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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcttccctgagatttgagctacttttcacttttgcgaatctttttaaaaaatgtggtgtaacattttcattcgttttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGCCCCAACTACTTGAAGGGTCTGGCAAACATGCGGGCTCTAAGTGAAGAGA

Basic information

species Physcomitrella patens
transcript PP1S63_54V6.2
intron # 12
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|208365149|gb|DC946778.1|DC946778
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|18339126|gb|BJ171152.1|BJ171152
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|162235867|gb|FC412418.1|FC412418
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|18336575|gb|BJ168597.1|BJ168597
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|208364467|gb|DC958036.1|DC958036
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|37846736|gb|BJ604744.1|BJ604744
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|22492495|gb|BU052418.1|BU052418
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|37849163|gb|BJ607171.1|BJ607171
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|37841322|gb|BJ599330.1|BJ599330
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|7648273|gb|AW739256.1|AW739256
EST:     GCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: GCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|67697641|gb|BJ957874.1|BJ957874
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|22132424|gb|BQ827155.1|BQ827155
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|208385420|gb|DC956632.1|DC956632
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|37845681|gb|BJ603689.1|BJ603689
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
EST: gi|162162206|gb|FC337988.1|FC337988
EST:     CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAG                         CAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC
genomic: CTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGC

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), 28 (downstream exon)
Score: 14

TGATGGCCGCAAGAGAGCTTTGGTTGTCGGTGGAGGCATTGCTAACTTCACTGATGTTGCAGCAACTTTCAACGGCATCATTCGAGCCATGCGTGAAAAGgtaagcttcc ... ttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGCCCCAACTACTTGAAGGGTCTGGCAAACATGCGGGCTCTAAGTGAAGAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcgaatctttttaaaaaatgtggtgtaacattttcattcgttttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGCCCCAACTACTTGAAGGGTCTGGCAAACATGCGGGCTCTAAGTGAAGAGA
                         gtgtaac  putative branch site (score: 14)
                                 ttttcattcgttttct  CT-rich tract
      aatctttttaaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcttccctgagatttgagctacttttcacttttgcgaatctttttaaaaaatgtggtgtaacattttcattcgttttctgttcagCAATCTCATTTAAAAGCAGCAAGGGTGAACATTTTCGTGCGGAGAGGAGGCCCCAACTACTTGAAGGGTCTGGCAAACATGCGGGCTCTAAGTGAAGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA