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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactcttggggcaacctaatctgcttccctgctgcgttgcattactgctgcgtccgagcattcaaatgtccccgaactgataggtttgttgacgattgtgggattgaatgatcgcgcagTATGTGGTGGTGGACTTCTTGTGGTACCGCAAATTTGAATTGGGTGCATCAGTGTGGTCAGCCGGTCACGACGTGATCGACGAATGGGGTCGTCCAATTC

Basic information

species Physcomitrella patens
transcript PP1S80_41V6.1
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|100394496|gb|BY972094.1|BY972094
EST:     TCGACAATGCTAAATTCGTCTCCCAAAATCTTCTCAAGTTCGGCTACGAG                         TATGTGGTGGTGGACTTCTTGTGGTACCGCAAATTTGAATTGGGTGCATCA
genomic: TCGACAATGCTAAATTCGTCTCCCAAAATCTTCTCAAGTTCGGCTACGAGgtactcttgg ... gatcgcgcagTATGTGGTGGTGGACTTCTTGTGGTACCGCAAATTTGAATTGGGTGCATCA
EST: gi|67716209|gb|BJ966469.1|BJ966469
EST:     TCGACAATGCTAAATTCGTCTCCCAAAATCTTCTCAAGCTCGGCTACGAG                         TATGTGGTGGTGGACTTCTTGTGGTACCGCAAATTTGAATTGGGTGCATCA
genomic: TCGACAATGCTAAATTCGTCTCCCAAAATCTTCTCAAGTTCGGCTACGAGgtactcttgg ... gatcgcgcagTATGTGGTGGTGGACTTCTTGTGGTACCGCAAATTTGAATTGGGTGCATCA
EST: gi|208344547|gb|DC909106.1|DC909106
EST:     TCGACAATGCTAAATTCGTCTCCCAAAATCTTCTCAAGTTCGGCTACGAG                         TATGTGGTGGTGGACTTCTTGTGGTACCGCAAATTTGAATTGGGTGCATCA
genomic: TCGACAATGCTAAATTCGTCTCCCAAAATCTTCTCAAGTTCGGCTACGAGgtactcttgg ... gatcgcgcagTATGTGGTGGTGGACTTCTTGTGGTACCGCAAATTTGAATTGGGTGCATCA
EST: gi|100354453|gb|BY945870.1|BY945870
EST:     TCGACAATGCTAAATTCGTCTCCCAAAATCTTCTCAAGTTCGGCTACGAG                         TATGTGGTGGTGGACTTCTTGTGGTACCGCAAATTTGAATTGGGTGCATCA
genomic: TCGACAATGCTAAATTCGTCTCCCAAAATCTTCTCAAGTTCGGCTACGAGgtactcttgg ... gatcgcgcagTATGTGGTGGTGGACTTCTTGTGGTACCGCAAATTTGAATTGGGTGCATCA
EST: gi|100451878|gb|CJ974987.1|CJ974987
EST:     TCGACAATGCTAAATTCGTCTCCCAAAATCTTCTCAAGTTCGGCTACGAG                         TATGTGGTGGTGGACTTCTTGTGGTACCGCAAATTTGAATTGGGTGCATCA
genomic: TCGACAATGCTAAATTCGTCTCCCAAAATCTTCTCAAGTTCGGCTACGAGgtactcttgg ... gatcgcgcagTATGTGGTGGTGGACTTCTTGTGGTACCGCAAATTTGAATTGGGTGCATCA
EST: gi|67709748|gb|BJ965564.1|BJ965564
EST:     TCGACAATGCTAAATTCGTCTCCCAAAATCTTCTCAAGTTCGGCTACGAG                         TATGTGGTGGTGGACTTCTTGTGGTACCGCAAATTTGAATTGGGTGCATCA
genomic: TCGACAATGCTAAATTCGTCTCCCAAAATCTTCTCAAGTTCGGCTACGAGgtactcttgg ... gatcgcgcagTATGTGGTGGTGGACTTCTTGTGGTACCGCAAATTTGAATTGGGTGCATCA

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: 35 (upstream exon), 30 (downstream exon)
Score: 12

ATGGAACTCGTACAACTCATTTTCGTGGATCGTCTCAGAAGCAGAATTCCTCGACAATGCTAAATTCGTCTCCCAAAATCTTCTCAAGTTCGGCTACGAGgtactcttgg ... gatcgcgcagTATGTGGTGGTGGACTTCTTGTGGTACCGCAAATTTGAATTGGGTGCATCAGTGTGGTCAGCCGGTCACGACGTGATCGACGAATGGGGTCGTCCAATTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgtccccgaactgataggtttgttgacgattgtgggattgaatgatcgcgcagTATGTGGTGGTGGACTTCTTGTGGTACCGCAAATTTGAATTGGGTGCATCAGTGTGGTCAGCCGGTCACGACGTGATCGACGAATGGGGTCGTCCAATTC
                      tgttgac  putative branch site (score: 12)
                                      attgaat  TA-rich tract