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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgaagtagtccgagtccccaatacatttcatcatattttacaattgttaagcaaaatactgctgtaagatatgttcacgtgcattagtatgcccgcagGATTTGATGGCAAACCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAGAG

Basic information

species Physcomitrella patens
transcript PP1S94_106V6.1
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|67693514|gb|BJ953747.1|BJ953747
EST:     TCGAAACTNAAGGTCGCGCTATCATTTGTGTAGCTGAGGGTGCCGGCCAG                         GATTTGATGGCAAACCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTC
genomic: TCGAAACTAAAGGTCGCGCTATCATTTGTGTAGCTGAGGGTGCCGGCCAGgttagttgtt ... atgcccgcagGATTTGATGGCAAACCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTC
EST: gi|162203811|gb|FC379908.1|FC379908
EST:     AAACTAAAGGTCGCGCTATCATTTGTGTAGCTGAGGGTGCCGGCCAG                         GATTTGATGGCAAACCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTC
genomic: AAACTAAAGGTCGCGCTATCATTTGTGTAGCTGAGGGTGCCGGCCAGgttagttgtt ... atgcccgcagGATTTGATGGCAAACCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTC
EST: gi|162203812|gb|FC379909.1|FC379909
EST:     TCGAAACTAAAGGTCGCGCTATCATTTGTGTAGCTGAGGGTGCCGGCCAG                         GATTTGATGGCAAACCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTC
genomic: TCGAAACTAAAGGTCGCGCTATCATTTGTGTAGCTGAGGGTGCCGGCCAGgttagttgtt ... atgcccgcagGATTTGATGGCAAACCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTC
EST: gi|37852524|gb|BJ610532.1|BJ610532
EST:     TCGAAACTAAAGGTCGCGCTATCATTTGTGTAGCTGAGGGTGCCGGCCAG                         GATTTGATGGCAAACCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTC
genomic: TCGAAACTAAAGGTCGCGCTATCATTTGTGTAGCTGAGGGTGCCGGCCAGgttagttgtt ... atgcccgcagGATTTGATGGCAAACCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTC
EST: gi|7648346|gb|AW739329.1|AW739329
EST:     TCGAAACTAAAGGTCGCGCTATCATTTGTGTAGCTGAGGGTGCCGGCCAG                         GATTTGATGGCAAACCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTC
genomic: TCGAAACTAAAGGTCGCGCTATCATTTGTGTAGCTGAGGGTGCCGGCCAGgttagttgtt ... atgcccgcagGATTTGATGGCAAACCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTC
EST: gi|162229043|gb|FC404753.1|FC404753
EST:     TAAAAGTCGCGCTATCATTTGTGTAGCTGAGGGTGCCGGCCAG                         GATTTGATGGCAAACCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTC
genomic: TAAAGGTCGCGCTATCATTTGTGTAGCTGAGGGTGCCGGCCAGgttagttgtt ... atgcccgcagGATTTGATGGCAAACCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTC
EST: gi|37850516|gb|BJ608524.1|BJ608524
EST:     GGTCGCGCTATCATTTGTGTAGCTGAGGGTGCCGGCCAG                         GATTTGATGGCAAACNTATCAAATAGCACTGATGCCTCTGGAAACCCAGTC
genomic: GGTCGCGCTATCATTTGTGTAGCTGAGGGTGCCGGCCAGgttagttgtt ... atgcccgcagGATTTGATGGCAAACCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTC
EST: gi|7648257|gb|AW739240.1|AW739240
EST:     TCGAAACTAAAGGTCGCGCTATCATTTGTGTAGCTGAAGGTGCCGGCCAG                         GATTTGATGGCAAACCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTC
genomic: TCGAAACTAAAGGTCGCGCTATCATTTGTGTAGCTGAGGGTGCCGGCCAGgttagttgtt ... atgcccgcagGATTTGATGGCAAACCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTC
EST: gi|100428968|gb|BY959524.1|BY959524
EST:     TCGAAACTAAAGGTCGCGCTATCATTTGTGTAGCTGAGGGTGCCGGCCAG                         GATTTGATGGCAA-CCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTC
genomic: TCGAAACTAAAGGTCGCGCTATCATTTGTGTAGCTGAGGGTGCCGGCCAGgttagttgtt ... atgcccgcagGATTTGATGGCAAACCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTC
EST: gi|162229044|gb|FC404754.1|FC404754
EST:     TCGAAACTAAAGGTCGCGCTATCATTTGTGTAGCTGAGGGTGCCGGCCAG                         GATTTGATGGCAAACCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTC
genomic: TCGAAACTAAAGGTCGCGCTATCATTTGTGTAGCTGAGGGTGCCGGCCAGgttagttgtt ... atgcccgcagGATTTGATGGCAAACCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTC

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), 34 (downstream exon)
Score: 12

ATTTACTGTGGACGGACCAGAGGGAATGTTGCAGCACGTTCAATATTTACTCGAAACTAAAGGTCGCGCTATCATTTGTGTAGCTGAGGGTGCCGGCCAGgttagttgtt ... atgcccgcagGATTTGATGGCAAACCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttaagcaaaatactgctgtaagatatgttcacgtgcattagtatgcccgcagGATTTGATGGCAAACCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAGAG
         aaaatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgaagtagtccgagtccccaatacatttcatcatattttacaattgttaagcaaaatactgctgtaagatatgttcacgtgcattagtatgcccgcagGATTTGATGGCAAACCTATCAAATAGCACTGATGCCTCTGGAAACCCAGTCCTGGGAGACATAGGCGTTCACCTTACAAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacgtgc