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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTCGAAATCTACCTCTGCGCCTTCTGCTCGCTCGCCCGCCCGCTCGCCCTCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgcttcgtctccctctctctctttacgtccttcgattattttgtcttgcatttttgaagtggagttgtcgaacaatgtggtttcgcgctgaataa...

Basic information

species Physcomitrella patens
transcript PP1S21_362V6.1
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|162205567|gb|FC381834.1|FC381834
EST:     TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|162191903|gb|FC366908.1|FC366908
EST:     TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|162205553|gb|FC381833.1|FC381833
EST:     TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|162200856|gb|FC377051.1|FC377051
EST:     TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|18367866|gb|BJ199949.1|BJ199949
EST:     TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|37848412|gb|BJ606420.1|BJ606420
EST:     TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|18369526|gb|BJ201613.1|BJ201613
EST:     TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|67723437|gb|BJ973696.1|BJ973696
EST:     TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|162199653|gb|FC375892.1|FC375892
EST:     TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|162228654|gb|FC405474.1|FC405474
EST:     TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|37827391|gb|BJ585403.1|BJ585403
EST:     TTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|162250020|gb|FC427121.1|FC427121
EST:     TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|19776818|gb|BQ039116.1|BQ039116
EST:     TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|162233115|gb|FC408938.1|FC408938
EST:     TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|18331708|gb|BJ163719.1|BJ163719
EST:     TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|162191902|gb|FC366907.1|FC366907
EST:     TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|67709361|gb|BJ965177.1|BJ965177
EST:     TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|162248540|gb|FC425316.1|FC425316
EST:     TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|162265173|gb|FC441260.1|FC441260
EST:     TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|162252421|gb|FC427815.1|FC427815
EST:     TCTGGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGTTCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|162252422|gb|FC427816.1|FC427816
EST:     TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|162220650|gb|FC396862.1|FC396862
EST:     TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|37850839|gb|BJ608847.1|BJ608847
EST:     TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|18335239|gb|BJ167257.1|BJ167257
EST:     TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
EST: gi|18348022|gb|BJ180069.1|BJ180069
EST:     TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATG                         GATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG
genomic: TCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGG

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: 28 (upstream exon), 35 (downstream exon)
Score: 18

AGTCGAAATCTACCTCTGCGCCTTCTGCTCGCTCGCCCGCCCGCTCGCCCTCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgctt ... gatcgtgcagGATTCAGCAGTGAAGCTGGCTATTGTAATGAAGGTGATCGGACGCACTGGGTCCCGAGGGCAGGTGACGCAGGTGCGCGTTAAGTTCTTGGATGACCAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTCGAAATCTACCTCTGCGCCTTCTGCTCGCTCGCCCGCCCGCTCGCCCTCTCGTTGTTCGCTTGCTACTGCAGGCTTTCTCGCTACTTGGCCACAATGgtttgcgcttcgtctccctctctctctttacgtccttcgattattttgtcttgcatttttgaagtggagttgtcgaacaatgtggtttcgcgctgaataa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG