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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACATTGTCTGTCCTGAAACTTTCTGAGAGGACAATTAAACCTCTCGCAGAGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgatcatacttctccgaaccctcccagtgtatctccatgattgcatatagaatagaatccatgaaaattccagtagaatttctctttcgctctc...

Basic information

species Physcomitrella patens
transcript PP1S4_75V6.1
intron # 2
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|67701024|gb|BJ961257.1|BJ961257
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|67572953|gb|BJ945777.1|BJ945777
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|162223589|gb|FC399713.1|FC399713
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|18351485|gb|BJ183537.1|BJ183537
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|18365447|gb|BJ197523.1|BJ197523
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|162228292|gb|FC404371.1|FC404371
EST:     GGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: GGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|162172794|gb|FC348383.1|FC348383
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|37845568|gb|BJ603576.1|BJ603576
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|15327270|gb|BI487856.1|BI487856
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|37839637|gb|BJ597645.1|BJ597645
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|162172793|gb|FC348382.1|FC348382
EST:     AGAATCCAGTTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|162249183|gb|FC421227.1|FC421227
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|67696335|gb|BJ956568.1|BJ956568
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|162209382|gb|FC385497.1|FC385497
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|162209383|gb|FC385498.1|FC385498
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|162235543|gb|FC411340.1|FC411340
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|37830831|gb|BJ588843.1|BJ588843
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|162235544|gb|FC411341.1|FC411341
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|162271170|gb|FC447159.1|FC447159
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|162223590|gb|FC399714.1|FC399714
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|162228293|gb|FC404372.1|FC404372
EST:     GGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: GGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|37852014|gb|BJ610022.1|BJ610022
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|162259933|gb|FC435236.1|FC435236
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|18362341|gb|BJ194411.1|BJ194411
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|162210449|gb|FC386537.1|FC386537
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|19778834|gb|BQ039368.1|BQ039368
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|162228470|gb|FC404120.1|FC404120
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|162258992|gb|FC435935.1|FC435935
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGGGAAGGCTTTATTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|67578157|gb|BJ950324.1|BJ950324
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|162259934|gb|FC435237.1|FC435237
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|67698062|gb|BJ958295.1|BJ958295
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|100444457|gb|BY964155.1|BY964155
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|162271171|gb|FC447160.1|FC447160
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|162245153|gb|FC421601.1|FC421601
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|162213088|gb|FC389512.1|FC389512
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|162258993|gb|FC435936.1|FC435936
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
EST: gi|67574646|gb|BJ947470.1|BJ947470
EST:     AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAG                         GTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG
genomic: AGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAG

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: 46

GACATTGTCTGTCCTGAAACTTTCTGAGAGGACAATTAAACCTCTCGCAGAGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgat ... atttgaacagGTTGTAGGTTGGAGGCTTGTGAATCTGGGCTCAAGCGAAGCAGGGCTTAAGCTCCAGTGCGATTGGCTTTTGAAAGATGCGGTTTCCGTGACTGAATTGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACATTGTCTGTCCTGAAACTTTCTGAGAGGACAATTAAACCTCTCGCAGAGAATACAGCTCCCATGACTGAGGGTGAGGCGAAGGCTTTACTCCGCAAGgtagtttgatcatacttctccgaaccctcccagtgtatctccatgattgcatatagaatagaatccatgaaaattccagtagaatttctctttcgctctc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC