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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAGgttcgatctcgtacttttctagcttgagttaacagggatcaatatgtgaacatggaagtctatttcgatctccagtgaagaaaatggagaaggcatgaat...

Basic information

species Physcomitrella patens
transcript PP1S505_6V6.2
intron # 12
splice site 5'
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|208394906|gb|DC924125.1|DC924125
EST:     GCAGGATTTGAG                         ATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
genomic: GCAGGATTTGAGgttcgatctc ... gattgatcagATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
EST: gi|208394780|gb|DC924083.1|DC924083
EST:     TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAG                         ATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
genomic: TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAGgttcgatctc ... gattgatcagATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
EST: gi|162166439|gb|FC342421.1|FC342421
EST:     TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATNTGAG                         ATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
genomic: TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAGgttcgatctc ... gattgatcagATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
EST: gi|208346584|gb|DC916850.1|DC916850
EST:     NTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAG                         ATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
genomic: TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAGgttcgatctc ... gattgatcagATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
EST: gi|208388484|gb|DC957066.1|DC957066
EST:     TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAG                         ATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
genomic: TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAGgttcgatctc ... gattgatcagATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
EST: gi|67727357|gb|BJ977616.1|BJ977616
EST:     TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAG                         ATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
genomic: TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAGgttcgatctc ... gattgatcagATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
EST: gi|208367883|gb|DC955346.1|DC955346
EST:     TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAG                         ATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
genomic: TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAGgttcgatctc ... gattgatcagATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
EST: gi|208387195|gb|DC945494.1|DC945494
EST:     TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAG                         ATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
genomic: TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAGgttcgatctc ... gattgatcagATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
EST: gi|208396976|gb|DC924658.1|DC924658
EST:     TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAG                         ATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
genomic: TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAGgttcgatctc ... gattgatcagATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
EST: gi|162166440|gb|FC342422.1|FC342422
EST:     TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAG                         ATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
genomic: TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAGgttcgatctc ... gattgatcagATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
EST: gi|208380622|gb|DC919380.1|DC919380
EST:     TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAG                         ATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
genomic: TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAGgttcgatctc ... gattgatcagATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
EST: gi|208386208|gb|DC952921.1|DC952921
EST:     CCTGAAAGACGCAGGATTTGAG                         ATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
genomic: CCTGAAAGACGCAGGATTTGAGgttcgatctc ... gattgatcagATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
EST: gi|37853228|gb|BJ611236.1|BJ611236
EST:     TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAG                         ATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
genomic: TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAGgttcgatctc ... gattgatcagATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
EST: gi|208371896|gb|DC951714.1|DC951714
EST:     TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAG                         ATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
genomic: TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAGgttcgatctc ... gattgatcagATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
EST: gi|208354679|gb|DC918705.1|DC918705
EST:     TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAG                         ATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
genomic: TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAGgttcgatctc ... gattgatcagATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG
EST: gi|67720489|gb|BJ970748.1|BJ970748
EST:     TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAG                         ATTCTCATGGAAGAGGATTTGGCAAAACGTTCGCAAGTGCCGTGGTATCAG
genomic: TTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAGgttcgatctc ... gattgatcagATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAG

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), 34 (downstream exon)
Score: 19

GAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAGgttcgatctc ... gattgatcagATTCTCATGGAAGAGGATTTGGCAAAACATTCGCAAGTGCCGTGGTATCAGCCTTTGGATCCCAACCATTTCTCACTTTCCACTCTTCGGCTTACCCCGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGAGATTGAACTCGGAAATGGTCTTCCTGACATTCGGTCCACACGTCAGGTTCTTCAAGCCCTGAAAGACGCAGGATTTGAGgttcgatctcgtacttttctagcttgagttaacagggatcaatatgtgaacatggaagtctatttcgatctccagtgaagaaaatggagaaggcatgaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagaaaa