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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTACTGGAGGAAACTGAGGATGAGgtaggctgcttctcttggatgacatttatacattactttttttatactagcaaatatcgtctgaattttcccgtttcttgacagctgtgttttgttatgaactatacagatctatcataatttagttaaaaatagggcctcatctagagctttttttggttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g02524.1
intron # 7
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|88530639|gb|CI459049.1|CI459049
EST:     AGGAAACTGAGGATGAG                         CTTTCTGAGTGGATAAAAACGAGCTCCGCAGAATCAGGAAATGTCAGCAGA
genomic: AGGAAACTGAGGATGAGgtaggctgct ... ttggttgcagCTTTCTGAGTGGATAAAAACGAGCTCCGCAGAATCAGGAAATGTCAGCAGA
EST: gi|88505777|gb|CI433283.1|CI433283
EST:     GTTACTGGAGGAAACTGAGGATGAG                         CTTTCTGAGTGGATAAAAACGAGCTCCGCAGAATCAGGAAATGTCAGCAGA
genomic: GTTACTGGAGGAAACTGAGGATGAGgtaggctgct ... ttggttgcagCTTTCTGAGTGGATAAAAACGAGCTCCGCAGAATCAGGAAATGTCAGCAGA
EST: gi|88555056|gb|CI485284.1|CI485284
EST:     CTGAGGATGAG                         CTTTCTGAGTGGATAAANACGAGCTCCGCAGAATCAGGAAATGTCAGCAGA
genomic: CTGAGGATGAGgtaggctgct ... ttggttgcagCTTTCTGAGTGGATAAAAACGAGCTCCGCAGAATCAGGAAATGTCAGCAGA
EST: gi|86539990|gb|CI180196.1|CI180196
EST:     GTTACTGGAGGAAACTGAGGATGAG                         CTTTCTGAGTGGATAAAAACGAGCTCCGCAGAATCAGGAAATGTCAGCAGA
genomic: GTTACTGGAGGAAACTGAGGATGAGgtaggctgct ... ttggttgcagCTTTCTGAGTGGATAAAAACGAGCTCCGCAGAATCAGGAAATGTCAGCAGA
EST: gi|88282038|gb|CI403434.1|CI403434
EST:     GTTACTGGAGGAAACTGAGGATGAG                         CTTTCTGAGTGGATAGAAACGAGCTCCGCAGAATCAGGAAATGTCAGCAGA
genomic: GTTACTGGAGGAAACTGAGGATGAGgtaggctgct ... ttggttgcagCTTTCTGAGTGGATAAAAACGAGCTCCGCAGAATCAGGAAATGTCAGCAGA
EST: gi|88527801|gb|CI455987.1|CI455987
EST:     GTTACTGGAGGAAACTGAGGATGAG                         CTTTCTGAGTGGATAAAAACGAGCTCCGCAGAATCAGGAAATGTCAGCAGA
genomic: GTTACTGGAGGAAACTGAGGATGAGgtaggctgct ... ttggttgcagCTTTCTGAGTGGATAAAAACGAGCTCCGCAGAATCAGGAAATGTCAGCAGA
EST: gi|427973|gb|D24119.1|D24119
EST:     GTTACTGGAGGANACTGAGGATGAG                         CTTTCTGAGTGGATAAAAACGAGCTCCGCAGAATCAGGAAATGTCAGCAGA
genomic: GTTACTGGAGGAAACTGAGGATGAGgtaggctgct ... ttggttgcagCTTTCTGAGTGGATAAAAACGAGCTCCGCAGAATCAGGAAATGTCAGCAGA
EST: gi|88271484|gb|CI387537.1|CI387537
EST:     GTTACTGGAGGAAACTGAGGATGAG                         CTTTCTGAGTGGATAAAAACGAGCTCCGCAGAATCAGGAAATGTCAGCAGA
genomic: GTTACTGGAGGAAACTGAGGATGAGgtaggctgct ... ttggttgcagCTTTCTGAGTGGATAAAAACGAGCTCCGCAGAATCAGGAAATGTCAGCAGA
EST: gi|3767712|gb|AU031739.1|AU031739
EST:     GTTACTGGAGGAAACTGAGGATGAG                         CTTTCTGAGTGGATNAAANCGA-NTCCGCAGAATCAGGAAATGTCAGCAGA
genomic: GTTACTGGAGGAAACTGAGGATGAGgtaggctgct ... ttggttgcagCTTTCTGAGTGGATAAAAACGAGCTCCGCAGAATCAGGAAATGTCAGCAGA
EST: gi|86538953|gb|CI179159.1|CI179159
EST:     GTTACTGGGAGGAAACTGAGGATGAG                         CTTTCTGAGTGGATAAAAACGAGCTCCGCAGAATCAGGAAATGTCAGCAGA
genomic: GTTACT-GGAGGAAACTGAGGATGAGgtaggctgct ... ttggttgcagCTTTCTGAGTGGATAAAAACGAGCTCCGCAGAATCAGGAAATGTCAGCAGA
EST: gi|88836249|gb|CI371354.1|CI371354
EST:     GTTACTGGAGGGAAACTGAGGATGAG                         CTTTCTGAGGTGGATAAAAAGCGAGCTCCGCAGAATCAGGAAATGTCAGCA
genomic: GTTACTGGA-GGAAACTGAGGATGAGgtaggctgct ... ttggttgcagCTTTCTGA-GTGGATAAAAA-CGAGCTCCGCAGAATCAGGAAATGTCAGCA
EST: gi|33678092|gb|CF306331.1|CF306331
EST:     GTTACTGGAGGAAACTGAGGATGAG                         CTTTNTGAGTGGATAAAAACGAGCTCCGCAGAATCAGGAAATGTCAGCAGA
genomic: GTTACTGGAGGAAACTGAGGATGAGgtaggctgct ... ttggttgcagCTTTCTGAGTGGATAAAAACGAGCTCCGCAGAATCAGGAAATGTCAGCAGA
EST: gi|88525538|gb|CI452543.1|CI452543
EST:     GTTACTGGAGGAAACTGAGGATGAG                         CTTTCTGAGTGGATAAAAACGAGCTCCGCAGAATCAGGAAATGTCAGCAGA
genomic: GTTACTGGAGGAAACTGAGGATGAGgtaggctgct ... ttggttgcagCTTTCTGAGTGGATAAAAACGAGCTCCGCAGAATCAGGAAATGTCAGCAGA

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), 71 (downstream exon)
Score: 20

GTTACTGGAGGAAACTGAGGATGAGgtaggctgct ... ttggttgcagCTTTCTGAGTGGATAAAAACGAGCTCCGCAGAATCAGGAAATGTCAGCAGAGCACTTTGTGAAGATATTAGCAAACACTGTCAGTCTACAAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTACTGGAGGAAACTGAGGATGAGgtaggctgcttctcttggatgacatttatacattactttttttatactagcaaatatcgtctgaattttcccgtttcttgacagctgtgttttgttatgaactatacagatctatcataatttagttaaaaatagggcctcatctagagctttttttggttgcag

- -  TGGAGG
- - - GGAGGA
- - - - - - - - GAGGAT
- - - - - - - -  AGGATG