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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTTAATGCAGTCCTGTTCACGGCCAGAGGACAGATGGAGGCACTTCTCCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTGgtatgtgaaattctcctcgacaactaattcttggcgaaacgtcaaagtagagagagtaggtttgtgttttctcacgaaggttgtagacagagcattcttc...

Basic information

species Physcomitrella patens
transcript PP1S475_26V6.1
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|100393374|gb|BY989844.1|BY989844
EST:     CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTG                         GCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
genomic: CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTGgtatgtgaaa ... ttatgcgcagGCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
EST: gi|100446414|gb|CJ970713.1|CJ970713
EST:     CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCANATGATCGCTG                         GCGCTGGANCCGGANTACCGTGCTCAATGNTGGCTTGCCCA-CTGAGCTTG
genomic: CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTGgtatgtgaaa ... ttatgcgcagGCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
EST: gi|162177172|gb|FC352601.1|FC352601
EST:     CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTG                         GCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
genomic: CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTGgtatgtgaaa ... ttatgcgcagGCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
EST: gi|208383658|gb|DC907049.1|DC907049
EST:     CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCANATGATCGCTG                         GCGCTGGANCCGGA
genomic: CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTGgtatgtgaaa ... ttatgcgcagGCGCTGGAGCCGGA
EST: gi|100362759|gb|BY947514.1|BY947514
EST:     CCGTGAATCCCC-GGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTG                         GCGCTGGAGCCGGAGTAGCGTGCTNCA-TGGTGGCT-GCCCAACTGAGCTT
genomic: CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTGgtatgtgaaa ... ttatgcgcagGCGCTGGAGCCGGAGTAGCGTGCT-CAATGGTGGCTTGCCCAACTGAGCTT
EST: gi|162154302|gb|FC330641.1|FC330641
EST:     CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTG                         GCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
genomic: CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTGgtatgtgaaa ... ttatgcgcagGCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
EST: gi|100415736|gb|BY992979.1|BY992979
EST:     CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTG                         GCGCTGGAGCCGGAGTAGCGTGCTNCA-TGGTGGCTTGCCCCACTGAGCTT
genomic: CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTGgtatgtgaaa ... ttatgcgcagGCGCTGGAGCCGGAGTAGCGTGCT-CAATGGTGGCTTGCCCAACTGAGCTT
EST: gi|100439205|gb|BY980146.1|BY980146
EST:     CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTG                         GCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
genomic: CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTGgtatgtgaaa ... ttatgcgcagGCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
EST: gi|208380180|gb|DC927459.1|DC927459
EST:     CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTG                         GCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
genomic: CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTGgtatgtgaaa ... ttatgcgcagGCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
EST: gi|162160511|gb|FC336901.1|FC336901
EST:     CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTG                         GCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCCACTGAGCTTG
genomic: CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTGgtatgtgaaa ... ttatgcgcagGCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
EST: gi|100362322|gb|BY947301.1|BY947301
EST:     CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTG                         GCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
genomic: CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTGgtatgtgaaa ... ttatgcgcagGCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
EST: gi|162158213|gb|FC335256.1|FC335256
EST:     GCAGATGATCGCTG                         GCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
genomic: GCAGATGATCGCTGgtatgtgaaa ... ttatgcgcagGCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
EST: gi|208348136|gb|DC920927.1|DC920927
EST:     GTGACCCAGCAGATGATCGCTG                         GCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCNTGCCCAACTGAGCTTG
genomic: GTGACCCAGCAGATGATCGCTGgtatgtgaaa ... ttatgcgcagGCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
EST: gi|162167490|gb|FC343687.1|FC343687
EST:     CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTG                         GCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
genomic: CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTGgtatgtgaaa ... ttatgcgcagGCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
EST: gi|162245674|gb|FC420419.1|FC420419
EST:     CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTG                         GCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
genomic: CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTGgtatgtgaaa ... ttatgcgcagGCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
EST: gi|162214875|gb|FC391010.1|FC391010
EST:     CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTG                         GCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
genomic: CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTGgtatgtgaaa ... ttatgcgcagGCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
EST: gi|162164666|gb|FC340713.1|FC340713
EST:     CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTG                         GCGCTGGAGCCGGAGTAGCGTGCTNCA-TGGTGGCTTGCCCAACTGAGCTT
genomic: CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTGgtatgtgaaa ... ttatgcgcagGCGCTGGAGCCGGAGTAGCGTGCT-CAATGGTGGCTTGCCCAACTGAGCTT
EST: gi|208370451|gb|DC952154.1|DC952154
EST:     CTGTGACCCAGCAGATGATCGCTG                         GCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
genomic: CTGTGACCCAGCAGATGATCGCTGgtatgtgaaa ... ttatgcgcagGCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG
EST: gi|100418198|gb|BY993381.1|BY993381
EST:     CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTG                         GCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCA-CTGAGCTTG
genomic: CCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTGgtatgtgaaa ... ttatgcgcagGCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTG

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), 35 (downstream exon)
Score: 85

GTTTTTAATGCAGTCCTGTTCACGGCCAGAGGACAGATGGAGGCACTTCTCCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTGgtatgtgaaa ... ttatgcgcagGCGCTGGAGCCGGAGTAGCGTGCTCAATGGTGGCTTGCCCAACTGAGCTTGTGAAGTGTCGTCTTCAAGCTCAAAGTGCACTTGCCACCACTGTGGAGGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTTAATGCAGTCCTGTTCACGGCCAGAGGACAGATGGAGGCACTTCTCCGTGAATCCCCCGGTGCTCCTCTCACTGTGACCCAGCAGATGATCGCTGgtatgtgaaattctcctcgacaactaattcttggcgaaacgtcaaagtagagagagtaggtttgtgttttctcacgaaggttgtagacagagcattcttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG