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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgtttagcactgtgaaaagctaatacgcctacaagatgtcttgttccttatcatttaagcatctacgctgatgtctgtatggcttcactctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCGCGTGGGCGTCACGATCCGTGTGTTGTCCCACGAG

Basic information

species Physcomitrella patens
transcript PP1S28_168V6.1
intron # 9
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|37822320|gb|BJ580386.1|BJ580386
EST:     GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACG                         CAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
genomic: GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
EST: gi|162156721|gb|FC333564.1|FC333564
EST:     GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACG                         CAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
genomic: GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
EST: gi|162191761|gb|FC367494.1|FC367494
EST:     GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACG                         CAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
genomic: GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
EST: gi|162156720|gb|FC333563.1|FC333563
EST:     GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACG                         CAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
genomic: GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
EST: gi|162150109|gb|FC326822.1|FC326822
EST:     GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACG                         CAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
genomic: GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
EST: gi|37821326|gb|BJ579392.1|BJ579392
EST:     GGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCCACG                         CAAAAGCAGAAAACTGTCACCCGGCGACAAGCCAGGAGACAGAGCTGCGG
genomic: GGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCAT-CACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCC-GCGACAAG-CAGGAGACAGAGCTGCGG
EST: gi|208346067|gb|DC921312.1|DC921312
EST:     GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACG                         CAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
genomic: GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
EST: gi|37826196|gb|BJ584208.1|BJ584208
EST:     GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACG                         CAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
genomic: GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
EST: gi|67695924|gb|BJ956157.1|BJ956157
EST:     GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACG                         CAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
genomic: GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
EST: gi|162194736|gb|FC371583.1|FC371583
EST:     ATTCAAGCCCACTTCTACCATCACG                         CAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
genomic: ATTCAAGCCCACTTCTACCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
EST: gi|37850822|gb|BJ608830.1|BJ608830
EST:     GGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTNTACCATCCACG                         CAAAAGCAGAAAACTGTCACCCGGCGACAAGCCAGGAGACAGAGCTGCGG
genomic: GGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCAT-CACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCC-GCGACAAG-CAGGAGACAGAGCTGCGG
EST: gi|208368432|gb|DC947875.1|DC947875
EST:     GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACG                         CAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
genomic: GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
EST: gi|162241958|gb|FC415769.1|FC415769
EST:     GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACG                         CAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
genomic: GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
EST: gi|162189600|gb|FC365822.1|FC365822
EST:     GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACG                         CAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
genomic: GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
EST: gi|162191762|gb|FC367495.1|FC367495
EST:     GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACG                         CAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
genomic: GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
EST: gi|37843534|gb|BJ601542.1|BJ601542
EST:     GGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCCATCCCG                         CAAAAGCAGAAAACTGTCACCCGNCGACAAGCCGGAGACAGAGCTGCGGG
genomic: GGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTA-CCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCG-CGACAAGCAGGAGACAGAGCTGCGGG
EST: gi|162152500|gb|FC328778.1|FC328778
EST:     GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACG                         CAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
genomic: GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
EST: gi|162241957|gb|FC415768.1|FC415768
EST:     GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACG                         CAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
genomic: GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
EST: gi|37823580|gb|BJ581646.1|BJ581646
EST:     GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACG                         CAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
genomic: GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
EST: gi|162159688|gb|FC336074.1|FC336074
EST:     TTCTTCCATCACG                         CAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
genomic: TTCTACCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
EST: gi|37826731|gb|BJ584743.1|BJ584743
EST:     GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACG                         CAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
genomic: GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
EST: gi|67699184|gb|BJ959417.1|BJ959417
EST:     GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACG                         CAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
genomic: GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
EST: gi|37825235|gb|BJ583301.1|BJ583301
EST:     GGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCCACG                         CAAAAGCAGAAAACTGTCACCCGGCGACAAGCCAGGAGACAGAGCTGCGG
genomic: GGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCAT-CACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCC-GCGACAAG-CAGGAGACAGAGCTGCGG
EST: gi|162150110|gb|FC326823.1|FC326823
EST:     GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACG                         CAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
genomic: GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
EST: gi|162194737|gb|FC371584.1|FC371584
EST:     ATTCAAGCCCACTTCTACCATCACG                         CAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
genomic: ATTCAAGCCCACTTCTACCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
EST: gi|208374737|gb|DC948681.1|DC948681
EST:     GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACG                         CAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG
genomic: GGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCG

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: 34 (upstream exon), 34 (downstream exon)
Score: 6

GCGAACTCGCACCAACAGATCTGGAGGAGTTCAAGGGGGGATCTCCAACGGGGAGATGATAGTGCTTCGGATTGCATTCAAGCCCACTTCTACCATCACGgtatgtcact ... tctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCGCGTGGGCGTCACGATCCGTGTGTTGTCCCACGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccttatcatttaagcatctacgctgatgtctgtatggcttcactctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCGCGTGGGCGTCACGATCCGTGTGTTGTCCCACGAG
                      cgctgat  putative branch site (score: 6)
                                       cttcactctc  putative PPT
     tatcatttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgtttagcactgtgaaaagctaatacgcctacaagatgtcttgttccttatcatttaagcatctacgctgatgtctgtatggcttcactctcatgcagCAAAAGCAGAAAACTGTCACCCGCGACAAGCAGGAGACAGAGCTGCGGGCGCGTGGGCGTCACGATCCGTGTGTTGTCCCACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC