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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTTACGACATGGAGCCCGCTTGCATCTGGTGTGCTTACAGGAAAATACATGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggattaatgattttgctatccttgcagaactagacctggtgatttttttgtctcttgagtaactctagggcagaatattgatagctaattcgtttgtgcgcag

Basic information

species Physcomitrella patens
transcript PP1S83_53V6.1
intron # 3
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|37842032|gb|BJ600040.1|BJ600040
EST:     TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAG                         CATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
genomic: TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggatt ... ttgtgcgcagCATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
EST: gi|208380713|gb|DC919429.1|DC919429
EST:     TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAG                         CATCTGGCAACCAAGTCCCTCGTTGNTGAGACTCTCGAGAAGGTAGAAGCT
genomic: TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggatt ... ttgtgcgcagCATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
EST: gi|208391694|gb|DC942284.1|DC942284
EST:     TGAACGGCGACATTCCCGAGGGCAGTCGCTT-GCGCTGAA-AACTATAA-                         CATCTGGCA-CCAA
genomic: TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggatt ... ttgtgcgcagCATCTGGCAACCAA
EST: gi|22492212|gb|BU052135.1|BU052135
EST:     TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAG                         CATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
genomic: TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggatt ... ttgtgcgcagCATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
EST: gi|13251450|gb|BG362353.1|BG362353
EST:     TGAACGGCGACATTCCCGTGGGCAGTCGCTTTGCGCTGGATAACTATAAG                         CATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
genomic: TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggatt ... ttgtgcgcagCATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
EST: gi|162207556|gb|FC384009.1|FC384009
EST:     TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAG                         CATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
genomic: TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggatt ... ttgtgcgcagCATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
EST: gi|162236472|gb|FC412839.1|FC412839
EST:     TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAG                         CATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
genomic: TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggatt ... ttgtgcgcagCATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
EST: gi|162260012|gb|FC435315.1|FC435315
EST:     TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAG                         CATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
genomic: TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggatt ... ttgtgcgcagCATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
EST: gi|208371173|gb|DC955979.1|DC955979
EST:     TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAG                         CATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
genomic: TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggatt ... ttgtgcgcagCATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
EST: gi|22131893|gb|BQ826862.1|BQ826862
EST:     TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAG                         CATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
genomic: TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggatt ... ttgtgcgcagCATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
EST: gi|162207555|gb|FC384008.1|FC384008
EST:     TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAG                         CATTTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
genomic: TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggatt ... ttgtgcgcagCATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
EST: gi|208395524|gb|DC928939.1|DC928939
EST:     TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAG                         CATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
genomic: TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggatt ... ttgtgcgcagCATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
EST: gi|208346033|gb|DC921278.1|DC921278
EST:     TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAG                         CATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
genomic: TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggatt ... ttgtgcgcagCATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
EST: gi|162248713|gb|FC424566.1|FC424566
EST:     TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAG                         CATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
genomic: TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggatt ... ttgtgcgcagCATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
EST: gi|37840709|gb|BJ598717.1|BJ598717
EST:     GAACGGCGACATTNCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAG                         CATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
genomic: GAACGGCGACATT-CCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggatt ... ttgtgcgcagCATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
EST: gi|162272930|gb|FC448047.1|FC448047
EST:     TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAG                         CATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
genomic: TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggatt ... ttgtgcgcagCATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
EST: gi|37845209|gb|BJ603217.1|BJ603217
EST:     TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAG                         CATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
genomic: TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggatt ... ttgtgcgcagCATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
EST: gi|208367179|gb|DC947857.1|DC947857
EST:     TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAG                         CATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
genomic: TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggatt ... ttgtgcgcagCATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
EST: gi|208366178|gb|DC955279.1|DC955279
EST:     TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAG                         CATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
genomic: TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggatt ... ttgtgcgcagCATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
EST: gi|208370555|gb|DC951591.1|DC951591
EST:     TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAG                         CATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
genomic: TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggatt ... ttgtgcgcagCATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
EST: gi|162236005|gb|FC412164.1|FC412164
EST:     TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAG                         CATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
genomic: TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggatt ... ttgtgcgcagCATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
EST: gi|208355973|gb|DC946189.1|DC946189
EST:     TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAG                         CATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT
genomic: TGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggatt ... ttgtgcgcagCATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCT

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), 32 (downstream exon)
Score: 5

TCTTACGACATGGAGCCCGCTTGCATCTGGTGTGCTTACAGGAAAATACATGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggatt ... ttgtgcgcagCATCTGGCAACCAAGTCCCTCGTTGCTGAGACTCTCGAGAAGGTAGAAGCTCTGAAGCCGATTGCCAAGGAGCTTGACGCTTCTTTAGCACAGTTGGCTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTTACGACATGGAGCCCGCTTGCATCTGGTGTGCTTACAGGAAAATACATGAACGGCGACATTCCCGAGGGCAGTCGCTTTGCGCTGGATAACTATAAGgtttgggattaatgattttgctatccttgcagaactagacctggtgatttttttgtctcttgagtaactctagggcagaatattgatagctaattcgtttgtgcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA