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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataatttcttttgttgatgctttcttttgcttgtactctacatgattatgtatgaaggctttgctggtacatgatgcaagtgaattttttttgaagt...

Basic information

species Physcomitrella patens
transcript PP1S9_103V6.1
intron # 4
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|208373828|gb|DC936599.1|DC936599
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|100436155|gb|BY979407.1|BY979407
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|100387442|gb|BY988313.1|BY988313
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|100379638|gb|BY949869.1|BY949869
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|100395304|gb|BY953670.1|BY953670
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGANAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|67712940|gb|BJ966389.1|BJ966389
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|100438224|gb|BY961716.1|BY961716
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|208369720|gb|DC932618.1|DC932618
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGAAAAGCTCAACCTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|208390018|gb|DC938073.1|DC938073
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|208376441|gb|DC932309.1|DC932309
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|208354269|gb|DC902483.1|DC902483
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAGCCAG                         GTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|208386847|gb|DC941565.1|DC941565
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|100365282|gb|BY966901.1|BY966901
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|100450378|gb|CJ974233.1|CJ974233
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGC
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGC
EST: gi|100379592|gb|BY949846.1|BY949846
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|67704790|gb|BJ965023.1|BJ965023
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|67719429|gb|BJ969688.1|BJ969688
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|208364000|gb|DC939593.1|DC939593
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|208393623|gb|DC904339.1|DC904339
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|100376654|gb|BY949400.1|BY949400
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGANAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|100385264|gb|BY950856.1|BY950856
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGANAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|100394556|gb|BY989846.1|BY989846
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|100444730|gb|BY982559.1|BY982559
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|100369353|gb|BY948059.1|BY948059
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGANAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|100356151|gb|BY946222.1|BY946222
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTGTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|67508667|gb|BJ941528.1|BJ941528
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAG                         GTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT
EST: gi|100363621|gb|BY966478.1|BY966478
EST:     AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAGA-CCGGTGAACCAG                         GTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGACATT
genomic: AGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATT

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: 19

GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataattt ... ttggattcagGTGTTTTTGTGTGAAAAGCTCAACTTAATCAACGAGATGTATTTTGCCATTGCTTTAGATCGAGCTAGTGCGGGGCCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAAATGCTTGGACAGGTCCTGGTGACTAAGCAGACTGGAGCAGAGGGAAAACCGGTGAACCAGgtgataatttcttttgttgatgctttcttttgcttgtactctacatgattatgtatgaaggctttgctggtacatgatgcaagtgaattttttttgaagt

- - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - -  GAGCAG