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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATGgtatatgaacacttatctcttcatttctattttattcttttcacttaataagttattttgattttaaagctgaagagaagtattttacttgtctattatgctgagacttgtgattaaaatccaaccgtcaattgagccgtgtagccatctctctcacccattaaattttgtacttgcag

Basic information

species Physcomitrella patens
transcript PP1S22_40V6.2
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S22_40V6.2 (Physcomitrella patens), 5'ss of exon 19
lower sequence: AT3G55610.1 (Arabidopsis thaliana), 5'ss of exon 19
GTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATGgtatatgaacacttatctcttcatttctattttattcttttcacttaataagttattttgattttaaagctgaagagaagtattttacttgtctattatgctgagacttgtgattaaaatccaaccgtcaattgagccgtgtagccatctctctcacccattaaattttgtacttgcag
||||||||||||||| ||||||||||||| ||||| || || ||||| |||||  |  | || || ||||||||     ||| ||   |  |    | | |||   ||| ||| | || |    |  ||||  |  |||||||   ||      ||||  ||  | |  || |||                                                                           
GTGGGAATAAGCACAAGCAGGATTCATGCCCGTGGTCCAGTTGGAGTTGAAGGATTATTGACAACAAGATGgtact---acaattgagttat----tttgtttctctctcttc-catagttcactgatttg--tcaaaagctgtgaag------tttaaatggttgtggtgatgaatgacag--------------------------------------------------------------------
















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|162197988|gb|FC373691.1|FC373691
EST:     ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG                         GTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
genomic: ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATGgtatatgaac ... gtacttgcagGTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
EST: gi|37835735|gb|BJ593747.1|BJ593747
EST:     ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG                         GTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
genomic: ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATGgtatatgaac ... gtacttgcagGTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
EST: gi|37829388|gb|BJ587400.1|BJ587400
EST:     ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG                         GTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
genomic: ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATGgtatatgaac ... gtacttgcagGTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
EST: gi|162154554|gb|FC330764.1|FC330764
EST:     ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG                         GTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
genomic: ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATGgtatatgaac ... gtacttgcagGTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
EST: gi|208396875|gb|DC920443.1|DC920443
EST:     ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG                         GTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
genomic: ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATGgtatatgaac ... gtacttgcagGTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
EST: gi|162167111|gb|FC343587.1|FC343587
EST:     ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG                         GTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
genomic: ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATGgtatatgaac ... gtacttgcagGTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
EST: gi|162154553|gb|FC330763.1|FC330763
EST:     ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG                         GTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
genomic: ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATGgtatatgaac ... gtacttgcagGTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
EST: gi|37839335|gb|BJ597343.1|BJ597343
EST:     ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG                         GTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
genomic: ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATGgtatatgaac ... gtacttgcagGTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
EST: gi|162167110|gb|FC343586.1|FC343586
EST:     ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG                         GTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
genomic: ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATGgtatatgaac ... gtacttgcagGTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
EST: gi|162276247|gb|FC452601.1|FC452601
EST:     ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG                         GTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
genomic: ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATGgtatatgaac ... gtacttgcagGTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
EST: gi|37821498|gb|BJ579564.1|BJ579564
EST:     ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG                         GTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
genomic: ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATGgtatatgaac ... gtacttgcagGTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
EST: gi|162197987|gb|FC373690.1|FC373690
EST:     ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG                         GTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
genomic: ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATGgtatatgaac ... gtacttgcagGTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
EST: gi|162191466|gb|FC367170.1|FC367170
EST:     ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG                         GTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
genomic: ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATGgtatatgaac ... gtacttgcagGTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
EST: gi|162159355|gb|FC335156.1|FC335156
EST:     AACTACCAGATG                         GTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
genomic: AACTACCAGATGgtatatgaac ... gtacttgcagGTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
EST: gi|162153152|gb|FC329558.1|FC329558
EST:     ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG                         GTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
genomic: ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATGgtatatgaac ... gtacttgcagGTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
EST: gi|162235435|gb|FC411570.1|FC411570
EST:     ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG                         GTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
genomic: ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATGgtatatgaac ... gtacttgcagGTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
EST: gi|162210538|gb|FC386834.1|FC386834
EST:     ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG                         GTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
genomic: ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATGgtatatgaac ... gtacttgcagGTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
EST: gi|162167790|gb|FC344520.1|FC344520
EST:     ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG                         GTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
genomic: ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATGgtatatgaac ... gtacttgcagGTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
EST: gi|18338412|gb|BJ170436.1|BJ170436
EST:     ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG                         GTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
genomic: ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATGgtatatgaac ... gtacttgcagGTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
EST: gi|162164179|gb|FC339602.1|FC339602
EST:     ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATG                         GTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA
genomic: ATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATGgtatatgaac ... gtacttgcagGTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATA

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: 32 (upstream exon), 35 (downstream exon)
Score: 20

GTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATGgtatatgaac ... gtacttgcagGTTGCTCAGAGGTAGTGGTCAGCTTGTTAATGGAGATAAGGGGGTGCAATATACACACAAAAAACTTCCAATTGGTGAAGATGAAGGTTTGGCAGCACTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGGAATAAGCACAGGCAGGATTCATGCACGTGGGCCTGTAGGAGTCGAAGGTCTTCTAACTACCAGATGgtatatgaacacttatctcttcatttctattttattcttttcacttaataagttattttgattttaaagctgaagagaagtattttacttgtctattatgctgagacttgtgattaaaatccaaccgtcaattgagccgtgtagccatctctctcacccattaaattttgtacttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG