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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacgggtggattgtgatttttgaacttgaattcgggttacttttttctctcttctcttcttccttgcactccctttttgactgttgttatgtatattcagTTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGACCCTGAATTCCGGCAGCAATTGTCTGAAACAGTTAACTCTCTCTTAGCGC

Basic information

species Physcomitrella patens
transcript PP1S22_40V6.2
intron # 4
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|100369280|gb|BY948029.1|BY948029
EST:     CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAG                         TTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGAC
genomic: CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAGgtactttatt ... gtatattcagTTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGAC
EST: gi|18372366|gb|BJ203968.1|BJ203968
EST:     CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAG                         TTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGAC
genomic: CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAGgtactttatt ... gtatattcagTTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGAC
EST: gi|18330622|gb|BJ162628.1|BJ162628
EST:     CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAG                         TTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGAC
genomic: CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAGgtactttatt ... gtatattcagTTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGAC
EST: gi|208355557|gb|DC906565.1|DC906565
EST:     CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAG                         TTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGAC
genomic: CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAGgtactttatt ... gtatattcagTTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGAC
EST: gi|18354264|gb|BJ186320.1|BJ186320
EST:     CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAG                         TTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAA
genomic: CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAGgtactttatt ... gtatattcagTTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAA
EST: gi|18360887|gb|BJ192950.1|BJ192950
EST:     CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAG                         TTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGAC
genomic: CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAGgtactttatt ... gtatattcagTTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGAC
EST: gi|18328179|gb|BJ160183.1|BJ160183
EST:     CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAG                         TTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGAC
genomic: CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAGgtactttatt ... gtatattcagTTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGAC
EST: gi|100436607|gb|BY961302.1|BY961302
EST:     CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAG                         TTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGAC
genomic: CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAGgtactttatt ... gtatattcagTTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGAC
EST: gi|18351918|gb|BJ183970.1|BJ183970
EST:     CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAG                         TTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGAC
genomic: CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAGgtactttatt ... gtatattcagTTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGAC
EST: gi|18361631|gb|BJ193697.1|BJ193697
EST:     CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAG                         TTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGAC
genomic: CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAGgtactttatt ... gtatattcagTTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGAC
EST: gi|18343880|gb|BJ175918.1|BJ175918
EST:     CANTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAG                         TTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCA
genomic: CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAGgtactttatt ... gtatattcagTTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCA
EST: gi|18358703|gb|BJ190762.1|BJ190762
EST:     CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAG                         TTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGAC
genomic: CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAGgtactttatt ... gtatattcagTTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGAC
EST: gi|208381231|gb|DC903065.1|DC903065
EST:     CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAG                         TTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGAC
genomic: CAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAGgtactttatt ... gtatattcagTTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGAC

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), 32 (downstream exon)
Score: 12

TGTAGATTTGCAAAAACCTCAAGTGGAACTGGATGGGAAACCTTGTGCAGCAGTGGGTCAAAGCGGACTTATGGCTCTGTATGACAGTTTGTTCAGCCAGgtactttatt ... gtatattcagTTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGACCCTGAATTCCGGCAGCAATTGTCTGAAACAGTTAACTCTCTCTTAGCGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctcttctcttcttccttgcactccctttttgactgttgttatgtatattcagTTGGACGTAGCATCTTCACAACTTCTCGTGACGGATAATGACTTCAAGGACCCTGAATTCCGGCAGCAATTGTCTGAAACAGTTAACTCTCTCTTAGCGC
                             ttttgac  putative branch site (score: 12)
                                      ttgttatgtatatt  TA-rich tract