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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaccctaatctaaaacttcattacaccttttcgtactccaagtgatcttgcactcaattttttagcgtggcttcctaggtcgaggagctgatgatctgtgggatgattgtttcaacagGACAAGAGCTAGAAGTAGGACCATATTTGCAAACAGCAGGGCTTGACTTGAGACCCATTTTGACGCTCTCCCGTTTTCCCACCATTGTCTTCTTCGCAAG

Basic information

species Physcomitrella patens
transcript PP1S9_406V6.1
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|162208966|gb|FC385310.1|FC385310
EST:     AATTCATGTAGAGGAAGCCTCAAACCCTGAGCTGTACACTGTCTCGGAGG                         GACAAGAGCTAGAAGTAGGACCATATTTGCAAACAGCAGGGCTTGACTTGA
genomic: AATTCATGTAGAGGAAGCCTCAAACCCTGAGCTGTACACTGTCTCGGAGGgtaagaaccc ... gtttcaacagGACAAGAGCTAGAAGTAGGACCATATTTGCAAACAGCAGGGCTTGACTTGA
EST: gi|100438303|gb|BY979889.1|BY979889
EST:     AATTCATGTAGAGGAAGCCTCAAACCCTGAGCTGTACACTGTCTCGGAGG                         GACAAGAGCTAGAAGTAGGACCATATTTGCAAACAGCAGGGCTTGACTTGA
genomic: AATTCATGTAGAGGAAGCCTCAAACCCTGAGCTGTACACTGTCTCGGAGGgtaagaaccc ... gtttcaacagGACAAGAGCTAGAAGTAGGACCATATTTGCAAACAGCAGGGCTTGACTTGA
EST: gi|19780118|gb|BQ039517.1|BQ039517
EST:     AATTCATGTAGAGGAAGCCTCAAACCCTGAGCTGTACACTGTCTCGGAGG                         GACAAGAGCTAGAAGTAGGACCATATTTGCAAACAGCAGGGCTTGACTTGA
genomic: AATTCATGTAGAGGAAGCCTCAAACCCTGAGCTGTACACTGTCTCGGAGGgtaagaaccc ... gtttcaacagGACAAGAGCTAGAAGTAGGACCATATTTGCAAACAGCAGGGCTTGACTTGA
EST: gi|100392187|gb|BY953237.1|BY953237
EST:     A-TTCATGTAGAGGAAGCCTCAA-CCCTGAGCTGTACACTGTCTCGGAAG                         GACAAGAGCTAGAAGTAGG
genomic: AATTCATGTAGAGGAAGCCTCAAACCCTGAGCTGTACACTGTCTCGGAGGgtaagaaccc ... gtttcaacagGACAAGAGCTAGAAGTAGG
EST: gi|162199066|gb|FC372391.1|FC372391
EST:     AATTCATGTAGAGGAAGCCTCAAACCCTGAGCTGTACACTGTCTCGGAGG                         GACAAGAGCTAGAAGTAGGACCATATTTGCAAACAGCAGGGCTTGACTTGA
genomic: AATTCATGTAGAGGAAGCCTCAAACCCTGAGCTGTACACTGTCTCGGAGGgtaagaaccc ... gtttcaacagGACAAGAGCTAGAAGTAGGACCATATTTGCAAACAGCAGGGCTTGACTTGA
EST: gi|162158901|gb|FC334787.1|FC334787
EST:     AATTCATGTAGAGGAAGCCTCAAACCCTGAGCTGTACACTGTCTCGGAGG                         GACAAGAGCTAGAAGTAGGACCATATTTGCAAACAGC
genomic: AATTCATGTAGAGGAAGCCTCAAACCCTGAGCTGTACACTGTCTCGGAGGgtaagaaccc ... gtttcaacagGACAAGAGCTAGAAGTAGGACCATATTTGCAAACAGC
EST: gi|162155129|gb|FC330923.1|FC330923
EST:     AATTCATGTAGAGGAAGCCTCAAACCCTGAGCTGTACACTGTCTCGGAGG                         GACAAGAGCTAGAAGTAGGACCATATTTGCAAACAGC
genomic: AATTCATGTAGAGGAAGCCTCAAACCCTGAGCTGTACACTGTCTCGGAGGgtaagaaccc ... gtttcaacagGACAAGAGCTAGAAGTAGGACCATATTTGCAAACAGC

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: 30 (upstream exon), 34 (downstream exon)
Score: 10

GGAATGATAAAGCTGCCTCAGTTTTCACTGTCTGTGAAGGCCCCAGTTGAAATTCATGTAGAGGAAGCCTCAAACCCTGAGCTGTACACTGTCTCGGAGGgtaagaaccc ... gtttcaacagGACAAGAGCTAGAAGTAGGACCATATTTGCAAACAGCAGGGCTTGACTTGAGACCCATTTTGACGCTCTCCCGTTTTCCCACCATTGTCTTCTTCGCAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcgtggcttcctaggtcgaggagctgatgatctgtgggatgattgtttcaacagGACAAGAGCTAGAAGTAGGACCATATTTGCAAACAGCAGGGCTTGACTTGAGACCCATTTTGACGCTCTCCCGTTTTCCCACCATTGTCTTCTTCGCAAG
                      agctgat  putative branch site (score: 10)
                                           ttgtttc  putative PPT
                                          attgttt  TA-rich tract