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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaattatgtgccaattcaatcattgtgtgattgcaaagtcgtgaatgagaacatagattatataatttcaatttagggacgatactgtcaattccactatccacttgcagaatcacagtaacgaggccctgtctattagatttaatgtaaggactttaagtggtgcttttgcttgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTGTGTATTGAAAAGAGCATATTAAGAAATGCTTTGGCTGCAGTGCAGGAGC

Basic information

species Physcomitrella patens
transcript PP1S181_117V6.1
intron # 10
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|37834676|gb|BJ592688.1|BJ592688
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|162198876|gb|FC372903.1|FC372903
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|162258112|gb|FC433894.1|FC433894
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|162177903|gb|FC355153.1|FC355153
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|162169196|gb|FC345163.1|FC345163
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|162162594|gb|FC338688.1|FC338688
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|162205687|gb|FC380771.1|FC380771
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|162221407|gb|FC397216.1|FC397216
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|162157457|gb|FC333520.1|FC333520
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|67697073|gb|BJ957306.1|BJ957306
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|162161113|gb|FC336461.1|FC336461
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|162228256|gb|FC404972.1|FC404972
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|162198877|gb|FC372904.1|FC372904
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCCAGAAAAACG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACG
EST: gi|162254786|gb|FC430763.1|FC430763
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|37829068|gb|BJ587080.1|BJ587080
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|162190739|gb|FC367001.1|FC367001
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|162254787|gb|FC430764.1|FC430764
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|208352660|gb|DC921394.1|DC921394
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|37838228|gb|BJ596236.1|BJ596236
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|18340613|gb|BJ172641.1|BJ172641
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|18338965|gb|BJ170991.1|BJ170991
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|162226196|gb|FC401656.1|FC401656
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|162205686|gb|FC380770.1|FC380770
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|162163084|gb|FC338474.1|FC338474
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|162169197|gb|FC345164.1|FC345164
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|18336588|gb|BJ168610.1|BJ168610
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|162205220|gb|FC380902.1|FC380902
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|162158625|gb|FC335525.1|FC335525
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|162157456|gb|FC333519.1|FC333519
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|162162496|gb|FC339214.1|FC339214
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
EST: gi|162233877|gb|FC409727.1|FC409727
EST:     AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAG                         GGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG
genomic: AGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTG

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: 32 (upstream exon), 35 (downstream exon)
Score: 15

GTAAGTGCTTGCAATGAGAGAGCTGTATTAGAACAATTAGAGCAGTACTTTGAGAAGCGCTTGGCAGGATACAAATCATCCCATGCAACGGAGgtgagaatta ... tgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTGTGTATTGAAAAGAGCATATTAAGAAATGCTTTGGCTGCAGTGCAGGAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtctattagatttaatgtaaggactttaagtggtgcttttgcttgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTGTGTATTGAAAAGAGCATATTAAGAAATGCTTTGGCTGCAGTGCAGGAGC
                                     cttttgctt  CT-rich tract
     tattagatttaatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaattatgtgccaattcaatcattgtgtgattgcaaagtcgtgaatgagaacatagattatataatttcaatttagggacgatactgtcaattccactatccacttgcagaatcacagtaacgaggccctgtctattagatttaatgtaaggactttaagtggtgcttttgcttgatgtacagGGTGGTGATGCCAAGAAAAACGCAAAGAAAAGAGTAGCGGAGAAGTTGCTGTGTATTGAAAAGAGCATATTAAGAAATGCTTTGGCTGCAGTGCAGGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG