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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaactcaatttttcttgctacttatttattgaatagaaatcgtgtatgtttctttactggggtgtgcagcaaaactcttgaacacgttttaaaatagtattggactcatcatctccatcactgttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAGCTGCTCTCGGAGCCTTGGACTCCTGAAAGTGGTCTGGTCACTGCAGCAA

Basic information

species Physcomitrella patens
transcript PP1S186_65V6.1
intron # 11
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|208354168|gb|DC957402.1|DC957402
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|37839451|gb|BJ597459.1|BJ597459
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|162275892|gb|FC451453.1|FC451453
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|162174770|gb|FC352186.1|FC352186
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|37848211|gb|BJ606219.1|BJ606219
EST:     NGTGTTCAAANCCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|208374594|gb|DC948608.1|DC948608
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|162213167|gb|FC389052.1|FC389052
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|37849759|gb|BJ607767.1|BJ607767
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|37827281|gb|BJ585293.1|BJ585293
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|37843445|gb|BJ601453.1|BJ601453
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|162196324|gb|FC374367.1|FC374367
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|162171718|gb|FC348179.1|FC348179
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|37839002|gb|BJ597010.1|BJ597010
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|37847762|gb|BJ605770.1|BJ605770
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|162273456|gb|FC449905.1|FC449905
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|162188838|gb|FC364852.1|FC364852
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|162196325|gb|FC374368.1|FC374368
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACG
EST: gi|37851541|gb|BJ609549.1|BJ609549
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|37839692|gb|BJ597700.1|BJ597700
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|7648069|gb|AW739052.1|AW739052
EST:     AAGAAGTCCTCTCCTTATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: AAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|162197910|gb|FC373652.1|FC373652
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|162171719|gb|FC348180.1|FC348180
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|162174769|gb|FC352185.1|FC352185
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|37838529|gb|BJ596537.1|BJ596537
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|37848377|gb|BJ606385.1|BJ606385
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCNTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCANCGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|37846229|gb|BJ604237.1|BJ604237
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|37846846|gb|BJ604854.1|BJ604854
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|37835874|gb|BJ593886.1|BJ593886
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|37824618|gb|BJ582684.1|BJ582684
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|37844789|gb|BJ602797.1|BJ602797
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|18338675|gb|BJ170699.1|BJ170699
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|18341761|gb|BJ173796.1|BJ173796
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|162165355|gb|FC341974.1|FC341974
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|162246877|gb|FC422766.1|FC422766
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
EST: gi|37848517|gb|BJ606525.1|BJ606525
EST:     TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAG                         GTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG
genomic: TGTGTTCAAAACCAGAAGCATGCAAAGAAGTCCTCTCCTCATTAAACCAGgtaagcaact ... gttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaacacgttttaaaatagtattggactcatcatctccatcactgttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAGCTGCTCTCGGAGCCTTGGACTCCTGAAAGTGGTCTGGTCACTGCAGCAA
                                           ctgtttt  CT-rich tract
         ttttaaaatagtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaactcaatttttcttgctacttatttattgaatagaaatcgtgtatgtttctttactggggtgtgcagcaaaactcttgaacacgttttaaaatagtattggactcatcatctccatcactgttttggcagGTGGCCAAAAATGGAAAGCTGGAAAGGTTTGAGATTCCAACGAAGATAAAGCTGCTCTCGGAGCCTTGGACTCCTGAAAGTGGTCTGGTCACTGCAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG