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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaatttttacgtcattgctgtgttgattggaataatggcttgttgcatttaaaacttaaatctctaaaaatgcgacgttgttggatggcactcgtcctactgcgaaggatgagtgtcgccacagagtgcgcgtcaagctagcactgaggcgccttgccgtggttgaatgcgcag

Basic information

species Physcomitrella patens
transcript PP1S424_22V6.2
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|208351125|gb|DC926017.1|DC926017
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|162278876|gb|FC454927.1|FC454927
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|208382870|gb|DC928295.1|DC928295
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|208381395|gb|DC927831.1|DC927831
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|162236682|gb|FC413777.1|FC413777
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|162259659|gb|FC436704.1|FC436704
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|162270768|gb|FC446381.1|FC446381
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|208397629|gb|DC912247.1|DC912247
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|162260192|gb|FC436327.1|FC436327
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|162263103|gb|FC440081.1|FC440081
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|162265463|gb|FC440789.1|FC440789
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|162263104|gb|FC440082.1|FC440082
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|162278875|gb|FC454926.1|FC454926
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|162273701|gb|FC449424.1|FC449424
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|162264249|gb|FC441351.1|FC441351
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|100389283|gb|BY971033.1|BY971033
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|162272167|gb|FC448676.1|FC448676
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGATTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|162275819|gb|FC451380.1|FC451380
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|162264248|gb|FC441350.1|FC441350
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|162265542|gb|FC441557.1|FC441557
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|100411270|gb|BY974553.1|BY974553
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|162265762|gb|FC443168.1|FC443168
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|162273702|gb|FC449425.1|FC449425
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|67575999|gb|BJ948823.1|BJ948823
EST:     CGGTGCAGCCCATGCTGCTTTGCNAGACACATTCCGTATCTTGAAGAGCG                         ANCNAGTGACTAAG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAG
EST: gi|67568787|gb|BJ941611.1|BJ941611
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|162273976|gb|FC450115.1|FC450115
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|162263098|gb|FC440076.1|FC440076
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|162273757|gb|FC449480.1|FC449480
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|18333294|gb|BJ165308.1|BJ165308
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|162260191|gb|FC436326.1|FC436326
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|162236681|gb|FC413776.1|FC413776
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|67691982|gb|BJ952215.1|BJ952215
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|208353927|gb|DC914081.1|DC914081
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
EST: gi|162265462|gb|FC440788.1|FC440788
EST:     CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCG                         AGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG
genomic: CGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTG

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: 101

GTCGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaattt ... gaatgcgcagAGCAAGTGACTAAGACCGACGTCGAGAAACTGGTTAAGAGGACTGGTTTTGAAGGTCTTCAATGGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCGGTGCAGCCCATGCTGCTTTGCAAGACACATTCCGTATCTTGAAGAGCGgtacgaatttttacgtcattgctgtgttgattggaataatggcttgttgcatttaaaacttaaatctctaaaaatgcgacgttgttggatggcactcgtcctactgcgaaggatgagtgtcgccacagagtgcgcgtcaagctagcactgaggcgccttgccgtggttgaatgcgcag

- - - - - -  ATGCTG
- - - - - - - TGCTGC
- - - - - - -  GCTGCT
- - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - -  TGAAGA