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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcgaggtttttctgccgcttttacgtcatttagatccctcgaagattttctgagcatgtttgaattggtgatcgaacttccttttctgcttgtaacgcagACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGCGACTGGGAGCACAAACTTTTGGATCGAAGGCAGCGACAGGTCTCTTCCG

Basic information

species Physcomitrella patens
transcript PP1S78_29V6.1
intron # 1
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|37822090|gb|BJ580156.1|BJ580156
EST:     GTGCAAAAGTGTGAGCGGAGGGAGCAGTTGCTGAGGAGATGTCCTGGCAG                         ACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC
genomic: GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAGgtcagattcg ... tgtaacgcagACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC
EST: gi|18355456|gb|BJ187515.1|BJ187515
EST:     TGCAAAAGTGTGAGCGGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAG                         ACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC
genomic: TGCAAAAGTGTGAGCGG-ACGGAGCAGTTGCTGAGGAGATGTCCTGGCAGgtcagattcg ... tgtaacgcagACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC
EST: gi|208368014|gb|DC955407.1|DC955407
EST:     GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAG                         ACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGCGATGCGGC
genomic: GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAGgtcagattcg ... tgtaacgcagACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC
EST: gi|100414188|gb|BY992654.1|BY992654
EST:     GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAG                         ACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC
genomic: GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAGgtcagattcg ... tgtaacgcagACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC
EST: gi|18342945|gb|BJ174981.1|BJ174981
EST:     GTGCAAAAGTGTGAGCGGAGGGAGCAGTTGCTGAGGAGATGTCCTGGCAG                         ACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC
genomic: GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAGgtcagattcg ... tgtaacgcagACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC
EST: gi|162239315|gb|FC415401.1|FC415401
EST:     GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAG                         ACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC
genomic: GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAGgtcagattcg ... tgtaacgcagACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC
EST: gi|67692911|gb|BJ953144.1|BJ953144
EST:     GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAG                         ACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC
genomic: GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAGgtcagattcg ... tgtaacgcagACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC
EST: gi|67576820|gb|BJ949644.1|BJ949644
EST:     GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAG                         ACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC
genomic: GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAGgtcagattcg ... tgtaacgcagACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC
EST: gi|67698870|gb|BJ959103.1|BJ959103
EST:     GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAG                         ACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC
genomic: GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAGgtcagattcg ... tgtaacgcagACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC
EST: gi|208392731|gb|DC942413.1|DC942413
EST:     GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAG                         ACCTGTTGAAGTTGTGAAATCTGAAACTGANTATACGGAAGGCGATGCGGC
genomic: GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAGgtcagattcg ... tgtaacgcagACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC
EST: gi|100410993|gb|BY956276.1|BY956276
EST:     GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAG                         ACCTGTTTGA-GTTGTGAAATCTGAAACTGAGTATACG
genomic: GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAGgtcagattcg ... tgtaacgcagACCTGTT-GAAGTTGTGAAATCTGAAACTGAGTATACG
EST: gi|67569644|gb|BJ942468.1|BJ942468
EST:     GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAG                         ACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC
genomic: GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAGgtcagattcg ... tgtaacgcagACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC
EST: gi|162239314|gb|FC415400.1|FC415400
EST:     GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAG                         ACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC
genomic: GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAGgtcagattcg ... tgtaacgcagACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC
EST: gi|37832401|gb|BJ590413.1|BJ590413
EST:     GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAG                         ACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC
genomic: GTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAGgtcagattcg ... tgtaacgcagACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGC

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), 33 (downstream exon)
Score: 8

TTAGGAAGTACAAGTGTTTCTTGGAAGGGAATGATTCTTCAGGGAATGCAGTGCAAAAGTGTGAGCGGACGGAGCAGTTGCTGAGGAGATGTCCTGGCAGgtcagattcg ... tgtaacgcagACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGCGACTGGGAGCACAAACTTTTGGATCGAAGGCAGCGACAGGTCTCTTCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttctgagcatgtttgaattggtgatcgaacttccttttctgcttgtaacgcagACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGCGACTGGGAGCACAAACTTTTGGATCGAAGGCAGCGACAGGTCTCTTCCG
                                            ttgtaac  putative branch site (score: 8)
                               cttccttttctgcttg  CT-rich tract
             tttgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcgaggtttttctgccgcttttacgtcatttagatccctcgaagattttctgagcatgtttgaattggtgatcgaacttccttttctgcttgtaacgcagACCTGTTGAAGTTGTGAAATCTGAAACTGAGTATACGGAAGGTGATGCGGCGACTGGGAGCACAAACTTTTGGATCGAAGGCAGCGACAGGTCTCTTCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA