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

...ccaaccatacactggttctaccatttcatgtcttttatatatcttatgatttcttttcttactccattgcggcatttacacttttgtttcttttcctcagCTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACTATTGAACACAGACGCTCCTGACTTGTACATTCGGCAGAACCCTGTTCCTAATGCTTACA

Basic information

species Oryza sativa
transcript LOC_Os01g73910.3
intron # 3
splice site 3'
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|58590372|gb|CF988680.1|CF988680
EST:     TTATGGTACTTCAGAACATTGGATCGTCTGTGCTAGTCTCTGAAAACCAG                         CTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACTATTGAACACA
genomic: TTATGGTACTTCAGAACATTGGATCGTCTGTGCTAGTCTCTGAAAACCAGgtgcgctttt ... ttttcctcagCTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACTATTGAACACA
EST: gi|29624825|gb|CB629836.1|CB629836
EST:     TTATGGTACTTCAGAACATTGGATCGTCTGTGCTAGTCTCTGAAAACCAG                         CTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACTATTGAACACA
genomic: TTATGGTACTTCAGAACATTGGATCGTCTGTGCTAGTCTCTGAAAACCAGgtgcgctttt ... ttttcctcagCTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACTATTGAACACA
EST: gi|2427812|gb|C72275.1|C72275
EST:     TTATGGTACTTCAGAACATTGGATCGTCTGTGCTAGTCTCTGAAAACCAG                         NTTTNAGATCTTCATAAGATCTT
genomic: TTATGGTACTTCAGAACATTGGATCGTCTGTGCTAGTCTCTGAAAACCAGgtgcgctttt ... ttttcctcagCTTTCAGATCTTCATCAGATCTT
EST: gi|88411775|gb|CI571267.1|CI571267
EST:     TTATGGTACTTCAGAACATTGGATCGTCTGTGCTAGTCTCTGAAAACCAG                         CTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACTATTGAACA
genomic: TTATGGTACTTCAGAACATTGGATCGTCTGTGCTAGTCTCTGAAAACCAGgtgcgctttt ... ttttcctcagCTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACTATTGAACA
EST: gi|13806000|gb|AU181304.1|AU181304
EST:     TTATGGTACTTCAGAACATTGGATCGTCTGTGCTAGTCTCTGAAAACCAG                         CTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACTATTGAACACA
genomic: TTATGGTACTTCAGAACATTGGATCGTCTGTGCTAGTCTCTGAAAACCAGgtgcgctttt ... ttttcctcagCTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACTATTGAACACA
EST: gi|88762070|gb|CI771626.1|CI771626
EST:     TTATGGTACTTCAGAACATTGGATCGTCTGTGCTAGTCTCTGAAAACCAG                         CTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACTATTGAACACA
genomic: TTATGGTACTTCAGAACATTGGATCGTCTGTGCTAGTCTCTGAAAACCAGgtgcgctttt ... ttttcctcagCTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACTATTGAACACA
EST: gi|58591227|gb|CF989535.1|CF989535
EST:     TTATGGTACTTCAGAACATTGGATCGTCTGTGCTAGTCTCTGAAAACCAG                         CTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACTATTGAACACA
genomic: TTATGGTACTTCAGAACATTGGATCGTCTGTGCTAGTCTCTGAAAACCAGgtgcgctttt ... ttttcctcagCTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACTATTGAACACA
EST: gi|88312036|gb|CI580201.1|CI580201
EST:     TTATGGTACTTCAGAACATTGGATCGTCTGTGCTAGTCTCTGAAAACCAG                         CTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACT
genomic: TTATGGTACTTCAGAACATTGGATCGTCTGTGCTAGTCTCTGAAAACCAGgtgcgctttt ... ttttcctcagCTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACT
EST: gi|29683738|gb|CB680013.1|CB680013
EST:     TTATGGTACTTCAGAACATTGGATCGTCTGTGCTAGTCTCTGAAAACCAT                         CTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACTATTGAACACA
genomic: TTATGGTACTTCAGAACATTGGATCGTCTGTGCTAGTCTCTGAAAACCAGgtgcgctttt ... ttttcctcagCTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACTATTGAACACA
EST: gi|88454163|gb|CI694086.1|CI694086
EST:     TTATGGTACTTCAGAACATTGGATCGTCTGTGCTAGTCTCTGAAAACCAG                         CTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACTATTGAACACA
genomic: TTATGGTACTTCAGAACATTGGATCGTCTGTGCTAGTCTCTGAAAACCAGgtgcgctttt ... ttttcctcagCTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACTATTGAACACA
EST: gi|13806135|gb|AU181375.1|AU181375
EST:     TTATGGTACTTCAGAACATTGGATCGTCTGTGCTAGTCTCTGAAAACCAG                         CTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACTATTGAACACA
genomic: TTATGGTACTTCAGAACATTGGATCGTCTGTGCTAGTCTCTGAAAACCAGgtgcgctttt ... ttttcctcagCTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACTATTGAACACA

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: 65 (upstream exon), 75 (downstream exon)
Score: 45

GACCAGTTTCTGAGCAAGTTATGGTACTTCAGAACATTGGATCGTCTGTGCTAGTCTCTGAAAACCAGgtgcgctttt ... ttttcctcagCTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACTATTGAACACAGACGCTCCTGACTTGTACATTCGGCAGAACCCTGTTCCTAATGCTTACA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatttcttttcttactccattgcggcatttacacttttgtttcttttcctcagCTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACTATTGAACACAGACGCTCCTGACTTGTACATTCGGCAGAACCCTGTTCCTAATGCTTACA
          ttcttac  putative branch site (score: 45)
                             tttacacttttgtttc  putative PPT
        ttttctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccaaccatacactggttctaccatttcatgtcttttatatatcttatgatttcttttcttactccattgcggcatttacacttttgtttcttttcctcagCTTTCAGATCTTCATCAGATCTTGACCGAGGCAGCAAAACTATTGAACACAGACGCTCCTGACTTGTACATTCGGCAGAACCCTGTTCCTAATGCTTACA

- - -catacac
- - - - - - tggttct
- - - - - - - - - - - -tttcatg
- - - - - - - - - - - - - - - - - - - - - cttatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttttgt