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

gtaaattacaaatctataaatagcaaattgcatctatatatacgatgtaagaactctgtttcatccatgtcatctaaattttagGTGAGCACAGCATGGGGGATAGGTCTTGTAGTTGGCCCAGCAACTGGGGGATACCTCGCACAG

Basic information

species Oryza sativa
transcript LOC_Os12g03860.6
intron # 6
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|33794568|gb|CF323171.1|CF323171
EST:     ACTCTATCGAAGTTTGCCGAGCTGAACATCAACCTTTGGGCCTATCAATT                         GTGAGCACAGCATGGGGGATAGGTCTT
genomic: ACTCTATCGAAGTTTGCCGAGCTGAACATCAACCTTTGGGCCTATCAATTgtaaattaca ... taaattttagGTGAGCACAGCATGGGGGATAGGTCTT
EST: gi|33797096|gb|CF324414.1|CF324414
EST:     ACTCTATCGAAGTTTGCCGAGCTGAACATCAACCTTTGGGCCTATCAATT                         GTGAGCACAGCATGGGGGATAGGTCTTGTAGTTGGCCCAGCAACTGGGGGA
genomic: ACTCTATCGAAGTTTGCCGAGCTGAACATCAACCTTTGGGCCTATCAATTgtaaattaca ... taaattttagGTGAGCACAGCATGGGGGATAGGTCTTGTAGTTGGCCCAGCAACTGGGGGA
EST: gi|33692622|gb|CF320861.1|CF320861
EST:     ACTCTATCGAAGTTTGCCGAGCTGAACATCAACCTTTGGGCCTATCAATT                         GTGAGCACAGCATGGGGGATAGGTCTTGTAGTTGGCCCAGCAACTGGGGGA
genomic: ACTCTATCGAAGTTTGCCGAGCTGAACATCAACCTTTGGGCCTATCAATTgtaaattaca ... taaattttagGTGAGCACAGCATGGGGGATAGGTCTTGTAGTTGGCCCAGCAACTGGGGGA

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: 60 (upstream exon), 41 (downstream exon)
Score: 29

GCGTACTCTATCGAAGTTTGCCGAGCTGAACATCAACCTTTGGGCCTATCAATTgtaaattaca ... taaattttagGTGAGCACAGCATGGGGGATAGGTCTTGTAGTTGGCCCAGCAACTGGGGGATACCTCGCACAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatctatatatacgatgtaagaactctgtttcatccatgtcatctaaattttagGTGAGCACAGCATGGGGGATAGGTCTTGTAGTTGGCCCAGCAACTGGGGGATACCTCGCACAG
                                          atctaaa  putative branch site (score: 29)
                                        tcatctaaatttta  TA-rich tract