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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatcggaatagctgggaaattcgtgttgtcgaagaacgtagaaggtttctgacttgatttttcacatggagtacctaaattactgttgaattggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAATGCCGTCACTTTCGGCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTG

Basic information

species Physcomitrella patens
transcript PP1S11_397V6.2
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|162186359|gb|FC361667.1|FC361667
EST:     CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAG                         GTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
genomic: CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAGgtattgccaa ... ttggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
EST: gi|18331540|gb|BJ163551.1|BJ163551
EST:     CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAG                         GTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
genomic: CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAGgtattgccaa ... ttggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
EST: gi|100429021|gb|BY977900.1|BY977900
EST:     CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAG                         GTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
genomic: CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAGgtattgccaa ... ttggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
EST: gi|100409989|gb|BY974354.1|BY974354
EST:     CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAG                         GTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
genomic: CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAGgtattgccaa ... ttggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
EST: gi|100425657|gb|BY958705.1|BY958705
EST:     CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAG                         GTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
genomic: CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAGgtattgccaa ... ttggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
EST: gi|100353689|gb|BY983261.1|BY983261
EST:     CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAG                         GTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGNAAGAGCACTAA
genomic: CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAGgtattgccaa ... ttggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATG-AAGAGCACTAA
EST: gi|100431493|gb|BY960225.1|BY960225
EST:     CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAG                         GTAGCGGGCTCAAGGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
genomic: CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAGgtattgccaa ... ttggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
EST: gi|100442976|gb|BY963471.1|BY963471
EST:     CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAG                         GTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
genomic: CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAGgtattgccaa ... ttggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
EST: gi|162195743|gb|FC371134.1|FC371134
EST:     CGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAG                         GTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
genomic: CGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAGgtattgccaa ... ttggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
EST: gi|100435524|gb|BY960955.1|BY960955
EST:     CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAG                         GTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
genomic: CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAGgtattgccaa ... ttggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
EST: gi|100452599|gb|CJ975350.1|CJ975350
EST:     CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAG                         GTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
genomic: CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAGgtattgccaa ... ttggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
EST: gi|18326329|gb|BJ158328.1|BJ158328
EST:     CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAG                         GTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
genomic: CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAGgtattgccaa ... ttggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
EST: gi|100385733|gb|BY987798.1|BY987798
EST:     CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAG                         GTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
genomic: CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAGgtattgccaa ... ttggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
EST: gi|100442351|gb|BY981375.1|BY981375
EST:     CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAG                         GTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
genomic: CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAGgtattgccaa ... ttggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
EST: gi|18346978|gb|BJ179024.1|BJ179024
EST:     CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAG                         GTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
genomic: CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAGgtattgccaa ... ttggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
EST: gi|100428306|gb|BY977737.1|BY977737
EST:     CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAG                         GTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
genomic: CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAGgtattgccaa ... ttggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
EST: gi|18350798|gb|BJ182849.1|BJ182849
EST:     CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAG                         GTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
genomic: CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAGgtattgccaa ... ttggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
EST: gi|100444603|gb|BY964301.1|BY964301
EST:     CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAG                         GTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
genomic: CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAGgtattgccaa ... ttggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
EST: gi|100451144|gb|CJ974619.1|CJ974619
EST:     CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAG                         GTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
genomic: CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAGgtattgccaa ... ttggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
EST: gi|100365549|gb|BY966651.1|BY966651
EST:     CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAG                         GTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
genomic: CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAGgtattgccaa ... ttggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
EST: gi|18350585|gb|BJ182636.1|BJ182636
EST:     CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAG                         GTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT
genomic: CTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAGgtattgccaa ... ttggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAAT

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: 29 (upstream exon), 35 (downstream exon)
Score: 99

GCAGCTCTCCCCTCACCGTCACATCTGATCGGAGCAGCGCTGCATCATGGCTGCCACCGCGTTCACGGCGGTCTCTGTGCCGAGCAATGCTTCCCTCAAGgtattgccaa ... ttggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAATGCCGTCACTTTCGGCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctgacttgatttttcacatggagtacctaaattactgttgaattggttacagGTAGCGGGCTCAAAGGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAATGCCGTCACTTTCGGCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTG
        ttgattttt  TA-rich tract