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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagagaatcacgggcctaataaattcatgcctttactattgtttcctgttgacatatgttgatgttaagagattgacgttttcctgttcaccttgttcagCAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTTGACGCTGCCGTACAGACCTCAAAGAACACGCTCGATCTGCGAGGAAAGC

Basic information

species Physcomitrella patens
transcript PP1S98_33V6.1
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|162159888|gb|FC336141.1|FC336141
EST:     CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAG                         CAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
genomic: CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAGgttggtaact ... ccttgttcagCAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
EST: gi|162156939|gb|FC333093.1|FC333093
EST:     CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAG                         CAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
genomic: CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAGgttggtaact ... ccttgttcagCAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
EST: gi|162242044|gb|FC414451.1|FC414451
EST:     CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAG                         CAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
genomic: CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAGgttggtaact ... ccttgttcagCAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
EST: gi|67573035|gb|BJ945859.1|BJ945859
EST:     AGGACTCCTACAGAGAATAAAATG-A-                         -AGCCTGCCAGAATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTT
genomic: AGGACTCCTACAGAGAATAAAATGAAGgttggtaact ... ccttgttcagCAGCCTGCCAG-ATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTT
EST: gi|67696416|gb|BJ956649.1|BJ956649
EST:     GATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATG-A-                         -AGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
genomic: GATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAGgttggtaact ... ccttgttcagCAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
EST: gi|162230336|gb|FC406900.1|FC406900
EST:     CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAG                         CAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
genomic: CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAGgttggtaact ... ccttgttcagCAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
EST: gi|162178131|gb|FC354849.1|FC354849
EST:     CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAG                         CAGCCTGCCAGATCAAGCAAGGGTGAGGCAGAACCAGAGGAGATCAAGTTG
genomic: CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAGgttggtaact ... ccttgttcagCAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
EST: gi|6102498|gb|AW126968.1|AW126968
EST:     CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAG                         CAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
genomic: CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAGgttggtaact ... ccttgttcagCAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
EST: gi|162242004|gb|FC414450.1|FC414450
EST:     CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAG                         CAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
genomic: CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAGgttggtaact ... ccttgttcagCAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
EST: gi|162165746|gb|FC340901.1|FC340901
EST:     CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAG                         CAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
genomic: CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAGgttggtaact ... ccttgttcagCAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
EST: gi|162178132|gb|FC354850.1|FC354850
EST:     CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAG                         CAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
genomic: CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAGgttggtaact ... ccttgttcagCAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
EST: gi|162165747|gb|FC340902.1|FC340902
EST:     CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAG                         CAGCCTGCCAGATCAAGCAAGGCTGAGGC
genomic: CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAGgttggtaact ... ccttgttcagCAGCCTGCCAGATCAAGCAAGGCTGAGGC
EST: gi|162271068|gb|FC446095.1|FC446095
EST:     CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAG                         CAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
genomic: CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAGgttggtaact ... ccttgttcagCAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
EST: gi|162175934|gb|FC351612.1|FC351612
EST:     CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAG                         CAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
genomic: CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAGgttggtaact ... ccttgttcagCAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
EST: gi|162175935|gb|FC351613.1|FC351613
EST:     CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAG                         CAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT
genomic: CAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAGgttggtaact ... ccttgttcagCAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTT

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), 35 (downstream exon)
Score: 17

GGGCACCATGAAGATGAGAGTTAAATTGAATGAAATTCTTTCAAGAGTAGCAAGATCGGCAAAAGGAGGTGCAAGGACTCCTACAGAGAATAAAATGAAGgttggtaact ... ccttgttcagCAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTTGACGCTGCCGTACAGACCTCAAAGAACACGCTCGATCTGCGAGGAAAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttgacatatgttgatgttaagagattgacgttttcctgttcaccttgttcagCAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTTGACGCTGCCGTACAGACCTCAAAGAACACGCTCGATCTGCGAGGAAAGC
                         gattgac  putative branch site (score: 17)
                                 ttttcctgttcacctt  CT-rich tract
        atatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagagaatcacgggcctaataaattcatgcctttactattgtttcctgttgacatatgttgatgttaagagattgacgttttcctgttcaccttgttcagCAGCCTGCCAGATCAAGCAAGGCTGAGGCAGAACCAGAGGAGATCAAGTTTGACGCTGCCGTACAGACCTCAAAGAACACGCTCGATCTGCGAGGAAAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC