCTACAAGGTGATACTGGACTGTTCTTTACTAATCTTCCAAGAGATGAT
genomic: GGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAGgtgacatttt ... ctgtatttagTTCCTACAAGGTGATACTGGACTGTTCTTTACTAATCTTCCAAGAGATGAT
EST: gi|33822729|gb|CF337172.1|CF337172
EST:     GGCGTTCATCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTNTCCAAG                         TTCCTACAAGGTGATACTGGACTGTTCTTTACTAATCTTCCAAGAGATGAT
genomic: GGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAGgtgacatttt ... ctgtatttagTTCCTACAAGGTGATACTGGACTGTTCTTTACTAATCTTCCAAGAGATGAT
EST: gi|33686639|gb|CF314878.1|CF314878
EST:     GGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAG                         TTCCTACAAGGTGATACTGGACTGTTCTTTACTAATCTTCCAAGAGATGAT
genomic: GGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAGgtgacatttt ... ctgtatttagTTCCTACAAGGTGATACTGGACTGTTCTTTACTAATCTTCCAAGAGATGAT
EST: gi|163918505|gb|EG711435.1|EG711435
EST:     GGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAG                         TTCCTACAAGGTGATACTGGACTGTTCTTTACTAATCTTCCAAGAGATGAT
genomic: GGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAGgtgacatttt ... ctgtatttagTTCCTACAAGGTGATACTGGACTGTTCTTTACTAATCTTCCAAGAGATGAT
EST: gi|55440809|gb|CV733716.1|CV733716
EST:     GGCGTTCATCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAG                         TTCCTACAAGGTGATACTGGACTGTTCTTTACTAATCTTCCAAGAGATGAT
genomic: GGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAGgtgacatttt ... ctgtatttagTTCCTACAAGGTGATACTGGACTGTTCTTTACTAATCTTCCAAGAGATGAT
EST: gi|88347469|gb|CI637409.1|CI637409
EST:     GGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAG                         TTCCTACAAGGTGATACTGGACTGTTC
genomic: GGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAGgtgacatttt ... ctgtatttagTTCCTACAAGGTGATACTGGACTGTTC
EST: gi|218490970|gb|FG950243.1|FG950243
EST:     GGCGTTCACCTGCTGATGAATCTAAAACAGGCCTTCATAAACTTTCCAAG                         TTCCTACAAGGTGATACTGGACTGTTCTTTACTA
genomic: GGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAGgtgacatttt ... ctgtatttagTTCCTACAAGGTGATACTGGACTGTTCTTTACTA
EST: gi|163925538|gb|EG713379.1|EG713379
EST:     GGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAG                         TTCCTACAAGGTGATACTGGACTGTTCTTTACTAATCTTCCAAGAGATGAT
genomic: GGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAGgtgacatttt ... ctgtatttagTTCCTACAAGGTGATACTGGACTGTTCTTTACTAATCTTCCAAGAGATGAT
EST: gi|88302253|gb|CI668099.1|CI668099
EST:     GGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAG                         TTCCTACAAGGTGATACTGGACTGTTCTTTACTAATCTTCCAAGAGATGAT
genomic: GGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAGgtgacatttt ... ctgtatttagTTCCTACAAGGTGATACTGGACTGTTCTTTACTAATCTTCCAAGAGATGAT
EST: gi|88302497|gb|CI668343.1|CI668343
EST:     GGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAG                         TTCCTACAAGGTGATACTGGACTGTTCTTTACTAATCTTCCAAGAGATGAT
genomic: GGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAGgtgacatttt ... ctgtatttagTTCCTACAAGGTGATACTGGACTGTTCTTTACTAATCTTCCAAGAGATGAT
EST: gi|88294157|gb|CI667131.1|CI667131
EST:     GGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAG                         TTCCTACAAGGTGATACTGGACTGTTCTTTACTAATCTTCCAAGAGATGAT
genomic: GGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAGgtgacatttt ... ctgtatttagTTCCTACAAGGTGATACTGGACTGTTCTTTACTAATCTTCCAAGAGATGAT
EST: gi|218498120|gb|FG965520.1|FG965520
EST:     GGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAG                         TTCCTACAAGGTGATACTGGACTGTTCTTTACTAATCTTCCAAGAGATGAT
genomic: GGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAGgtgacatttt ... ctgtatttagTTCCTACAAGGTGATACTGGACTGTTCTTTACTAATCTTCCAAGAGATGAT

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: 19

GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAGgtgacatttt ... ctgtatttagTTCCTACAAGGTGATACTGGACTGTTCTTTACTAATCTTCCAAGAGATGATGTAGAGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATATTCCTTGCTGGAAAGAAGGTCATGCAGATAGCGTTGGGGCGTTCACCTGCTGATGAAGCTAAAACAGGCCTTCATAAACTTTCCAAGgtgacattttcctttcttaacacttggcatataatacaatccacaccattcctttgaattatgagctcttacttgatgtatgttttctgtatttag

- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC