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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtacctctcaaccttccctccttttttttacttcgttgttgctcaaggtggtcccttacactctgataaatcctgagtaatgaaagtaccctgatcttctctcgtccattgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAGAGTACAATGCCTGTTCAATGAGCACCGGCAAGAAGTATCTATCCGGAGG

Basic information

species Physcomitrella patens
transcript PP1S4_171V6.2
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|208348692|gb|DC926367.1|DC926367
EST:     CGGCAGGGGACAACNTAG                         TATTTTCATACACTCCTNGTGCACATGATGTGCAAGTNGTAAGTGCGACAG
genomic: CGGCAGGGGACAACCTAGgtaagtacct ... attgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
EST: gi|67725866|gb|BJ976125.1|BJ976125
EST:     AGGAGACGTTCACGGCAGGGGACAACCTAG                         TATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
genomic: AGGAGACGTTCACGGCAGGGGACAACCTAGgtaagtacct ... attgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
EST: gi|208354559|gb|DC934135.1|DC934135
EST:     CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAG                         TATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
genomic: CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAGgtaagtacct ... attgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
EST: gi|162218077|gb|FC394134.1|FC394134
EST:     GGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAG                         TATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
genomic: GGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAGgtaagtacct ... attgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
EST: gi|67573232|gb|BJ946056.1|BJ946056
EST:     CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAG                         TATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
genomic: CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAGgtaagtacct ... attgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
EST: gi|100403651|gb|BY955033.1|BY955033
EST:     CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAG                         TATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
genomic: CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAGgtaagtacct ... attgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
EST: gi|162261800|gb|FC437089.1|FC437089
EST:     CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAG                         TATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
genomic: CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAGgtaagtacct ... attgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
EST: gi|162160996|gb|FC337514.1|FC337514
EST:     CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAG                         TATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
genomic: CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAGgtaagtacct ... attgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
EST: gi|100362946|gb|BY947608.1|BY947608
EST:     CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAG                         TATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
genomic: CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAGgtaagtacct ... attgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
EST: gi|208383223|gb|DC928237.1|DC928237
EST:     NTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAG                         TATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
genomic: CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAGgtaagtacct ... attgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
EST: gi|100442813|gb|BY981638.1|BY981638
EST:     CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAG                         TATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
genomic: CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAGgtaagtacct ... attgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
EST: gi|208373400|gb|DC956490.1|DC956490
EST:     TACGACACTTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAG                         TATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
genomic: TACGACAC-TTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAGgtaagtacct ... attgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
EST: gi|67696616|gb|BJ956849.1|BJ956849
EST:     GGGACAACCTAG                         TATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
genomic: GGGACAACCTAGgtaagtacct ... attgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
EST: gi|162218078|gb|FC394135.1|FC394135
EST:     CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAG                         TATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
genomic: CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAGgtaagtacct ... attgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
EST: gi|208381407|gb|DC927843.1|DC927843
EST:     CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAG                         TATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
genomic: CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAGgtaagtacct ... attgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
EST: gi|208354174|gb|DC957408.1|DC957408
EST:     NTACGACACTTGGGCATCGGAGGAGACGTTCACGGCAGGGGACAACCTAG                         TATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
genomic: CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAGgtaagtacct ... attgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
EST: gi|208361698|gb|DC954132.1|DC954132
EST:     CATCGNAGGAGACGNTCACGGCANGGGACAACCTAG                         TATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
genomic: CATCGAAGGAGACGTTCACGGCAGGGGACAACCTAGgtaagtacct ... attgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
EST: gi|100421774|gb|BY993637.1|BY993637
EST:     CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAG                         TATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
genomic: CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAGgtaagtacct ... attgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
EST: gi|162219363|gb|FC396399.1|FC396399
EST:     CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAG                         TATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
genomic: CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAGgtaagtacct ... attgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
EST: gi|67717349|gb|BJ967608.1|BJ967608
EST:     CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAG                         TATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
genomic: CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAGgtaagtacct ... attgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
EST: gi|208392119|gb|DC957240.1|DC957240
EST:     NTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAG                         TATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
genomic: CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAGgtaagtacct ... attgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
EST: gi|100420537|gb|BY976068.1|BY976068
EST:     CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAG                         TATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
genomic: CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAGgtaagtacct ... attgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
EST: gi|100380102|gb|BY968848.1|BY968848
EST:     CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGNGACAACCTAG                         TATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG
genomic: CTACGACACTTGGGCATCGAAGGAGACGTTCACGGCAGGGGACAACCTAGgtaagtacct ... attgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgataaatcctgagtaatgaaagtaccctgatcttctctcgtccattgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAGAGTACAATGCCTGTTCAATGAGCACCGGCAAGAAGTATCTATCCGGAGG
                          ccctgat  putative branch site (score: 4)
                                tcttctctcgtccatt  CT-rich tract
               taatgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtacctctcaaccttccctccttttttttacttcgttgttgctcaaggtggtcccttacactctgataaatcctgagtaatgaaagtaccctgatcttctctcgtccattgtcgcagTATTCTCATACACTCCTGGTGCACATGATGTGCAAGTCGTAAGTGCGACAGAGTACAATGCCTGTTCAATGAGCACCGGCAAGAAGTATCTATCCGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT