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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAGgtcagttctgagcttgactattcctccacttcttgtattgagatccagttttgcgaaccccttgtaatgaggatatcagttggtcatttccaaactcttt...

Basic information

species Physcomitrella patens
transcript PP1S100_23V6.1
intron # 12
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|37840302|gb|BJ598310.1|BJ598310
EST:     AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAG                         AATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG
genomic: AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAGgtcagttctg ... atggatgcagAATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG
EST: gi|208373324|gb|DC944967.1|DC944967
EST:     AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAG                         AATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG
genomic: AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAGgtcagttctg ... atggatgcagAATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG
EST: gi|162159099|gb|FC334270.1|FC334270
EST:     AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAG                         AATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG
genomic: AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAGgtcagttctg ... atggatgcagAATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG
EST: gi|208372810|gb|DC956211.1|DC956211
EST:     AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAG                         AATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG
genomic: AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAGgtcagttctg ... atggatgcagAATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG
EST: gi|67698955|gb|BJ959188.1|BJ959188
EST:     AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAG                         AATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG
genomic: AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAGgtcagttctg ... atggatgcagAATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG
EST: gi|37837357|gb|BJ595365.1|BJ595365
EST:     AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAG                         AATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG
genomic: AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAGgtcagttctg ... atggatgcagAATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG
EST: gi|18335062|gb|BJ167080.1|BJ167080
EST:     AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAG                         AATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG
genomic: AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAGgtcagttctg ... atggatgcagAATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG
EST: gi|162225721|gb|FC401863.1|FC401863
EST:     AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAG                         AATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG
genomic: AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAGgtcagttctg ... atggatgcagAATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG
EST: gi|37847853|gb|BJ605861.1|BJ605861
EST:     AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAG                         AATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG
genomic: AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAGgtcagttctg ... atggatgcagAATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG
EST: gi|208371608|gb|DC952250.1|DC952250
EST:     AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAG                         AATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG
genomic: AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAGgtcagttctg ... atggatgcagAATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG
EST: gi|162159100|gb|FC334271.1|FC334271
EST:     AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAG                         AATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG
genomic: AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAGgtcagttctg ... atggatgcagAATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG
EST: gi|37852235|gb|BJ610243.1|BJ610243
EST:     AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAG                         AATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG
genomic: AGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAGgtcagttctg ... atggatgcagAATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAG

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-Seq library.


Block sizes: 35 (upstream exon), 14 (downstream exon)
Score: 3

AGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAGgtcagttctg ... atggatgcagAATCTGGATCTGAGCGTGGACCTAAGCGCAGCAAGCGCTGCCGAGGAGTAGTGATGGATGTTACAAATTTAGGTGTTTTCTCCCAGTAGACCATGAGAGT





























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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTACGATCCAACAACTCACTTCGAGACGACAGTGCAAGATGTACTTTCAATGTATACCAAAATCACTGGAAAGgtcagttctgagcttgactattcctccacttcttgtattgagatccagttttgcgaaccccttgtaatgaggatatcagttggtcatttccaaactcttt

- - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - -  AAGATG