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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gataaatcccttgtcaacaagaagaaaaagattgctttagatgtttggtaaattttattctttatcatgagtatgaatttcgtggtgttgcaaagtgcagCCCGACATGAACTTGCCCTTGGTAATACCTATGTCTCTAAGAACGGAGTAGCTCCGCCCAAGTCCGAGGTTGACCCAAAG

Basic information

species Physcomitrella patens
transcript PP1S9_51V6.2
intron # 2
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|18360845|gb|BJ192908.1|BJ192908
EST:     TGAAGAGTACCTACTACAAGATGCACCGACACTCAAGAATTTCTGGGCAG                         CCCGACATGAACTTGCCCTTGGTAATACCTATGTCTCTAAGAA
genomic: TGAAGAGTACCTACTACAAGATGCACCGACACTCAAGAATTTCTGGGCAGgtcagttata ... caaagtgcagCCCGACATGAACTTGCCCTTGGTAATACCTATGTCTCTAAGAA
EST: gi|100378952|gb|BY986500.1|BY986500
EST:     TGAAGAGTACCTACTACAAGATGCACCGACACTCAAGAATTTCTGGGCAG                         CCCGACATGAACTTGCCCTTGGTAATACCTATGTCTCTAAGAACGGAGTAG
genomic: TGAAGAGTACCTACTACAAGATGCACCGACACTCAAGAATTTCTGGGCAGgtcagttata ... caaagtgcagCCCGACATGAACTTGCCCTTGGTAATACCTATGTCTCTAAGAACGGAGTAG
EST: gi|100353188|gb|BY945650.1|BY945650
EST:     TGAAGAGTACCTACTACAAGATGCACCGACACTCAAGAATTTCTGGGCAG                         CCCGACATGAACTTGCCCTTGGTAATACCTATGTCTCTAAGAACGGAGTAG
genomic: TGAAGAGTACCTACTACAAGATGCACCGACACTCAAGAATTTCTGGGCAGgtcagttata ... caaagtgcagCCCGACATGAACTTGCCCTTGGTAATACCTATGTCTCTAAGAACGGAGTAG
EST: gi|162227522|gb|FC403464.1|FC403464
EST:     TGAAGAGTACCTACTACAAGATGCACCGACACTCAAGAATTTCTGGGCAG                         CCCGACATGAACTTGCCCTTGGTAATACCTATGTCTCT
genomic: TGAAGAGTACCTACTACAAGATGCACCGACACTCAAGAATTTCTGGGCAGgtcagttata ... caaagtgcagCCCGACATGAACTTGCCCTTGGTAATACCTATGTCTCT
EST: gi|100402906|gb|BY973411.1|BY973411
EST:     TGAAGAGTACCTACTACAAGATGCACCGACACTCAAGAATTTCTGGGCAG                         CCCGACATGAACTTGCCCTTGGTAATACCTATGTCTCTAAGAACGGAGTAG
genomic: TGAAGAGTACCTACTACAAGATGCACCGACACTCAAGAATTTCTGGGCAGgtcagttata ... caaagtgcagCCCGACATGAACTTGCCCTTGGTAATACCTATGTCTCTAAGAACGGAGTAG
EST: gi|100374390|gb|BY985771.1|BY985771
EST:     TGAAGAGTACCTACTACAAGATGCACCGACACTCAAGAATTTCTGGGCAG                         CCCGACATGAACTTGCCCTTGGTAATACCTATGTCTCTAAGAACGGAGTAG
genomic: TGAAGAGTACCTACTACAAGATGCACCGACACTCAAGAATTTCTGGGCAGgtcagttata ... caaagtgcagCCCGACATGAACTTGCCCTTGGTAATACCTATGTCTCTAAGAACGGAGTAG

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), 33 (downstream exon)
Score: 8

TTCGACCCCTCATCTACACCATCAGGTGCTGCACAAGTTATGGGTGCTGATGAAGAGTACCTACTACAAGATGCACCGACACTCAAGAATTTCTGGGCAGgtcagttata ... caaagtgcagCCCGACATGAACTTGCCCTTGGTAATACCTATGTCTCTAAGAACGGAGTAGCTCCGCCCAAGTCCGAGGTTGACCCAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtaaattttattctttatcatgagtatgaatttcgtggtgttgcaaagtgcagCCCGACATGAACTTGCCCTTGGTAATACCTATGTCTCTAAGAACGGAGTAGCTCCGCCCAAGTCCGAGGTTGACCCAAAG
     aattttattctttatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gataaatcccttgtcaacaagaagaaaaagattgctttagatgtttggtaaattttattctttatcatgagtatgaatttcgtggtgttgcaaagtgcagCCCGACATGAACTTGCCCTTGGTAATACCTATGTCTCTAAGAACGGAGTAGCTCCGCCCAAGTCCGAGGTTGACCCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC