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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAAGCTGAAGGGCTATGTCAGAAAGGTGCAGTCATGGCCGACTCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGGgtaagtttgtccttgtgtttatgtatcgctaattgcatgtaccatattcttgttttaggtgcgtttacatgaggttttcattttctgcatagttaaaagttggcgttttccaaaatttggtgttgacag

Basic information

species Physcomitrella patens
transcript PP1S60_42V6.1
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|208392581|gb|DC933967.1|DC933967
EST:     TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGG                         ATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
genomic: TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGGgtaagtttgt ... gtgttgacagATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
EST: gi|100413646|gb|BY974920.1|BY974920
EST:     TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGG                         ATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
genomic: TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGGgtaagtttgt ... gtgttgacagATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
EST: gi|100448832|gb|CJ973131.1|CJ973131
EST:     TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGG                         ATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
genomic: TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGGgtaagtttgt ... gtgttgacagATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
EST: gi|100390427|gb|BY952835.1|BY952835
EST:     TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGG                         ATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
genomic: TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGGgtaagtttgt ... gtgttgacagATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
EST: gi|100438768|gb|BY961793.1|BY961793
EST:     TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGG                         ATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
genomic: TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGGgtaagtttgt ... gtgttgacagATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
EST: gi|100441852|gb|BY981075.1|BY981075
EST:     TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGG                         ATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
genomic: TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGGgtaagtttgt ... gtgttgacagATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
EST: gi|208383581|gb|DC903538.1|DC903538
EST:     TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGG                         ATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
genomic: TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGGgtaagtttgt ... gtgttgacagATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
EST: gi|100444602|gb|BY964300.1|BY964300
EST:     TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGTG                         ATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAG-AATTCTACA
genomic: TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGGgtaagtttgt ... gtgttgacagATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
EST: gi|162206537|gb|FC382906.1|FC382906
EST:     TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGG                         ATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
genomic: TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGGgtaagtttgt ... gtgttgacagATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
EST: gi|208379088|gb|DC911613.1|DC911613
EST:     TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGG                         ATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
genomic: TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGGgtaagtttgt ... gtgttgacagATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
EST: gi|208348401|gb|DC905573.1|DC905573
EST:     TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGG                         ATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
genomic: TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGGgtaagtttgt ... gtgttgacagATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
EST: gi|18375100|gb|BJ206678.1|BJ206678
EST:     TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGG                         ATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
genomic: TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGGgtaagtttgt ... gtgttgacagATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
EST: gi|18352971|gb|BJ185026.1|BJ185026
EST:     TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGG                         ATACCCAGCAGACGTGCGGGAAGTGATTCTA
genomic: TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGGgtaagtttgt ... gtgttgacagATACCCAGCAGACGTGCGGGAAGTGATTCTA
EST: gi|208381135|gb|DC903935.1|DC903935
EST:     TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGG                         ATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
genomic: TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGGgtaagtttgt ... gtgttgacagATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
EST: gi|162193509|gb|FC370412.1|FC370412
EST:     TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGG                         ATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
genomic: TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGGgtaagtttgt ... gtgttgacagATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
EST: gi|208353554|gb|DC929681.1|DC929681
EST:     TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGG                         ATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
genomic: TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGGgtaagtttgt ... gtgttgacagATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
EST: gi|100387723|gb|BY951723.1|BY951723
EST:     TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGG                         ATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
genomic: TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGGgtaagtttgt ... gtgttgacagATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
EST: gi|208352111|gb|DC901674.1|DC901674
EST:     TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGG                         ATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
genomic: TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGGgtaagtttgt ... gtgttgacagATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
EST: gi|100449406|gb|CJ973705.1|CJ973705
EST:     TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGG                         ATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA
genomic: TCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGGgtaagtttgt ... gtgttgacagATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACA

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: 35 (upstream exon), 30 (downstream exon)
Score: 15

CAAAGCTGAAGGGCTATGTCAGAAAGGTGCAGTCATGGCCGACTCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGGgtaagtttgt ... gtgttgacagATACCCAGCAGACGTGCGGGAAGTGATTCTAGGAGAGAAAGGAATTCTACAAACTCTTCGTCCGGGTGGAATT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAGCTGAAGGGCTATGTCAGAAAGGTGCAGTCATGGCCGACTCTCCAAGTGCTGTTGCTGAAAATAGCGATGTAGTCTTCATGATCGTGGGgtaagtttgtccttgtgtttatgtatcgctaattgcatgtaccatattcttgttttaggtgcgtttacatgaggttttcattttctgcatagttaaaagttggcgttttccaaaatttggtgttgacag

- - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT