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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccgcaatgaaacaaaaacattgaaaaatacttcttagagccgcacaactcatgcaattctgttctgcagTCGCACTACTCTCAGCCAGCATCGGCTTCTTCAAGTTTGCCTTCTGCTGGAAGTGCAGTATTGCCAGACCTCAGCTCCCAGGCAGCTCAATATGGGCTTC

Basic information

species Oryza sativa
transcript LOC_Os01g02090.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g02090.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G051622_T02 (Zea mays), 3'ss of exon 3
----------gtaccgcaatgaaacaaaaacattgaaaaatacttctt-agagccgcacaactcatgcaattctgttctgcagTCGCACTACTCTCAGCCAGCATCGGCTTCTTCAAGTTTGCCTTCTGCTGGAAGTGCAGTATTGCCAGACCTCAGCTCCCAGGCAGCTCAATATGGGCTTC
           ||||   || ||| | | |   || ||  | |  ||| |  || ||  | ||||   ||  ||||||||||||| || || ||||| ||||||||  | || |||| ||||||||| |||||  ||||||| || |||||||||||||||||||||| ||||||||||||||
gtgccaccatataccagtataaaatagacaacctgtaatctgccccttcatggctgcttagctcaca-aacgctgttctgcagTCACATTATTCTCAACCAGCATCAACATCGTCAAATTTGCCTTCCGCTGGGGGTGCAGTTTTACCAGACCTCAGCTCCCAGGCAGTTCAATATGGGCTTC

upper sequence: LOC_Os01g02090.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G132796_T01 (Zea mays), 3'ss of exon 3
----------gtaccgcaatgaaacaaaaacattgaaaaatacttcttagagccgcacaactcatgcaattctgttctgcagTCGCACTACTCTCAGCCAGCATCGGCTTCTTCAAGTTTGCCTTCTGCTGGAAGTGCAGTATTGCCAGACCTCAGCTCCCAGGCAGCTCAATATGGGCTTC
           |||    || ||   | ||| |         ||  | |  || ||  | || ||  ||  ||||| ||||||| || || ||||| || |||||  | || |||||||||||||| |||||  ||||||| || |||||| | ||||||||||||| ||||||||||||||
gtactatcatatacaagtataaatagataacctgttctgtgtctcttcatggctgcttagctaata-aacactgttttgcagTCACATTATTCTCAACCTGCATCAACGTCATCAAGTTTGCCTTCAGCTGGGGGTGCAGTTTTACCAGACTTTAGCTCCCAGGCAGTTCAATATGGGCTTC

upper sequence: LOC_Os01g02090.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AC190588.3_FGT003 (Zea mays), 3'ss of exon 3
--------gtaccgcaatg-aaacaaaaacattgaaaaatacttctt-agagccgcacaactcatgcaattctgttctgcagTCGCACTACTCTCAGCCAGCATCGGCTTCTTCAAGTTTGCCTTCTGCTGGAAGTGCAGTATTGCCAGACCTCAGCTCCCAGGCAGCTCAATATGGGCTTC----------------------------------------------------------
         ||   || || ||| | | |  |||     |   |||| |  || ||  | || |   ||  || || ||||||| || || ||||| || |||||  | || ||||||||||||||  ||||  ||||||| || |||||| |||||||| |||||| ||||||||||||||                                                          
gtactatcatataccagtgtaaatagataacttgttctgtgtctcttcatggctgcttagctaaca-aacactattttgcagtcacattattctcaacctgcatcaacgtcatcaagtttgccttcaactgggggtgcagTTTTACCAGACTTCAGCTCCTAGGCAGTTCAATATGGGCTTCAGAGGCCAACCTTCCAGAGTAACCTTCCTCTCTACCAACCAGGGAATACTCTGTGGGG

upper sequence: LOC_Os01g02090.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G120584_T01 (Zea mays), 3'ss of exon 3
----------gtaccgcaatgaaacaaaaacattgaaaaatacttcttagagccgcacaactcatgcaattctgttctgcagTCGCACTACTCTCAGCCAGCATCGGCTTCTTCAAGTTTGCCTTCTGCTGGAAGTGCAGTATTGCCAGACCTCAGCTCCCAGGCAGCTCAATATGGGCTTC
           ||||   || ||   | ||| |         ||  | |  || ||  | || |   ||  ||||| ||||||| || || ||||| || |||||  | || ||||||||||||||  ||||  ||||||| || |||||| ||||||||||||||| ||||||||||||||
gtactatcctataccagtataaatagataacctgttttgtgtctcttcatggctgcttagctaaca-aacactgttttgcagTCACATTATTCTCAACCTGCATCAACGTCATCAAGTTTGCCTTCAACTGGGGGTGCAGTTTTACCAGACTTCAGCTCCCAGGCAGTTCAATATGGGCTTC

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|29638811|gb|CB643820.1|CB643820
EST:     CGCCACCACCACAACCAGCTGCCCCGCACAATGATCCTGCCATAATACAG                         TCGCACTACTCTCAGCCAGCATCGGCTTCTTCAAGTTTGCCTTCTGCTGGA
genomic: CGCCACCACCACAACCAGCTGCCCCGCACAATGATCCTGCCATAATACAGgtaccgcaat ... tgttctgcagTCGCACTACTCTCAGCCAGCATCGGCTTCTTCAAGTTTGCCTTCTGCTGGA
EST: gi|218502808|gb|FG943217.1|FG943217
EST:     CGCCACCACCACAACCAGCTGCCCCGCACAATGATCCTGCCATAATACAG                         TCACACTACTCTCAGCCAGCATCGGCTTCTTCAAGTTTGCCTTCTGCTGGA
genomic: CGCCACCACCACAACCAGCTGCCCCGCACAATGATCCTGCCATAATACAGgtaccgcaat ... tgttctgcagTCGCACTACTCTCAGCCAGCATCGGCTTCTTCAAGTTTGCCTTCTGCTGGA
EST: gi|29638770|gb|CB643779.1|CB643779
EST:     CGCCACCACCACAACCAGCTGCCCCGCACAATGATCCTGCCATAATACAG                         TCGCACTACTCTCAGCCAGCATCGGCTTCTTCAAGTTTGCCTTCTGCTGGA
genomic: CGCCACCACCACAACCAGCTGCCCCGCACAATGATCCTGCCATAATACAGgtaccgcaat ... tgttctgcagTCGCACTACTCTCAGCCAGCATCGGCTTCTTCAAGTTTGCCTTCTGCTGGA
EST: gi|29636683|gb|CB641692.1|CB641692
EST:     CGCCACCACCACAACCAGCTGCCCCGCACAATGATCCTGCCATAATACAG                         TCGCACTACTCTCAGCCAGCATCGGCTTCTTCAAGTTTGCCTTCTGCTGGA
genomic: CGCCACCACCACAACCAGCTGCCCCGCACAATGATCCTGCCATAATACAGgtaccgcaat ... tgttctgcagTCGCACTACTCTCAGCCAGCATCGGCTTCTTCAAGTTTGCCTTCTGCTGGA
EST: gi|88723859|gb|CI745556.1|CI745556
EST:     CGCCACCACCACAACCAGCTGCCCCGCACAATGATCCTGCCATAATACAG                         TCGCACTACTCTCAGCCAGCATCGGCTTCTTCAAGTTTGCCTTCTGCTGGA
genomic: CGCCACCACCACAACCAGCTGCCCCGCACAATGATCCTGCCATAATACAGgtaccgcaat ... tgttctgcagTCGCACTACTCTCAGCCAGCATCGGCTTCTTCAAGTTTGCCTTCTGCTGGA
EST: gi|58671766|gb|CK060452.1|CK060452
EST:     CGCCACCACCACAACCAGCTGCCCCGCACAATGATCCTGCCATAATACAG                         TCGCACTACTCTCAGCCAGCATCGGCTTCTTCAAGTTTGCCTTCTGCTGGA
genomic: CGCCACCACCACAACCAGCTGCCCCGCACAATGATCCTGCCATAATACAGgtaccgcaat ... tgttctgcagTCGCACTACTCTCAGCCAGCATCGGCTTCTTCAAGTTTGCCTTCTGCTGGA

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: 14 (upstream exon), 75 (downstream exon)
Score: 15

GATTTGCAAGTTAAGTCATCACCACCTCCACCGCCACCACCACAACCAGCTGCCCCGCACAATGATCCTGCCATAATACAGgtaccgcaat ... tgttctgcagTCGCACTACTCTCAGCCAGCATCGGCTTCTTCAAGTTTGCCTTCTGCTGGAAGTGCAGTATTGCCAGACCTCAGCTCCCAGGCAGCTCAATATGGGCTTC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacattgaaaaatacttcttagagccgcacaactcatgcaattctgttctgcagTCGCACTACTCTCAGCCAGCATCGGCTTCTTCAAGTTTGCCTTCTGCTGGAAGTGCAGTATTGCCAGACCTCAGCTCCCAGGCAGCTCAATATGGGCTTC
                                          ttctgttct  CT-rich tract
        aaaaatacttctta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccgcaatgaaacaaaaacattgaaaaatacttcttagagccgcacaactcatgcaattctgttctgcagTCGCACTACTCTCAGCCAGCATCGGCTTCTTCAAGTTTGCCTTCTGCTGGAAGTGCAGTATTGCCAGACCTCAGCTCCCAGGCAGCTCAATATGGGCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA