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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actggcttatttacggttcaatatgttcgaaatacccttttaaaaagacgttttgaaaaaccttgattttaagctgatttattgattacttgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGATGTGTTGCAGCCTGGCACTGCAATGCTTGCTGCTGGCTATTGTATGTATG

Basic information

species Physcomitrella patens
transcript PP1S1_300V6.1
intron # 5
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|18325673|gb|BJ157670.1|BJ157670
EST:     ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|100391045|gb|BY953055.1|BY953055
EST:     ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|100404176|gb|BY955293.1|BY955293
EST:     ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|100396704|gb|BY953785.1|BY953785
EST:     ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|100445852|gb|CJ970151.1|CJ970151
EST:     ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|208373427|gb|DC931872.1|DC931872
EST:     ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|208393616|gb|DC904332.1|DC904332
EST:     ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|162278601|gb|FC454999.1|FC454999
EST:     ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|100372971|gb|BY949374.1|BY949374
EST:     ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|100352928|gb|BY945520.1|BY945520
EST:     ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|208391526|gb|DC937674.1|DC937674
EST:     ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|208352123|gb|DC906268.1|DC906268
EST:     ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|208378504|gb|DC927201.1|DC927201
EST:     ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|208396143|gb|DC924609.1|DC924609
EST:     TCTTCCAACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: TCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|208348185|gb|DC920976.1|DC920976
EST:     CACTTGATGGTTC-TCCCACATCGACTGCGGAGTTTNTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: CACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|208384630|gb|DC907103.1|DC907103
EST:     ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|162152140|gb|FC328730.1|FC328730
EST:     ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|100353087|gb|BY945599.1|BY945599
EST:     ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|208394809|gb|DC920152.1|DC920152
EST:     ATCCAC-TGATGG-TTTTCCCACATCGACTGCGGAGTTTCTA-TNGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|208380958|gb|DC903870.1|DC903870
EST:     ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|208352801|gb|DC917765.1|DC917765
EST:     ATCCACNTGATGGATCTTCC-ACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|208385201|gb|DC923581.1|DC923581
EST:     TCCACTTGATNGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: TCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|208352520|gb|DC918229.1|DC918229
EST:     TCCACTTGATGG-TTTTCCAACATTCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: TCCACTTGATGGATCTTCCAACA-TCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|208350215|gb|DC901599.1|DC901599
EST:     ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCANGCACTGTTGAGGAT
genomic: ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|208398545|gb|DC916516.1|DC916516
EST:     TCCACTTGATGG-TTTTNCC-ACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: TCCACTTGATGGATCTT-CCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|208376930|gb|DC910792.1|DC910792
EST:     ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|208358947|gb|DC946376.1|DC946376
EST:     ACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATTTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: ACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|208378151|gb|DC902624.1|DC902624
EST:     ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|162193916|gb|FC371729.1|FC371729
EST:     ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACG                         ATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: ATCCACTTGATGGATCTTCCAACATCGACTGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
EST: gi|208349119|gb|DC925902.1|DC925902
EST:     TGCGGAGTTTCTA-TNGAACG                         A-TTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT
genomic: TGCGGAGTTTCTATTGGAACGgtaaagcgca ... tgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agacgttttgaaaaaccttgattttaagctgatttattgattacttgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGATGTGTTGCAGCCTGGCACTGCAATGCTTGCTGCTGGCTATTGTATGTATG
                                  tattgat  putative branch site (score: 3)
                               atttattgattactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actggcttatttacggttcaatatgttcgaaatacccttttaaaaagacgttttgaaaaaccttgattttaagctgatttattgattacttgggtctcagATTTTTGGAATCTATATGCTCAAGGAAGGAGCATCAGGCACTGTTGAGGATGTGTTGCAGCCTGGCACTGCAATGCTTGCTGCTGGCTATTGTATGTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT