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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGAACCGATGCTTGGAGAGTCTTCAAGAAAACGTTAACCGGCTGAACACCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctctttacgatattacagacagtctcgtcctcttgtcggacattctcttatcatcactaaatttgaacctacttgatgcgttaaactgttacgt...

Basic information

species Physcomitrella patens
transcript PP1S47_277V6.1
intron # 4
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|18349800|gb|BJ181850.1|BJ181850
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|208380153|gb|DC927432.1|DC927432
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|67698997|gb|BJ959230.1|BJ959230
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|208396407|gb|DC920073.1|DC920073
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|162258306|gb|FC434233.1|FC434233
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|162192959|gb|FC371942.1|FC371942
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCC
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCC
EST: gi|100374751|gb|BY949051.1|BY949051
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|7046907|gb|AW476744.1|AW476744
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|37834559|gb|BJ592571.1|BJ592571
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|37845862|gb|BJ603870.1|BJ603870
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|162228814|gb|FC404685.1|FC404685
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATTTGCGGAGGAATTGTTTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|67717319|gb|BJ967578.1|BJ967578
EST:     CCTGCAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|22133342|gb|BQ827686.1|BQ827686
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|208352405|gb|DC906188.1|DC906188
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|37851577|gb|BJ609585.1|BJ609585
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|162228815|gb|FC404686.1|FC404686
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|208349966|gb|DC913674.1|DC913674
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|162237413|gb|FC412716.1|FC412716
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATTTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|67572247|gb|BJ945071.1|BJ945071
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|18358961|gb|BJ191021.1|BJ191021
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|162237414|gb|FC412717.1|FC412717
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|37850492|gb|BJ608500.1|BJ608500
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|37850237|gb|BJ608245.1|BJ608245
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAGGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|18371408|gb|BJ203010.1|BJ203010
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|18368948|gb|BJ201033.1|BJ201033
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAGGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|67575451|gb|BJ948275.1|BJ948275
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|208387241|gb|DC945540.1|DC945540
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|37828765|gb|BJ586777.1|BJ586777
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|67725836|gb|BJ976095.1|BJ976095
EST:     CCTGCAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|67721490|gb|BJ971749.1|BJ971749
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|18361266|gb|BJ193331.1|BJ193331
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|67698918|gb|BJ959151.1|BJ959151
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
EST: gi|67695614|gb|BJ955847.1|BJ955847
EST:     CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAG                         GCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT
genomic: CCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGT

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: 22 (upstream exon), 34 (downstream exon)
Score: 5

CAAGAACCGATGCTTGGAGAGTCTTCAAGAAAACGTTAACCGGCTGAACACCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctct ... ttgtgctcagGCTGGAGATGCATCTGCGGAGGAATTGTCTAGCGTCACCCAAGCCACTGGTGAATTTTTGCCAATTGTGAAACCAAGGCCATCAGCCGAGATTGTGTCCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGAACCGATGCTTGGAGAGTCTTCAAGAAAACGTTAACCGGCTGAACACCTACAGAGCGAAGCTGGTGGTTTTCCCTAGACTATCAAAGAAGACGAAGgtatgtctctttacgatattacagacagtctcgtcctcttgtcggacattctcttatcatcactaaatttgaacctacttgatgcgttaaactgttacgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG