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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATCTTTGGAGACGAAGGCATGGACGAGCTGGCAGGGATGAGCCCGGAAGATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctgcgccttgagtatggcgcgcctggttcatggttggatatgtatgttagtctgaggtcttgctgggggggtgtagtagcatggggttgtgtcgaggtgtgaattatcaatgatcggatgggtgggattggatttcag

Basic information

species Physcomitrella patens
transcript PP1S218_133V6.1
intron # 1
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|162173415|gb|FC349794.1|FC349794
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|162176626|gb|FC352471.1|FC352471
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|100393599|gb|BY953447.1|BY953447
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|208384557|gb|DC915029.1|DC915029
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|208393155|gb|DC907978.1|DC907978
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAGCGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|100386909|gb|BY988178.1|BY988178
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|208367277|gb|DC939835.1|DC939835
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|100362918|gb|BY947594.1|BY947594
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|208373514|gb|DC931917.1|DC931917
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|18357560|gb|BJ189619.1|BJ189619
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGNNNNNNNT
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAG-AAAAAAT
EST: gi|100423272|gb|BY958215.1|BY958215
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGGAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|162260448|gb|FC435061.1|FC435061
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|208351808|gb|DC910362.1|DC910362
EST:     ATATTCANCGCANAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|7207601|gb|AW561648.1|AW561648
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|100377926|gb|BY986463.1|BY986463
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGGAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|67702569|gb|BJ962802.1|BJ962802
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|67572938|gb|BJ945762.1|BJ945762
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|100445050|gb|BY964349.1|BY964349
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|100386534|gb|BY951330.1|BY951330
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|208357259|gb|DC910656.1|DC910656
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|208378607|gb|DC903638.1|DC903638
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|100447329|gb|CJ971628.1|CJ971628
EST:     ATATTCAACGCAGGAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|162155457|gb|FC330953.1|FC330953
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGNNNNNNNT
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAG-AAAAAAT
EST: gi|100445979|gb|CJ970278.1|CJ970278
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|162167872|gb|FC344810.1|FC344810
EST:     CGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: CGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|100382441|gb|BY969105.1|BY969105
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|162162468|gb|FC339199.1|FC339199
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|100386348|gb|BY988015.1|BY988015
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|100361517|gb|BY984045.1|BY984045
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|100399109|gb|BY954204.1|BY954204
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|162168240|gb|FC344970.1|FC344970
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
EST: gi|100418425|gb|BY957412.1|BY957412
EST:     ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAG                         GACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC
genomic: ATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATC

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: 26 (upstream exon), 35 (downstream exon)
Score: 20

TATCTTTGGAGACGAAGGCATGGACGAGCTGGCAGGGATGAGCCCGGAAGATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctg ... tggatttcagGACGAAACGCACAGACTTTCACTGGAACACGATGCTACGAAAGAAAAAATCAAGGAGAATCAAGAGAAGATCAAGCTGAATAAGCAGCTGCCTTACCTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATCTTTGGAGACGAAGGCATGGACGAGCTGGCAGGGATGAGCCCGGAAGATATTCAACGCAGAAGTCGTCTGCTCGAAAACGAGATCCGTGTCTTGAAGgttttttctgcgccttgagtatggcgcgcctggttcatggttggatatgtatgttagtctgaggtcttgctgggggggtgtagtagcatggggttgtgtcgaggtgtgaattatcaatgatcggatgggtgggattggatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG