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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtttcggttccttgtgtcaacttcctctagtaccttcgatattgacctaattaacgatcttcgtatctattcttctactgttgctaaataagcatgcttttctatgaggttggcaccagaacttgtggaacatgctcgatctaataattggatgcttctttatgggcggccagTCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGACTGGTGCCTTGAGGGTTGGCGCAGAGTTCATATCGAGGCATTATGCCAAG

Basic information

species Physcomitrella patens
transcript PP1S132_95V6.1
intron # 5
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|67718471|gb|BJ968730.1|BJ968730
EST:     ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAG                         TCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
genomic: ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAGgtgtgtttcg ... gggcggccagTCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
EST: gi|100356048|gb|BY946170.1|BY946170
EST:     ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAG                         TCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
genomic: ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAGgtgtgtttcg ... gggcggccagTCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
EST: gi|100380016|gb|BY968804.1|BY968804
EST:     ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAG                         TCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
genomic: ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAGgtgtgtttcg ... gggcggccagTCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
EST: gi|18351892|gb|BJ183944.1|BJ183944
EST:     ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAG                         TCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
genomic: ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAGgtgtgtttcg ... gggcggccagTCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
EST: gi|100446010|gb|CJ970309.1|CJ970309
EST:     ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAG                         TCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
genomic: ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAGgtgtgtttcg ... gggcggccagTCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
EST: gi|100390341|gb|BY952749.1|BY952749
EST:     ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAG                         TCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
genomic: ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAGgtgtgtttcg ... gggcggccagTCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
EST: gi|100448896|gb|CJ973195.1|CJ973195
EST:     ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAG                         TCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
genomic: ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAGgtgtgtttcg ... gggcggccagTCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
EST: gi|162267156|gb|FC443387.1|FC443387
EST:     ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAG                         TCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
genomic: ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAGgtgtgtttcg ... gggcggccagTCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
EST: gi|100417339|gb|BY957283.1|BY957283
EST:     ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAG                         TCCAGCAATTGCAGAGAACTGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
genomic: ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAGgtgtgtttcg ... gggcggccagTCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
EST: gi|18365276|gb|BJ197350.1|BJ197350
EST:     ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAG                         TCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
genomic: ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAGgtgtgtttcg ... gggcggccagTCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
EST: gi|208344839|gb|DC912673.1|DC912673
EST:     ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAG                         TCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
genomic: ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAGgtgtgtttcg ... gggcggccagTCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
EST: gi|208397779|gb|DC912002.1|DC912002
EST:     ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAG                         TCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
genomic: ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAGgtgtgtttcg ... gggcggccagTCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
EST: gi|208352476|gb|DC910190.1|DC910190
EST:     ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAG                         TCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
genomic: ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAGgtgtgtttcg ... gggcggccagTCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
EST: gi|18361573|gb|BJ193639.1|BJ193639
EST:     ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAG                         TCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
genomic: ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAGgtgtgtttcg ... gggcggccagTCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
EST: gi|208384190|gb|DC911298.1|DC911298
EST:     ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAG                         TCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTACCCGGGAC
genomic: ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAGgtgtgtttcg ... gggcggccagTCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
EST: gi|18371678|gb|BJ203280.1|BJ203280
EST:     ATTTCTCAGTTCAACAAACTTATCGCAAAGCTTATTCTGGGCGCTAATAG                         TCCAGCAATTGCAGATAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
genomic: ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAGgtgtgtttcg ... gggcggccagTCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
EST: gi|18332250|gb|BJ164263.1|BJ164263
EST:     ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAG                         TCCAGCAATTGCAGA-A-CCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
genomic: ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAGgtgtgtttcg ... gggcggccagTCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
EST: gi|162263809|gb|FC438428.1|FC438428
EST:     ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAG                         TCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC
genomic: ATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAGgtgtgtttcg ... gggcggccagTCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGAC

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: 31 (upstream exon), 34 (downstream exon)
Score: 8

ATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAGgtgtgtttcg ... gggcggccagTCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGACTGGTGCCTTGAGGGTTGGCGCAGAGTTCATATCGAGGCATTATGCCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaacttgtggaacatgctcgatctaataattggatgcttctttatgggcggccagTCCAGCAATTGCAGAGAACCGTGTTGCCACCGTGCAAGCCTTATCCGGGACTGGTGCCTTGAGGGTTGGCGCAGAGTTCATATCGAGGCATTATGCCAAG
                    atctaat  putative branch site (score: 8)
                    atctaataatt  TA-rich tract