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

gtgagttacatttttcttttatcttttgcaattatatattaatgcgaataaaatgtgttttgtgatttcttatcttcctattgctagGCTGAGATGGAAGTTCATTGATAATCCTGCACAAGAAGGGCAAGATATGATTGGACTTTGTAGATATGGTCAGTGATGTAGAACTTTGTTTTGCTATCTA

Basic information

species Oryza sativa
transcript LOC_Os02g27594.1
intron # 4
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|13896996|gb|AU183332.1|AU183332
EST:     GCCATTGCAACAGCAATACGAGTTTTAATGAGCCTGTAAAGAATGTTATT                         GCTGAGATGGAAGTTCATTGATAATCCTGCACAAGAAGGGCAAGATATGAT
genomic: GCCATTGCAACAGCAATACGAGTTTTAATGAGCCTGTAAAGAATGTTATTgtgagttaca ... ctattgctagGCTGAGATGGAAGTTCATTGATAATCCTGCACAAGAAGGGCAAGATATGAT
EST: gi|27577231|gb|CA999925.1|CA999925
EST:     GCCATTGCAACAGCAATACGAGTTTTAATGAGCCTGTAAAGAATGTTATT                         GCTGAGATGGAAGTTCATTGATAATCCTGCACAAGAAGGGCAAGATATGAT
genomic: GCCATTGCAACAGCAATACGAGTTTTAATGAGCCTGTAAAGAATGTTATTgtgagttaca ... ctattgctagGCTGAGATGGAAGTTCATTGATAATCCTGCACAAGAAGGGCAAGATATGAT
EST: gi|38480502|gb|CF964591.1|CF964591
EST:     GCCATTGCAACAGCAATACGAGTTTTAATGAGCCTGTAAAGAATGTTATT                         GCTGAGATGGAAGTTCATTGATGGTCCTGCACAAGAAGGGCAAGATATGAT
genomic: GCCATTGCAACAGCAATACGAGTTTTAATGAGCCTGTAAAGAATGTTATTgtgagttaca ... ctattgctagGCTGAGATGGAAGTTCATTGATAATCCTGCACAAGAAGGGCAAGATATGAT
EST: gi|88257092|gb|CI359480.1|CI359480
EST:     GCCATTGCAACAGCAATACGAGTTTTAATGAGCCTGTAAAGAATGTTATT                         GCTGAGATGGAAGTTCATTGATAATCCTGCACAAGAAGGGCAAGATATGAT
genomic: GCCATTGCAACAGCAATACGAGTTTTAATGAGCCTGTAAAGAATGTTATTgtgagttaca ... ctattgctagGCTGAGATGGAAGTTCATTGATAATCCTGCACAAGAAGGGCAAGATATGAT
EST: gi|88374682|gb|CI518549.1|CI518549
EST:     GCCATTGCAACAGCAATACGAGTTTTAATGAGCCTGTAAAGAATGTTATT                         GCTGAGATGGAAGTTCATTGATAATCCTGCACAAGAAGGGCAAGATATGAT
genomic: GCCATTGCAACAGCAATACGAGTTTTAATGAGCCTGTAAAGAATGTTATTgtgagttaca ... ctattgctagGCTGAGATGGAAGTTCATTGATAATCCTGCACAAGAAGGGCAAGATATGAT
EST: gi|86496213|gb|CI138846.1|CI138846
EST:     GCCATTGCAACAGCAATACGAGTTTTAATGAGCCTGTAAAGAATGTTATT                         GCTGAGATGGAAGTTCATTGATAATCCTGCACAAGAAGGGCAAGATATGAT
genomic: GCCATTGCAACAGCAATACGAGTTTTAATGAGCCTGTAAAGAATGTTATTgtgagttaca ... ctattgctagGCTGAGATGGAAGTTCATTGATAATCCTGCACAAGAAGGGCAAGATATGAT

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: 71 (upstream exon), 69 (downstream exon)
Score: 41

AACTAAGTATAAGGATGCTCCACCCACTGCATTTGATCTTTTCAAGATGTGCCATTGCAACAGCAATACGAGTTTTAATGAGCCTGTAAAGAATGTTATTgtgagttaca ... ctattgctagGCTGAGATGGAAGTTCATTGATAATCCTGCACAAGAAGGGCAAGATATGATTGGACTTTGTAGATATGGTCAGTGATGTAGAACTTTGTTTTGCTATCTA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatattaatgcgaataaaatgtgttttgtgatttcttatcttcctattgctagGCTGAGATGGAAGTTCATTGATAATCCTGCACAAGAAGGGCAAGATATGATTGGACTTTGTAGATATGGTCAGTGATGTAGAACTTTGTTTTGCTATCTA
    tattaat  putative branch site (score: 41)
                                 tttcttatcttcctat  putative PPT
              aataaaatgtgtttt  TA-rich tract