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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttcagttgttctaggaggttcagaattcccacttcatgctacagttctcttgttgcaccatcagttgttgtaacttatgctcgcctaaggtctggtttgcctggccattgacagGATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCCCAAGACAAGGGGATCCAAGCCAAAGACGGCGTCAGCCGCATGGTGACGC

Basic information

species Physcomitrella patens
transcript PP1S69_87V6.1
intron # 1
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|162270030|gb|FC446730.1|FC446730
EST:     CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAA                         GATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
genomic: CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAAgtacgttcag ... ccattgacagGATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
EST: gi|162269988|gb|FC445453.1|FC445453
EST:     CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAA                         GATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
genomic: CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAAgtacgttcag ... ccattgacagGATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
EST: gi|162265698|gb|FC443104.1|FC443104
EST:     CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAA                         GATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
genomic: CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAAgtacgttcag ... ccattgacagGATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
EST: gi|162268302|gb|FC444591.1|FC444591
EST:     CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAA                         GATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
genomic: CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAAgtacgttcag ... ccattgacagGATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
EST: gi|162270031|gb|FC446731.1|FC446731
EST:     CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAA                         GATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
genomic: CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAAgtacgttcag ... ccattgacagGATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
EST: gi|162265699|gb|FC443105.1|FC443105
EST:     CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAA                         GATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
genomic: CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAAgtacgttcag ... ccattgacagGATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
EST: gi|162272486|gb|FC448488.1|FC448488
EST:     CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAA                         GATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
genomic: CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAAgtacgttcag ... ccattgacagGATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
EST: gi|162259358|gb|FC435716.1|FC435716
EST:     CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAA                         GATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
genomic: CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAAgtacgttcag ... ccattgacagGATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
EST: gi|67574105|gb|BJ946929.1|BJ946929
EST:     CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAA                         GATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
genomic: CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAAgtacgttcag ... ccattgacagGATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
EST: gi|162266266|gb|FC442198.1|FC442198
EST:     CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAA                         GATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
genomic: CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAAgtacgttcag ... ccattgacagGATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
EST: gi|67697497|gb|BJ957730.1|BJ957730
EST:     CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAA                         GATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
genomic: CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAAgtacgttcag ... ccattgacagGATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
EST: gi|162272386|gb|FC449038.1|FC449038
EST:     CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAA                         GATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
genomic: CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAAgtacgttcag ... ccattgacagGATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
EST: gi|162273356|gb|FC449597.1|FC449597
EST:     CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAA                         GATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
genomic: CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAAgtacgttcag ... ccattgacagGATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
EST: gi|162269989|gb|FC445454.1|FC445454
EST:     CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAA                         GATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
genomic: CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAAgtacgttcag ... ccattgacagGATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
EST: gi|162271098|gb|FC447139.1|FC447139
EST:     CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAA                         GATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
genomic: CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAAgtacgttcag ... ccattgacagGATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
EST: gi|67578078|gb|BJ950245.1|BJ950245
EST:     CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAA                         GATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
genomic: CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAAgtacgttcag ... ccattgacagGATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
EST: gi|162273355|gb|FC449596.1|FC449596
EST:     AAGGGCGCCGCTCAA                         GATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
genomic: AAGGGCGCCGCTCAAgtacgttcag ... ccattgacagGATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
EST: gi|162272385|gb|FC449037.1|FC449037
EST:     GGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAA                         GATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
genomic: GGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAAgtacgttcag ... ccattgacagGATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
EST: gi|67575864|gb|BJ948688.1|BJ948688
EST:     CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAA                         GATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
genomic: CCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAAgtacgttcag ... ccattgacagGATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
EST: gi|67700942|gb|BJ961175.1|BJ961175
EST:     AACCAAGGGCGCCGCTCAA                         GATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC
genomic: AACCAAGGGCGCCGCTCAAgtacgttcag ... ccattgacagGATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCC

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: 33 (upstream exon), 14 (downstream exon)
Score: 2

CCTTTCTCGGTTCCCAATCTTCTTCATCAGCATGTCGACCTATGATGATACCAAGGCTGCTGCAGCTCAGAAGAGTGAGGAAACCAAGGGCGCCGCTCAAgtacgttcag ... ccattgacagGATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCCCAAGACAAGGGGATCCAAGCCAAAGACGGCGTCAGCCGCATGGTGACGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcagttgttgtaacttatgctcgcctaaggtctggtttgcctggccattgacagGATTTTACCGGAGCAGCTCAGCAGAAGGCTGGCGAAGCTGGCGGATTCGCCCAAGACAAGGGGATCCAAGCCAAAGACGGCGTCAGCCGCATGGTGACGC
        ttgtaac  putative branch site (score: 2)
           taacttat  TA-rich tract