Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGTTCGTTGCAATTGGGCAACAAAGGGTGCTAATGCTGGTGAAGAGAAACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAGgtgaatatacatgccttttgtcctggcccacttgttttggtttaagtcaatacatgattgtaatatgtaatgtaacaatcaactgagcaagagctctgttaaatggctagaaagtactgaactgtaaagtattccatgttcttttttatgcag

Basic information

species Oryza sativa
transcript LOC_Os11g40510.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g40510.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM5G835213_T02 (Zea mays), 5'ss of exon 9
------CAAGTTCGTTGCAATTGGGCAACAAAGGGTGCTAATGCTGGTGAAGAGAAACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAGgtgaatatacatgccttttgtcctggcccacttgttttggtttaagtcaatacatgattgtaatatgt--aatgtaacaatcaactgagcaagagctctgttaaatggctagaaagtactgaactgtaaagtattccatgttcttttttatgcag
      ||| ||||||||||||||||||| || |||||||||||||||||||||||||| | |   ||| | |||| |      ||  || |||||||||||||||||||||| |  ||| ||   | || |    ||| | ||  | | |||   |  |  | ||  |   |    | ||  | | ||||  ||   | |||| | |                                                     
AACCGTCAAATTCGTTGCAATTGGGCAACGAAAGGTGCTAATGCTGGTGAAGAGAAACAGATTCTGGACACTAAGGTT------GACCTGTCAAATGGTTCATCAGgtgaatacatgtgctttggcttcttga--gcttctctttttctgagtgtttcaaaaagtgctagccgctagacgtgcctagcaacctaggtggtgctcaggt-----------------------------------------------------
















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|218488516|gb|FG953157.1|FG953157
EST:     ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAG                         AAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
genomic: ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAGgtgaatatac ... ttttatgcagAAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
EST: gi|58688359|gb|CK077046.1|CK077046
EST:     ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAG                         AAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
genomic: ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAGgtgaatatac ... ttttatgcagAAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
EST: gi|58687280|gb|CK075967.1|CK075967
EST:     ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAG                         AAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
genomic: ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAGgtgaatatac ... ttttatgcagAAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
EST: gi|29640531|gb|CB645540.1|CB645540
EST:     TGATAGAG-TGGCAAAATGGTTCATCAG                         AAGGTGGAAAGGATAATGCAAATGAAGATGGTCC-GAAAACAACCCACAGT
genomic: TGATAGAGTTGAC-AAATGGTTCATCAGgtgaatatac ... ttttatgcagAAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
EST: gi|58602505|gb|CK013033.1|CK013033
EST:     ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAG                         AAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
genomic: ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAGgtgaatatac ... ttttatgcagAAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
EST: gi|33680119|gb|CF308358.1|CF308358
EST:     ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAG                         AGGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
genomic: ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAGgtgaatatac ... ttttatgcagAAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
EST: gi|88572117|gb|CI663688.1|CI663688
EST:     ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAG                         AAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
genomic: ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAGgtgaatatac ... ttttatgcagAAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
EST: gi|58678674|gb|CK067361.1|CK067361
EST:     ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAG                         AAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
genomic: ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAGgtgaatatac ... ttttatgcagAAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
EST: gi|58690866|gb|CK079553.1|CK079553
EST:     ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAG                         AAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAAGCCACAGT
genomic: ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAGgtgaatatac ... ttttatgcagAAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
EST: gi|218482201|gb|FG960522.1|FG960522
EST:     ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAG                         AAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
genomic: ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAGgtgaatatac ... ttttatgcagAAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
EST: gi|218500911|gb|FG960833.1|FG960833
EST:     ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAG                         AAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
genomic: ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAGgtgaatatac ... ttttatgcagAAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
EST: gi|58597389|gb|CK007917.1|CK007917
EST:     ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAG                         AAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
genomic: ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAGgtgaatatac ... ttttatgcagAAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
EST: gi|325494350|gb|JG458874.1|JG458874
EST:     CCAAAATACAGACTCCAAGGGTATGATAGAGTCGACAAATGGTTCATCAG                         AAGGTGGAAAG
genomic: ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAGgtgaatatac ... ttttatgcagAAGGTGGAAAG
EST: gi|58606512|gb|CK034545.1|CK034545
EST:     ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCTG                         AAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
genomic: ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAGgtgaatatac ... ttttatgcagAAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
EST: gi|58601763|gb|CK012291.1|CK012291
EST:     ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAG                         AAGGTGGAAAGGATCATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
genomic: ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAGgtgaatatac ... ttttatgcagAAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
EST: gi|86596642|gb|CI286555.1|CI286555
EST:     ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAG                         AAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
genomic: ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAGgtgaatatac ... ttttatgcagAAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
EST: gi|87004665|gb|CI300987.1|CI300987
EST:     ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAG                         AAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT
genomic: ACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAGgtgaatatac ... ttttatgcagAAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGT

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: 72 (upstream exon), 73 (downstream exon)
Score: 180

CAAGTTCGTTGCAATTGGGCAACAAAGGGTGCTAATGCTGGTGAAGAGAAACAAAATACAGACTCCAAGGGTATGATAGAGTTGACAAATGGTTCATCAGgtgaatatac ... ttttatgcagAAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT




<











<


<