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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctgccgacacttcacacgcttgctcactacacttgagacactgtcagaatgagataaaatctgcctggtgcaggcagtatgctgaaggcacccttttgtttctagaaacaaacaaggcatgtgggatttcacaataacggggtgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGCGACTGCAGCTTCGCTAGGGACAAGATGGTACAGCATGCCCTGACTGGGG

Basic information

species Physcomitrella patens
transcript PP1S424_22V6.2
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|208351125|gb|DC926017.1|DC926017
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|162278876|gb|FC454927.1|FC454927
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|208382870|gb|DC928295.1|DC928295
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|208381395|gb|DC927831.1|DC927831
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|162236682|gb|FC413777.1|FC413777
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|162259659|gb|FC436704.1|FC436704
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|162270768|gb|FC446381.1|FC446381
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|208397629|gb|DC912247.1|DC912247
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|162260192|gb|FC436327.1|FC436327
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|162263103|gb|FC440081.1|FC440081
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|162265463|gb|FC440789.1|FC440789
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|162263104|gb|FC440082.1|FC440082
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|162278875|gb|FC454926.1|FC454926
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|162273701|gb|FC449424.1|FC449424
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|162264249|gb|FC441351.1|FC441351
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|100389283|gb|BY971033.1|BY971033
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|162272167|gb|FC448676.1|FC448676
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|162275819|gb|FC451380.1|FC451380
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAAGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|162264248|gb|FC441350.1|FC441350
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|162265542|gb|FC441557.1|FC441557
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|100411270|gb|BY974553.1|BY974553
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|162265762|gb|FC443168.1|FC443168
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|162273702|gb|FC449425.1|FC449425
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|67568787|gb|BJ941611.1|BJ941611
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|162273976|gb|FC450115.1|FC450115
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|162263098|gb|FC440076.1|FC440076
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|162273757|gb|FC449480.1|FC449480
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|18333294|gb|BJ165308.1|BJ165308
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|162260191|gb|FC436326.1|FC436326
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|162236681|gb|FC413776.1|FC413776
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|67691982|gb|BJ952215.1|BJ952215
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|208353927|gb|DC914081.1|DC914081
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|18334976|gb|BJ166994.1|BJ166994
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
EST: gi|162265462|gb|FC440788.1|FC440788
EST:     ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGG                         AAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC
genomic: ACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGC

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: 35 (upstream exon), 35 (downstream exon)
Score: 164

GAGCGGTAGCTGGAGTATACGCCGGGGTCGAATACTCGTTGGAGAAGGCGCGTTCAAAACAGGACTGGgtaagctgcc ... tgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGCGACTGCAGCTTCGCTAGGGACAAGATGGTACAGCATGCCCTGACTGGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttctagaaacaaacaaggcatgtgggatttcacaataacggggtgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGCGACTGCAGCTTCGCTAGGGACAAGATGGTACAGCATGCCCTGACTGGGG
                                  caataac  putative branch site (score: 164)
        aaacaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctgccgacacttcacacgcttgctcactacacttgagacactgtcagaatgagataaaatctgcctggtgcaggcagtatgctgaaggcacccttttgtttctagaaacaaacaaggcatgtgggatttcacaataacggggtgatgtgcagAAAAATGCCGCCATTGGAGGAGCGGTGACGGGAGCCCTGCTGTCGGTGAGCGACTGCAGCTTCGCTAGGGACAAGATGGTACAGCATGCCCTGACTGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG