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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggataacgccaataagaagcttcattttccaagagacggcaagtggatttcaaaactattcggccatgaatctaattgttagttgatcacttgtgcagTCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAAAAAAGCTTGATGACGAGACAGATGTTCTTGCTC

Basic information

species Physcomitrella patens
transcript PP1S96_94V6.2
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|67578500|gb|BJ950667.1|BJ950667
EST:     TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAAT                         TCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
genomic: TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAATgtatatttct ... acttgtgcagTCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
EST: gi|162261021|gb|FC437428.1|FC437428
EST:     TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAAT                         TCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
genomic: TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAATgtatatttct ... acttgtgcagTCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
EST: gi|37826092|gb|BJ584104.1|BJ584104
EST:     TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAAT                         TCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
genomic: TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAATgtatatttct ... acttgtgcagTCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
EST: gi|67578369|gb|BJ950536.1|BJ950536
EST:     TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAAT                         TCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
genomic: TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAATgtatatttct ... acttgtgcagTCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
EST: gi|67695053|gb|BJ955286.1|BJ955286
EST:     TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAAT                         TCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
genomic: TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAATgtatatttct ... acttgtgcagTCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
EST: gi|67574919|gb|BJ947743.1|BJ947743
EST:     TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAAT                         TCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
genomic: TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAATgtatatttct ... acttgtgcagTCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
EST: gi|67701255|gb|BJ961488.1|BJ961488
EST:     TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAAT                         TCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
genomic: TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAATgtatatttct ... acttgtgcagTCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
EST: gi|67698680|gb|BJ958913.1|BJ958913
EST:     TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAAT                         TCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
genomic: TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAATgtatatttct ... acttgtgcagTCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
EST: gi|67574035|gb|BJ946859.1|BJ946859
EST:     TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAAT                         TCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
genomic: TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAATgtatatttct ... acttgtgcagTCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
EST: gi|67698346|gb|BJ958579.1|BJ958579
EST:     TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAAT                         TCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
genomic: TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAATgtatatttct ... acttgtgcagTCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
EST: gi|67697424|gb|BJ957657.1|BJ957657
EST:     TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAAT                         TCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
genomic: TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAATgtatatttct ... acttgtgcagTCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
EST: gi|67697361|gb|BJ957594.1|BJ957594
EST:     TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAAT                         TCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
genomic: TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAATgtatatttct ... acttgtgcagTCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
EST: gi|37828988|gb|BJ587000.1|BJ587000
EST:     TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAAT                         TCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
genomic: TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAATgtatatttct ... acttgtgcagTCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
EST: gi|22491864|gb|BU051787.1|BU051787
EST:     TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAAT                         TCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
genomic: TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAATgtatatttct ... acttgtgcagTCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
EST: gi|37830434|gb|BJ588446.1|BJ588446
EST:     TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAAT                         TCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
genomic: TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAATgtatatttct ... acttgtgcagTCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
EST: gi|67575221|gb|BJ948045.1|BJ948045
EST:     TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAAT                         TCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA
genomic: TGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAATgtatatttct ... acttgtgcagTCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAA

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

GTTGTCAGGAAGAAGGCCCCAACTTCGTCTGCAAAAAAAGATGAGGGTGCTGTTAATGCAGCGCGACGAGCTGGCGCCCCTATCGAGACCATTAAGAAATgtatatttct ... acttgtgcagTCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAAAAAAGCTTGATGACGAGACAGATGTTCTTGCTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggatttcaaaactattcggccatgaatctaattgttagttgatcacttgtgcagTCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAAAAAAGCTTGATGACGAGACAGATGTTCTTGCTC
        aaaactatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggataacgccaataagaagcttcattttccaagagacggcaagtggatttcaaaactattcggccatgaatctaattgttagttgatcacttgtgcagTCAACGCTGGATCAAACAAGGCAGCTACTAGTGCGACTGGCTTGAATACAAAAAAGCTTGATGACGAGACAGATGTTCTTGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG