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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgtatttgcttgatgctgactggcgcacaagtgctaatggttggtatgtgtagtacttctcaatgctatgaaataaccctcttattatgtacaacgcagATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACTGCAACTGAAAGAACACTGTGCTGCATTCTTGAGAACTACCAAACACCAG

Basic information

species Physcomitrella patens
transcript PP1S142_120V6.1
intron # 6
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|208396648|gb|DC929027.1|DC929027
EST:     GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAA                         ATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
genomic: GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAAgtgagttcta ... tacaacgcagATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
EST: gi|162204299|gb|FC380487.1|FC380487
EST:     GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAA                         ATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
genomic: GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAAgtgagttcta ... tacaacgcagATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
EST: gi|67724461|gb|BJ974720.1|BJ974720
EST:     GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAA                         ATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
genomic: GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAAgtgagttcta ... tacaacgcagATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
EST: gi|37842186|gb|BJ600194.1|BJ600194
EST:     GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAA                         ATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
genomic: GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAAgtgagttcta ... tacaacgcagATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
EST: gi|208353284|gb|DC926167.1|DC926167
EST:     GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAA                         ATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
genomic: GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAAgtgagttcta ... tacaacgcagATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
EST: gi|15728767|gb|BI740962.1|BI740962
EST:     GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAA                         ATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
genomic: GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAAgtgagttcta ... tacaacgcagATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
EST: gi|67697454|gb|BJ957687.1|BJ957687
EST:     GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAA                         ATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
genomic: GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAAgtgagttcta ... tacaacgcagATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
EST: gi|7584284|gb|AW700180.1|AW700180
EST:     GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAA                         ATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
genomic: GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAAgtgagttcta ... tacaacgcagATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
EST: gi|162204300|gb|FC380488.1|FC380488
EST:     GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAA                         ATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
genomic: GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAAgtgagttcta ... tacaacgcagATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
EST: gi|37839193|gb|BJ597201.1|BJ597201
EST:     GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAA                         ATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
genomic: GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAAgtgagttcta ... tacaacgcagATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
EST: gi|15728849|gb|BI741008.1|BI741008
EST:     GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAA                         ATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
genomic: GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAAgtgagttcta ... tacaacgcagATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
EST: gi|162243432|gb|FC425128.1|FC425128
EST:     GAAATTCGCTACGGCCAAAAGAAA                         ATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
genomic: GAAATTCGCTACGGCCAAAAGAAAgtgagttcta ... tacaacgcagATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
EST: gi|208368352|gb|DC955535.1|DC955535
EST:     GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAA                         ATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
genomic: GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAAgtgagttcta ... tacaacgcagATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
EST: gi|37838367|gb|BJ596375.1|BJ596375
EST:     GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAA                         ATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
genomic: GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAAgtgagttcta ... tacaacgcagATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
EST: gi|67725840|gb|BJ976099.1|BJ976099
EST:     GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAA                         ATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT
genomic: GTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAAgtgagttcta ... tacaacgcagATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACT

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: 33 (upstream exon), 35 (downstream exon)
Score: 13

ATGGTTTCCAGCTTCCAAGACGTTTCGTGAGCTTGTGTCGTGCTCAAATTGTACAGATTTCCAATCAAGGAATCTCGAAATTCGCTACGGCCAAAAGAAAgtgagttcta ... tacaacgcagATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACTGCAACTGAAAGAACACTGTGCTGCATTCTTGAGAACTACCAAACACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtgtagtacttctcaatgctatgaaataaccctcttattatgtacaacgcagATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACTGCAACTGAAAGAACACTGTGCTGCATTCTTGAGAACTACCAAACACCAG
                          aaataac  putative branch site (score: 13)
                      tatgaaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtatttgcttgatgctgactggcgcacaagtgctaatggttggtatgtgtagtacttctcaatgctatgaaataaccctcttattatgtacaacgcagATGAATGATCAAGTCAAGAACTATTGTCATCTGCTTAACTCCACTCTCACTGCAACTGAAAGAACACTGTGCTGCATTCTTGAGAACTACCAAACACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC