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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGCATATATCCTTCACTACATCAAAAATTGGTTCCCTTCTTGATGTACAGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAGgtacgtttattgaagaattgtgttacctctctgtgctggacttcaacgtggcttcaactttagggtatcccttttaacacctggaggtcctttgcttgaa...

Basic information

species Physcomitrella patens
transcript PP1S63_105V6.1
intron # 2
splice site 5'
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|67571935|gb|BJ944759.1|BJ944759
EST:     AGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAG                         GACTTGAAATGCTTCGTTTTTTCGCTCATCGGTCTGCATTTCAAGATTAAG
genomic: AGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAGgtacgtttat ... tattttgcagGACTTGAAATGCTTCGTTTTTTCGCTCATCGGTCTGCATTTCAAGATTAAG
EST: gi|22132523|gb|BQ827211.1|BQ827211
EST:     AGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAG                         GACTTGAAATGCTTCGTTTTTTCGCTCATCGGTCTGCATTTCAAGATTAAG
genomic: AGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAGgtacgtttat ... tattttgcagGACTTGAAATGCTTCGTTTTTTCGCTCATCGGTCTGCATTTCAAGATTAAG
EST: gi|22492561|gb|BU052477.1|BU052477
EST:     AGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAG                         GACTTGAAATGCTTCGTTTTTTCGCTCATCGGTCTGCATTTCAAGATTAAG
genomic: AGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAGgtacgtttat ... tattttgcagGACTTGAAATGCTTCGTTTTTTCGCTCATCGGTCTGCATTTCAAGATTAAG
EST: gi|67695301|gb|BJ955534.1|BJ955534
EST:     AGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAG                         GACTTGAAATGCTTCGTTTTTTCGCTCATCGGTCTGCATTTCAAGATTAAG
genomic: AGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAGgtacgtttat ... tattttgcagGACTTGAAATGCTTCGTTTTTTCGCTCATCGGTCTGCATTTCAAGATTAAG
EST: gi|37823748|gb|BJ581814.1|BJ581814
EST:     AGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAG                         GACTTGAAATGCTTCGTTTTTTCGCTCATCGGTCTGCATTTCAAGATTAAG
genomic: AGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAGgtacgtttat ... tattttgcagGACTTGAAATGCTTCGTTTTTTCGCTCATCGGTCTGCATTTCAAGATTAAG
EST: gi|162212818|gb|FC388618.1|FC388618
EST:     AGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAG                         GACTTGAAATGCTTCGTTTTTTCGCTCATCGGTCTGCATTTCAAGATTAAG
genomic: AGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAGgtacgtttat ... tattttgcagGACTTGAAATGCTTCGTTTTTTCGCTCATCGGTCTGCATTTCAAGATTAAG
EST: gi|18368122|gb|BJ200207.1|BJ200207
EST:     AGAGCAGCANGGATCCTGANGGTCTTCGGATTTTTTACTATCTTGTCCAG                         GACTTGAAATGCTTCGTTTTTTCGCTCATCGGTCTGCATTTCAAGATTAAG
genomic: AGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAGgtacgtttat ... tattttgcagGACTTGAAATGCTTCGTTTTTTCGCTCATCGGTCTGCATTTCAAGATTAAG
EST: gi|162262151|gb|FC436880.1|FC436880
EST:     AGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAG                         GACTTGAAATGCTTCGTTTTTTCGCTCATCGGTCTGCATTTCAAGATTAAG
genomic: AGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAGgtacgtttat ... tattttgcagGACTTGAAATGCTTCGTTTTTTCGCTCATCGGTCTGCATTTCAAGATTAAG
EST: gi|7286363|gb|AW598904.1|AW598904
EST:     AGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAG                         GACTTGAAATGCTTCGTTTTTTCGCTCATCGGTCTGCATTTCAAGATTAAG
genomic: AGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAGgtacgtttat ... tattttgcagGACTTGAAATGCTTCGTTTTTTCGCTCATCGGTCTGCATTTCAAGATTAAG
EST: gi|162212817|gb|FC388617.1|FC388617
EST:     AGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAG                         GACTTGAAATGCTTCGTTTTTTCGCTCATCGGTCTGCATTTCAAGATTAAG
genomic: AGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAGgtacgtttat ... tattttgcagGACTTGAAATGCTTCGTTTTTTCGCTCATCGGTCTGCATTTCAAGATTAAG
EST: gi|18344548|gb|BJ176589.1|BJ176589
EST:     AGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAG                         GACTTGAAATGCTTCGTTTTTTCGCTCATCGGTCTGCATTTCAAGATTAAG
genomic: AGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAGgtacgtttat ... tattttgcagGACTTGAAATGCTTCGTTTTTTCGCTCATCGGTCTGCATTTCAAGATTAAG

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), 35 (downstream exon)
Score: 27

CGAGCATATATCCTTCACTACATCAAAAATTGGTTCCCTTCTTGATGTACAGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAGgtacgtttat ... tattttgcagGACTTGAAATGCTTCGTTTTTTCGCTCATCGGTCTGCATTTCAAGATTAAGCCTATCTAAGTTTTGCTCCCATGATTGTTATCAATGGTGGATGTCGGTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAGCATATATCCTTCACTACATCAAAAATTGGTTCCCTTCTTGATGTACAGAGCAGCAAGGATCCTGAAGGTCTTCGGATTTTTTACTATCTTGTCCAGgtacgtttattgaagaattgtgttacctctctgtgctggacttcaacgtggcttcaactttagggtatcccttttaacacctggaggtcctttgcttgaa

- - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG