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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttcttctgatgctcttcagtgtctacttcagtgaacaatcgtgtttatatcctagatctgcagcaattttattcatctatatgattgtgtgggagcagATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAG

Basic information

species Physcomitrella patens
transcript PP1S132_95V6.1
intron # 4
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|67718471|gb|BJ968730.1|BJ968730
EST:     CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAG                         ATCGAGGAACAAGGAGTACCCGCCCATTACAGGAATTTCTCAGTTCAACAA
genomic: CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAGgtgatttatg ... gtgggagcagATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
EST: gi|100356048|gb|BY946170.1|BY946170
EST:     CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAG                         ATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
genomic: CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAGgtgatttatg ... gtgggagcagATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
EST: gi|100380016|gb|BY968804.1|BY968804
EST:     CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAG                         ATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
genomic: CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAGgtgatttatg ... gtgggagcagATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
EST: gi|18351892|gb|BJ183944.1|BJ183944
EST:     CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAG                         ATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
genomic: CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAGgtgatttatg ... gtgggagcagATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
EST: gi|100446010|gb|CJ970309.1|CJ970309
EST:     CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAG                         ATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
genomic: CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAGgtgatttatg ... gtgggagcagATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
EST: gi|100390341|gb|BY952749.1|BY952749
EST:     CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAG                         ATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
genomic: CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAGgtgatttatg ... gtgggagcagATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
EST: gi|100448896|gb|CJ973195.1|CJ973195
EST:     CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAG                         ATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
genomic: CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAGgtgatttatg ... gtgggagcagATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
EST: gi|162267156|gb|FC443387.1|FC443387
EST:     CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAG                         ATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
genomic: CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAGgtgatttatg ... gtgggagcagATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
EST: gi|100417339|gb|BY957283.1|BY957283
EST:     CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAG                         ATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
genomic: CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAGgtgatttatg ... gtgggagcagATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
EST: gi|18365276|gb|BJ197350.1|BJ197350
EST:     CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAG                         ATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
genomic: CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAGgtgatttatg ... gtgggagcagATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
EST: gi|208344839|gb|DC912673.1|DC912673
EST:     CTTGTTCTCAATGTGGTACGGCGAGCANAACAACAGTTGGTTGCAGATAG                         ATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
genomic: CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAGgtgatttatg ... gtgggagcagATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
EST: gi|208397779|gb|DC912002.1|DC912002
EST:     CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAG                         ATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
genomic: CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAGgtgatttatg ... gtgggagcagATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
EST: gi|208352476|gb|DC910190.1|DC910190
EST:     CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAG                         ATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
genomic: CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAGgtgatttatg ... gtgggagcagATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
EST: gi|18361573|gb|BJ193639.1|BJ193639
EST:     CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAG                         ATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
genomic: CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAGgtgatttatg ... gtgggagcagATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
EST: gi|208384190|gb|DC911298.1|DC911298
EST:     CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAG                         ATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
genomic: CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAGgtgatttatg ... gtgggagcagATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
EST: gi|18371678|gb|BJ203280.1|BJ203280
EST:     CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAG                         ATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
genomic: CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAGgtgatttatg ... gtgggagcagATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
EST: gi|18332250|gb|BJ164263.1|BJ164263
EST:     CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAG                         ATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
genomic: CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAGgtgatttatg ... gtgggagcagATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
EST: gi|162263809|gb|FC438428.1|FC438428
EST:     CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAG                         ATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA
genomic: CTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAGgtgatttatg ... gtgggagcagATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAA

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: 31 (upstream exon), 33 (downstream exon)
Score: 24

GAAGGCAAACCACTTGTTCTCAATGTGGTACGGCGAGCAGAACAACAGTTGGTTGCAGATAGgtgatttatg ... gtgggagcagATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatatcctagatctgcagcaattttattcatctatatgattgtgtgggagcagATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAG
                     aattttattcatctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttcttctgatgctcttcagtgtctacttcagtgaacaatcgtgtttatatcctagatctgcagcaattttattcatctatatgattgtgtgggagcagATCGAGGAACAAGGAGTACCAGCCCATTACAGGAATTTCTCAGTTCAACAAACTTAGCGCAAAGCTTATTCTGGGCGCTAATAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG