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'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTTTATGCCTGCTCACTGGATCCTGAAATCTGTGGCCTTGAATTCGCTCTCTTCCTCTCTGATATCTTTATTAAAAAGGAAGAGGATTCAATTTCTAGgtatttttttcccatatcatgcatacagctaacgtgcataccttgtatttctttgtcttgtgaacttgtgatcatagctggcattgggtgctgagtgatt...

Basic information

species Oryza sativa
transcript LOC_Os06g47350.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g47350.2 (Oryza sativa), 5'ss of exon 11
lower sequence: AT2G34750.1 (Arabidopsis thaliana), 5'ss of exon 11
TGTTTTATGCCTGCTCACTGGATCCTGAAATCTGTGGCCTTGAATTCGCTCTCTTCCTCTCTGATATCTTTATTAAAAAGGAAGAGGATTCAATTTCTAGgta--tttttttcccatatcatgcatacagctaacgtgcataccttgtatt-tctttgtcttgtgaacttgtgatcatagctggcattgggtgctgagtgatt-----
| || |||||||||||||||||||||||||  |||||  |  |||| |||      ||    || || ||| |    |   |  || ||  |  | ||||| |    |   | |  | | |    |   | |  | |||||    |||  | || ||||  |    | |    | | | | ||   ||  ||         ||     
TATTCTATGCCTGCTCACTGGATCCTGAAAATTGTGGTGTGAAATTTGCTAGTAAGCTAGTGGAGATTTTTCTCTCCAGCAACAAGCATGTAGCTACTAGgcaagcatcccttcggtttaaattttctcgttcgc-tgcatgatatgttctgtcattgttct----aatcacaaacttggttgtgcttttgtctctcccccttaacag
















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|58676719|gb|CK065406.1|CK065406
EST:     TAAAAAGGAAGAGGATTCAATTTCTAG                         AATGTCTGCAGTTTCATATGTTGGAAGCTATCTGTCTCGGGCAAGGTTCAT
genomic: TAAAAAGGAAGAGGATTCAATTTCTAGgtattttttt ... ttaagtgcagAATGTCTGCAGTTTCATATGTTGGAAGCTATTTGTCTCGGGCAAGGTTCAT
EST: gi|58668152|gb|CK056838.1|CK056838
EST:     GAGG-TTCAATTTCTAG                         AATGTCTGCAGTTTCATATGTTGGAAGCTATCTGTCTCGGGCAAGGTTCAT
genomic: GAGGATTCAATTTCTAGgtattttttt ... ttaagtgcagAATGTCTGCAGTTTCATATGTTGGAAGCTATTTGTCTCGGGCAAGGTTCAT
EST: gi|66922574|gb|CX109422.1|CX109422
EST:     CTCTTCCTCTCTGATATCTTTATTAAAAAGGAAGAGGATTCAATTTCTAG                         AATGTCTGCAGTTTCATATGTTGGAAGCTATCTGTCTCGGGCAAGGTTCAT
genomic: CTCTTCCTCTCTGATATCTTTATTAAAAAGGAAGAGGATTCAATTTCTAGgtattttttt ... ttaagtgcagAATGTCTGCAGTTTCATATGTTGGAAGCTATTTGTCTCGGGCAAGGTTCAT
EST: gi|29628119|gb|CB633130.1|CB633130
EST:     CTCTTCCTCTCTGATATCTTTATTAAAAAGGAAGAGGATTCAATTTCTAG                         AATGTCTGCAGTTTCATATGTTGGAAGCTATCTGTCTCGGGCAAGGTTCAT
genomic: CTCTTCCTCTCTGATATCTTTATTAAAAAGGAAGAGGATTCAATTTCTAGgtattttttt ... ttaagtgcagAATGTCTGCAGTTTCATATGTTGGAAGCTATTTGTCTCGGGCAAGGTTCAT
EST: gi|29689750|gb|CB686025.1|CB686025
EST:     CTCTTCCTCTCTGATATCTTTATTAAAAAGGAAGAGGATTCAATTTCTAG                         AATGTCTGCAGTTTCATATGTTGGAAGCTATTTGTCTCGGGNCA-GGTTCA
genomic: CTCTTCCTCTCTGATATCTTTATTAAAAAGGAAGAGGATTCAATTTCTAGgtattttttt ... ttaagtgcagAATGTCTGCAGTTTCATATGTTGGAAGCTATTTGTCTCGGG-CAAGGTTCA
EST: gi|218492292|gb|FG954140.1|FG954140
EST:     CTCTTCCTCTCTGATATCTTTATTAAAAAGGAAGAGGATTCAATTTCTAG                         AATGTCTGCAGTTTCATATGTTGGAAGCTATCTGTCTCGGGCAAGGTTCAT
genomic: CTCTTCCTCTCTGATATCTTTATTAAAAAGGAAGAGGATTCAATTTCTAGgtattttttt ... ttaagtgcagAATGTCTGCAGTTTCATATGTTGGAAGCTATTTGTCTCGGGCAAGGTTCAT

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: 75 (upstream exon), 75 (downstream exon)
Score: 163

TGTTTTATGCCTGCTCACTGGATCCTGAAATCTGTGGCCTTGAATTCGCTCTCTTCCTCTCTGATATCTTTATTAAAAAGGAAGAGGATTCAATTTCTAGgtattttttt ... ttaagtgcagAATGTCTGCAGTTTCATATGTTGGAAGCTATTTGTCTCGGGCAAGGTTCATTTCTGCTGATACGGTGGTTGGTATACTCAAAAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTTTATGCCTGCTCACTGGATCCTGAAATCTGTGGCCTTGAATTCGCTCTCTTCCTCTCTGATATCTTTATTAAAAAGGAAGAGGATTCAATTTCTAGgtatttttttcccatatcatgcatacagctaacgtgcataccttgtatttctttgtcttgtgaacttgtgatcatagctggcattgggtgctgagtgatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT