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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTCGGTGTCGCTGGCTCTCGACATCACTGTGTCCACTCTCACTCTAAACGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAAgtaagggattagtgattactctcttgctttgggtcaattgttgaactgcactcctgtgtcgtaccccctgtttcaactattggggattgagtaaccttttcctgattttgcacctccag

Basic information

species Physcomitrella patens
transcript PP1S215_25V6.1
intron # 1
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|208376363|gb|DC932273.1|DC932273
EST:     CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAA                         ATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
genomic: CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAAgtaagggatt ... gcacctccagATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
EST: gi|18356615|gb|BJ188674.1|BJ188674
EST:     CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAA                         ATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
genomic: CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAAgtaagggatt ... gcacctccagATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
EST: gi|208345629|gb|DC909299.1|DC909299
EST:     CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAA                         ATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
genomic: CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAAgtaagggatt ... gcacctccagATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
EST: gi|162259779|gb|FC436759.1|FC436759
EST:     CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAA                         ATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
genomic: CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAAgtaagggatt ... gcacctccagATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
EST: gi|18343486|gb|BJ175524.1|BJ175524
EST:     CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAA                         ATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
genomic: CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAAgtaagggatt ... gcacctccagATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
EST: gi|18357148|gb|BJ189207.1|BJ189207
EST:     CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAA                         ATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
genomic: CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAAgtaagggatt ... gcacctccagATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
EST: gi|208371667|gb|DC932496.1|DC932496
EST:     CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAA                         ATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
genomic: CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAAgtaagggatt ... gcacctccagATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
EST: gi|162221749|gb|FC397081.1|FC397081
EST:     CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAA                         ATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
genomic: CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAAgtaagggatt ... gcacctccagATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
EST: gi|67578005|gb|BJ950172.1|BJ950172
EST:     CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAA                         ATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
genomic: CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAAgtaagggatt ... gcacctccagATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
EST: gi|22492644|gb|BU052567.1|BU052567
EST:     CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAA                         ATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
genomic: CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAAgtaagggatt ... gcacctccagATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
EST: gi|67570549|gb|BJ943373.1|BJ943373
EST:     CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAA                         ATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
genomic: CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAAgtaagggatt ... gcacctccagATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
EST: gi|208354986|gb|DC914250.1|DC914250
EST:     CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAA                         ATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
genomic: CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAAgtaagggatt ... gcacctccagATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
EST: gi|208382460|gb|DC927994.1|DC927994
EST:     CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAA                         ATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
genomic: CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAAgtaagggatt ... gcacctccagATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
EST: gi|18350245|gb|BJ182296.1|BJ182296
EST:     CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAA                         ATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
genomic: CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAAgtaagggatt ... gcacctccagATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
EST: gi|18332428|gb|BJ164441.1|BJ164441
EST:     CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAA                         ATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA
genomic: CGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAAgtaagggatt ... gcacctccagATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCA

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: 15 (upstream exon), 21 (downstream exon)
Score: 1

ATCTCGGTGTCGCTGGCTCTCGACATCACTGTGTCCACTCTCACTCTAAACGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAAgtaagggatt ... gcacctccagATTCTCTTCCGAGGAGGTGACGGGGCAGAATCAAGTGAAGGCCTCGGTGCAGAGGAAAATCCGGCAAAACATCGCCGATGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTCGGTGTCGCTGGCTCTCGACATCACTGTGTCCACTCTCACTCTAAACGATTTTGTTGGGAGAATTGTGTAGAGTTACAATCCACCATGTTCAAGAAgtaagggattagtgattactctcttgctttgggtcaattgttgaactgcactcctgtgtcgtaccccctgtttcaactattggggattgagtaaccttttcctgattttgcacctccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA