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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatgcagagagtaactttatactcctctacattgaactgttggtgtcaggatttagatgccaccttgagttttcgtaacctatgtttctggttttgtagAATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAAGAAGTGATATCTGGAGCTTATGCAGTGCCGCCTTTGGCTAACTCGAAAG

Basic information

species Physcomitrella patens
transcript PP1S43_166V6.1
intron # 22
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|37852255|gb|BJ610263.1|BJ610263
EST:     AACCTTTAAAGGTCGAGGTTCGGCATTTCGACAAGCTTTTCAAAGCAGAG                         AATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAA
genomic: AACCTTTAAAGGTCGAGGTTCGGCATTTCGACAAGCTTTTCAAAGCAGAGgtatgcttct ... ggttttgtagAATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAA
EST: gi|162222919|gb|FC399381.1|FC399381
EST:     AACCTTTAAAGGTCGAGGTTCGGCATTTCGACAAGCTTTTCAAAGCAGAG                         AATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAA
genomic: AACCTTTAAAGGTCGAGGTTCGGCATTTCGACAAGCTTTTCAAAGCAGAGgtatgcttct ... ggttttgtagAATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAA
EST: gi|37842145|gb|BJ600153.1|BJ600153
EST:     AACCTTTAAAGGTCGAGGTTCGGCATTTCGACAAGCTTTTCAAAGCAGAG                         AATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAA
genomic: AACCTTTAAAGGTCGAGGTTCGGCATTTCGACAAGCTTTTCAAAGCAGAGgtatgcttct ... ggttttgtagAATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAA
EST: gi|37836849|gb|BJ594857.1|BJ594857
EST:     AACCTTTAAAGGTCGAGGTTCGGCATTTCGACAAGCTTTTCAAAGCAGAG                         AATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAA
genomic: AACCTTTAAAGGTCGAGGTTCGGCATTTCGACAAGCTTTTCAAAGCAGAGgtatgcttct ... ggttttgtagAATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAA
EST: gi|162184430|gb|FC359176.1|FC359176
EST:     AACCTTTAAAGGTCGAGGTTCGGCATTTCGACAAGCTTTTCAAAGCAGAG                         AATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAA
genomic: AACCTTTAAAGGTCGAGGTTCGGCATTTCGACAAGCTTTTCAAAGCAGAGgtatgcttct ... ggttttgtagAATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAA
EST: gi|162254784|gb|FC430761.1|FC430761
EST:     AACCTTTAAAGGTCGAGGTTCGGCATTTCGACAAGCTTTTCAAAGCAGAG                         AATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAA
genomic: AACCTTTAAAGGTCGAGGTTCGGCATTTCGACAAGCTTTTCAAAGCAGAGgtatgcttct ... ggttttgtagAATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAA
EST: gi|37828726|gb|BJ586738.1|BJ586738
EST:     AACCTTTAAAGGTCGAGGTTCGGCATTTCGACAAGCTTTTCAAAGCAGAG                         AATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAA
genomic: AACCTTTAAAGGTCGAGGTTCGGCATTTCGACAAGCTTTTCAAAGCAGAGgtatgcttct ... ggttttgtagAATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAA
EST: gi|162255906|gb|FC431982.1|FC431982
EST:     AACCTTTAAAGGTCGAGGTTCGGCATTTCGACAAGCTTTTCAAAGCAGAG                         AATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAA
genomic: AACCTTTAAAGGTCGAGGTTCGGCATTTCGACAAGCTTTTCAAAGCAGAGgtatgcttct ... ggttttgtagAATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAA
EST: gi|67697565|gb|BJ957798.1|BJ957798
EST:     AACCTTTAAAGGTCGAGGTTCGGCATTTCGACAAGCTTTTCAAAGCAGAG                         AATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAA
genomic: AACCTTTAAAGGTCGAGGTTCGGCATTTCGACAAGCTTTTCAAAGCAGAGgtatgcttct ... ggttttgtagAATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAA
EST: gi|37841870|gb|BJ599878.1|BJ599878
EST:     AACCTTTAAAGGTCGAGGTTCGGCATTTCGACAAGCTTTTCAAAGCAGAG                         AATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAA
genomic: AACCTTTAAAGGTCGAGGTTCGGCATTTCGACAAGCTTTTCAAAGCAGAGgtatgcttct ... ggttttgtagAATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAA
EST: gi|37851142|gb|BJ609150.1|BJ609150
EST:     AACCTTTAAAGGTCGAGGTTCGGCATTTCGACAAGCTTTTCAAAGCAGAG                         AATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAA
genomic: AACCTTTAAAGGTCGAGGTTCGGCATTTCGACAAGCTTTTCAAAGCAGAGgtatgcttct ... ggttttgtagAATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAA

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: 34 (upstream exon), 27 (downstream exon)
Score: 3

GGTGTTATTCACTGGGTGTCAGAGCCATCTCCTGGTGTTGAACCTTTAAAGGTCGAGGTTCGGCATTTCGACAAGCTTTTCAAAGCAGAGgtatgcttct ... ggttttgtagAATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAAGAAGTGATATCTGGAGCTTATGCAGTGCCGCCTTTGGCTAACTCGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcaggatttagatgccaccttgagttttcgtaacctatgtttctggttttgtagAATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAAGAAGTGATATCTGGAGCTTATGCAGTGCCGCCTTTGGCTAACTCGAAAG
                            tcgtaac  putative branch site (score: 3)
      atttagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatgcagagagtaactttatactcctctacattgaactgttggtgtcaggatttagatgccaccttgagttttcgtaacctatgtttctggttttgtagAATCCGAATGAACTTGAAGACTGGCTTGGTGATTTCAATACCAATTCCAAAGAAGTGATATCTGGAGCTTATGCAGTGCCGCCTTTGGCTAACTCGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT