Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaatttctatatcagcttattcatcaatgtgctaccttcttgataccctgtttatccattgggtcctgatactttcacgatctgttttgaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAATTGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGG

Basic information

species Oryza sativa
transcript LOC_Os01g59730.1
intron # 2
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|88213116|gb|CI212780.1|CI212780
EST:     GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTGATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|88364526|gb|CI644604.1|CI644604
EST:     GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|88736541|gb|CI760049.1|CI760049
EST:     GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|88735499|gb|CI759007.1|CI759007
EST:     GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|42591806|gb|CK738292.1|CK738292
EST:     AGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: AGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|88375923|gb|CI528227.1|CI528227
EST:     GTACACCCTCGGGTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|58687548|gb|CK076235.1|CK076235
EST:     GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|427564|gb|D23632.1|D23632
EST:     GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|88722313|gb|CI745823.1|CI745823
EST:     GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|88690331|gb|CI734410.1|CI734410
EST:     GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|287274|gb|D16076.1|D16076
EST:     GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|58585744|gb|CF984052.1|CF984052
EST:     GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACGGNCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|87004301|gb|CI298833.1|CI298833
EST:     GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA

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: 64 (upstream exon), 63 (downstream exon)
Score: 12

AACGCGGAGGGGATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAATTGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccctgtttatccattgggtcctgatactttcacgatctgttttgaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAATTGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGG
                    tcctgat  putative branch site (score: 12)
                                                tcttc  putative PPT
                                         ttttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaatttctatatcagcttattcatcaatgtgctaccttcttgataccctgtttatccattgggtcctgatactttcacgatctgttttgaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAATTGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - -tgctacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgttt