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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagacgacataaacaaagcttctgaaatcactaagtgcatcaccttgttcgggtcgttactaacatgaacctgtcacattctctttactttgtgctgcagCAAGGGTTAGGAAACATGCTTGGGAACATGCAGGGTCTATATGACACAGTGAGGAAAGCCCAACAGGTAGTTCAAGTCGAGGCTGTCCGCGTCCAGAAAG

Basic information

species Physcomitrella patens
transcript PP1S76_146V6.1
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|37833535|gb|BJ591547.1|BJ591547
EST:     GCTTGTGGGGTGGGAAAAAAGAGGAGAACCCAGACGATGCCGCCAAGAAG                         CAAGGGTTAGGAAACATGCTTGGGAACATGCAGGGTCTATATGACACAGTG
genomic: GCTTGTGGGGTGGGAAAAAAGAGGAGAACCCAGACGATGCCGCCAAGAAGgtgaatttcg ... tgtgctgcagCAAGGGTTAGGAAACATGCTTGGGAACATGCAGGGTCTATATGACACAGTG
EST: gi|162204037|gb|FC379406.1|FC379406
EST:     GCTTGTGGGGTGGGAAAAAAGAGGAGAACCCAGACGATGCCGCCAAGAAG                         CAAGGGTTAGGAAACATGCTTGGGAACATGCAGGGTCTATATGACACAGTG
genomic: GCTTGTGGGGTGGGAAAAAAGAGGAGAACCCAGACGATGCCGCCAAGAAGgtgaatttcg ... tgtgctgcagCAAGGGTTAGGAAACATGCTTGGGAACATGCAGGGTCTATATGACACAGTG
EST: gi|162228920|gb|FC404206.1|FC404206
EST:     GCTTGTGGGGTGGGAAAAAAGAGGAGAACCCAGACGATGCCGCCAAGAAG                         CAAGGGTTAGGAAACATGCTTGGGAACATGCAGGGTCTATATGACACAGTG
genomic: GCTTGTGGGGTGGGAAAAAAGAGGAGAACCCAGACGATGCCGCCAAGAAGgtgaatttcg ... tgtgctgcagCAAGGGTTAGGAAACATGCTTGGGAACATGCAGGGTCTATATGACACAGTG
EST: gi|67570323|gb|BJ943147.1|BJ943147
EST:     GCTTGTGGGGTGGGAAAAAAGAGGAGAACCCAGACGATGCCGCCAAGAAG                         CAAGGGTTAGGAAACATGCTTGGGAACATGCAGGGTCTATATGACACAGTG
genomic: GCTTGTGGGGTGGGAAAAAAGAGGAGAACCCAGACGATGCCGCCAAGAAGgtgaatttcg ... tgtgctgcagCAAGGGTTAGGAAACATGCTTGGGAACATGCAGGGTCTATATGACACAGTG
EST: gi|67703026|gb|BJ963259.1|BJ963259
EST:     GCTTGTGGGGTGGGAAAAAAGAGGAGAACCCAGACGATGCCGCCAAGAAG                         CAAGGGTTAGGAAACATGCTTGGGAACATGCAGGGTCTATATGACACA
genomic: GCTTGTGGGGTGGGAAAAAAGAGGAGAACCCAGACGATGCCGCCAAGAAGgtgaatttcg ... tgtgctgcagCAAGGGTTAGGAAACATGCTTGGGAACATGCAGGGTCTATATGACACA
EST: gi|162226667|gb|FC402738.1|FC402738
EST:     GCTTGTGGGGTGGGAAAAAAGAGGAGAACCCAGACGATGCCGCCAAGAAG                         CAAGGGTTAGGAAACATGCTTGGGAACATGCAGGGTCTATATGACACAGTG
genomic: GCTTGTGGGGTGGGAAAAAAGAGGAGAACCCAGACGATGCCGCCAAGAAGgtgaatttcg ... tgtgctgcagCAAGGGTTAGGAAACATGCTTGGGAACATGCAGGGTCTATATGACACAGTG
EST: gi|162204038|gb|FC379407.1|FC379407
EST:     GCTTGTGGGGTGGGAAAAAAGAGGAGAACCCAGACGATGCCGCCAAGAAG                         CAAGGGTTAGGAAACATGCTTGGGAACATGCAGGGTCTATATGACACAGTG
genomic: GCTTGTGGGGTGGGAAAAAAGAGGAGAACCCAGACGATGCCGCCAAGAAGgtgaatttcg ... tgtgctgcagCAAGGGTTAGGAAACATGCTTGGGAACATGCAGGGTCTATATGACACAGTG
EST: gi|67693595|gb|BJ953828.1|BJ953828
EST:     GCTTGTGGGGTGGGAAAAAAGAGGAGAACCCAGACGATGCCGCCAAGAAG                         CAAGGGTTAGGAAACATGCTTGGGAACATGCAGGGTCTATATGACACAGTG
genomic: GCTTGTGGGGTGGGAAAAAAGAGGAGAACCCAGACGATGCCGCCAAGAAGgtgaatttcg ... tgtgctgcagCAAGGGTTAGGAAACATGCTTGGGAACATGCAGGGTCTATATGACACAGTG
EST: gi|67569434|gb|BJ942258.1|BJ942258
EST:     GCTTGTGGGGTGGGAAAAAAGAGGAGAACCCAGACGATGCCGCCAAGAAG                         CAAGGGTTAGGAAACATGCTTGGGAACATGCAGGGTCTATATGACACAGTG
genomic: GCTTGTGGGGTGGGAAAAAAGAGGAGAACCCAGACGATGCCGCCAAGAAGgtgaatttcg ... tgtgctgcagCAAGGGTTAGGAAACATGCTTGGGAACATGCAGGGTCTATATGACACAGTG
EST: gi|67692697|gb|BJ952930.1|BJ952930
EST:     GCTTGTGGGGTGGGAAAAAAGAGGAGAACCCAGACGATGCCGCCAAGAAG                         CAAGGGTTAGGAAACATGCTTGGGAACATGCAGGGTCTATATGACACAGTG
genomic: GCTTGTGGGGTGGGAAAAAAGAGGAGAACCCAGACGATGCCGCCAAGAAGgtgaatttcg ... tgtgctgcagCAAGGGTTAGGAAACATGCTTGGGAACATGCAGGGTCTATATGACACAGTG

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: 35 (upstream exon), 34 (downstream exon)
Score: 15

GAGAACACATCGGTCATTCTGCTTTAATCAGCGCTCTCTGAACGTTACCAGCTTGTGGGGTGGGAAAAAAGAGGAGAACCCAGACGATGCCGCCAAGAAGgtgaatttcg ... tgtgctgcagCAAGGGTTAGGAAACATGCTTGGGAACATGCAGGGTCTATATGACACAGTGAGGAAAGCCCAACAGGTAGTTCAAGTCGAGGCTGTCCGCGTCCAGAAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttcgggtcgttactaacatgaacctgtcacattctctttactttgtgctgcagCAAGGGTTAGGAAACATGCTTGGGAACATGCAGGGTCTATATGACACAGTGAGGAAAGCCCAACAGGTAGTTCAAGTCGAGGCTGTCCGCGTCCAGAAAG
            tactaac  putative branch site (score: 15)
                               cattctctttacttt  putative PPT
                                      tttacttt  TA-rich tract