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

AAAGTATCAGCAGCTTCTACCACCATCTGAGGAAGATCAAAATAAGCAGCAAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAGgtaaaagagacattagcattaaccacgtttcacacaatggtcctaatctcctgaaatattttttgtcaggatgtactgcaattagaaaacgtaactgttg...

Basic information

species Oryza sativa
transcript LOC_Os01g03144.1
intron # 11
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|163927173|gb|EG715194.1|EG715194
EST:     AAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAG                         AGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGAATGAGAGGATCA
genomic: AAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAGgtaaaagaga ... ttcttatcagAGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGAATGAGAGGATCA
EST: gi|88226038|gb|CI225954.1|CI225954
EST:     AAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAG                         AGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGAATGAGAGGATCA
genomic: AAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAGgtaaaagaga ... ttcttatcagAGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGAATGAGAGGATCA
EST: gi|88236675|gb|CI235877.1|CI235877
EST:     AAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAG                         AGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGAATGAGAGGATCA
genomic: AAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAGgtaaaagaga ... ttcttatcagAGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGAATGAGAGGATCA
EST: gi|88236563|gb|CI235765.1|CI235765
EST:     AAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAG                         AGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGAATGAGAGGATCA
genomic: AAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAGgtaaaagaga ... ttcttatcagAGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGAATGAGAGGATCA
EST: gi|88463772|gb|CI527099.1|CI527099
EST:     AAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAG                         AGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGAATGAGAGGATCA
genomic: AAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAGgtaaaagaga ... ttcttatcagAGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGAATGAGAGGATCA
EST: gi|25806937|gb|CA762898.1|CA762898
EST:     AAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAG                         AGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGAATGAGAGGATCA
genomic: AAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAGgtaaaagaga ... ttcttatcagAGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGAATGAGAGGATCA
EST: gi|86535396|gb|CI175602.1|CI175602
EST:     AAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAG                         AGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGGATGAGAGGATCA
genomic: AAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAGgtaaaagaga ... ttcttatcagAGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGAATGAGAGGATCA
EST: gi|87038312|gb|CI192934.1|CI192934
EST:     AAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAG                         AGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGAATGAGAGGATCA
genomic: AAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAGgtaaaagaga ... ttcttatcagAGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGAATGAGAGGATCA
EST: gi|88273962|gb|CI394368.1|CI394368
EST:     AAGTTAAGGAAGTGAAATGAAGTGCTG-CAGCAACATTTTGCCAGCAAAG                         AGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGAATGAGAGGATCA
genomic: AAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAGgtaaaagaga ... ttcttatcagAGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGAATGAGAGGATCA
EST: gi|88476226|gb|CI413497.1|CI413497
EST:     AAGTTAAGGAAGTTAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAG                         AGAGAAGCTGCACCTTGTTCACAGCATCTCGGCATGAGAATGAGAGGATCA
genomic: AAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAGgtaaaagaga ... ttcttatcagAGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGAATGAGAGGATCA
EST: gi|86851387|gb|CI313985.1|CI313985
EST:     AAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAG                         AGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGAATGAGAGGATCA
genomic: AAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAGgtaaaagaga ... ttcttatcagAGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGAATGAGAGGATCA
EST: gi|87039299|gb|CI193921.1|CI193921
EST:     AAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAG                         AGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGAATGAGAGGATCA
genomic: AAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAGgtaaaagaga ... ttcttatcagAGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGAATGAGAGGATCA

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: 43 (upstream exon), 67 (downstream exon)
Score: 4

AAAGTATCAGCAGCTTCTACCACCATCTGAGGAAGATCAAAATAAGCAGCAAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAGgtaaaagaga ... ttcttatcagAGAGAAGCTGCACCTTCTTCACAGCATCTCGGCATGAGAATGAGAGGATCACTAAATCATGCGGCAATAAAACAATTAGCCGCCCAAGCCCATCACTTTG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGTATCAGCAGCTTCTACCACCATCTGAGGAAGATCAAAATAAGCAGCAAGTTAAGGAAGTGAAATGAAGTGCTGCCAGCAACATTTTGCCAGCAAAGgtaaaagagacattagcattaaccacgtttcacacaatggtcctaatctcctgaaatattttttgtcaggatgtactgcaattagaaaacgtaactgttg

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG