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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcagcagcaatggacggggcattttttaaccttgaacattctcaagggaggaaatgtttgtaataatcgttgtttcatgtacccttccatttgtgtgcagATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACCAGCACAGCCTTTTGGGTGGCTGGCCTTCTACTTTTCGAATCTGCTGCAG

Basic information

species Physcomitrella patens
transcript PP1S295_6V6.1
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|208388026|gb|DC933146.1|DC933146
EST:     CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCA                         ATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
genomic: CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCAgtacgtgtcg ... ttgtgtgcagATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
EST: gi|100418471|gb|BY957435.1|BY957435
EST:     CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCA                         ATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
genomic: CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCAgtacgtgtcg ... ttgtgtgcagATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
EST: gi|162152799|gb|FC329805.1|FC329805
EST:     CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCA                         ATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
genomic: CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCAgtacgtgtcg ... ttgtgtgcagATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
EST: gi|100357878|gb|BY946619.1|BY946619
EST:     CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCA                         ATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
genomic: CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCAgtacgtgtcg ... ttgtgtgcagATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
EST: gi|18332273|gb|BJ164286.1|BJ164286
EST:     CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCA                         ATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
genomic: CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCAgtacgtgtcg ... ttgtgtgcagATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
EST: gi|67569350|gb|BJ942174.1|BJ942174
EST:     CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCA                         ATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
genomic: CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCAgtacgtgtcg ... ttgtgtgcagATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
EST: gi|67570400|gb|BJ943224.1|BJ943224
EST:     CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCA                         ATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
genomic: CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCAgtacgtgtcg ... ttgtgtgcagATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
EST: gi|162275561|gb|FC451303.1|FC451303
EST:     CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCA                         ATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
genomic: CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCAgtacgtgtcg ... ttgtgtgcagATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
EST: gi|208399505|gb|DC908502.1|DC908502
EST:     CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCA                         ATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
genomic: CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCAgtacgtgtcg ... ttgtgtgcagATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
EST: gi|162270005|gb|FC446705.1|FC446705
EST:     CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCA                         ATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
genomic: CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCAgtacgtgtcg ... ttgtgtgcagATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
EST: gi|67578461|gb|BJ950628.1|BJ950628
EST:     CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCA                         ATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
genomic: CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCAgtacgtgtcg ... ttgtgtgcagATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
EST: gi|100447905|gb|CJ972204.1|CJ972204
EST:     CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCA                         ATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
genomic: CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCAgtacgtgtcg ... ttgtgtgcagATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
EST: gi|100353517|gb|BY964846.1|BY964846
EST:     CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCA                         ATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACNAGATTCACC
genomic: CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCAgtacgtgtcg ... ttgtgtgcagATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
EST: gi|18357428|gb|BJ189487.1|BJ189487
EST:     CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCA                         ATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC
genomic: CCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCAgtacgtgtcg ... ttgtgtgcagATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACC

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: 14

GCTGCTACAGAAGAAGCAAACGTTCGAAGTTGCTGCGAAAGCTCTAACTACCATTGTCCAGGAACGCTATGTACGAGCAACTCCAGCAGAGCAGCACTCAgtacgtgtcg ... ttgtgtgcagATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACCAGCACAGCCTTTTGGGTGGCTGGCCTTCTACTTTTCGAATCTGCTGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggaggaaatgtttgtaataatcgttgtttcatgtacccttccatttgtgtgcagATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACCAGCACAGCCTTTTGGGTGGCTGGCCTTCTACTTTTCGAATCTGCTGCAG
                                    cccttccattt  CT-rich tract
      aaatgtttgtaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcagcagcaatggacggggcattttttaaccttgaacattctcaagggaggaaatgtttgtaataatcgttgtttcatgtacccttccatttgtgtgcagATTTACGGAGCAGTGTGCAGGGCAGCCACACTTTTGACTACAAGATTCACCAGCACAGCCTTTTGGGTGGCTGGCCTTCTACTTTTCGAATCTGCTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG