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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTAAAGGCGATCGTGGTGTTGGGGAAGTTTTGAAGGTATAGGTGTGGCGTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgttgtttgtattgaattgtggttgatgacttcccaagcaatgcatgcgtcgtcgcttcagttgtagcatttttcgtttcggaacgccctcct...

Basic information

species Physcomitrella patens
transcript PP1S209_114V6.1
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|162262384|gb|FC437711.1|FC437711
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCT-G                         --GAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tgttctctagCAGAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
EST: gi|162246361|gb|FC422419.1|FC422419
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCT-G                         --GAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tgttctctagCAGAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
EST: gi|162225361|gb|FC401165.1|FC401165
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCT-G                         --GAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tgttctctagCAGAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
EST: gi|162264864|gb|FC440639.1|FC440639
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCT-G                         --GAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tgttctctagCAGAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
EST: gi|162215670|gb|FC391710.1|FC391710
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCT-G                         --GAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tgttctctagCAGAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
EST: gi|162216854|gb|FC393036.1|FC393036
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCT-G                         --GAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tgttctctagCAGAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
EST: gi|162270438|gb|FC447554.1|FC447554
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCT-G                         --GAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tgttctctagCAGAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
EST: gi|162246388|gb|FC422420.1|FC422420
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCT-G                         --GAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tgttctctagCAGAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
EST: gi|162238593|gb|FC418163.1|FC418163
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCT-G                         --GAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tgttctctagCAGAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
EST: gi|162238594|gb|FC418164.1|FC418164
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCT-G                         --GAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tgttctctagCAGAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
EST: gi|67575443|gb|BJ948267.1|BJ948267
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCT-G                         --GAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tgttctctagCAGAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
EST: gi|162233638|gb|FC409397.1|FC409397
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCT-G                         --GAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tgttctctagCAGAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
EST: gi|67698910|gb|BJ959143.1|BJ959143
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCT-G                         --GAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tgttctctagCAGAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
EST: gi|162200692|gb|FC377875.1|FC377875
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCT-G                         --GAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tgttctctagCAGAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
EST: gi|162200693|gb|FC377876.1|FC377876
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCT-G                         --GAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tgttctctagCAGAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
EST: gi|100416767|gb|BY993077.1|BY993077
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCT-G                         --GAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tgttctctagCAGAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
EST: gi|6102504|gb|AW126974.1|AW126974
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         CAGAGAAAAGGCAGGCGGAGGCTTCAAGGGATTCGTGACAAATATCCCGAC
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tgttctctagCAGAGAAAAGGCAGGCGGAGGCTTCAAGG-ATTCGTGACAAATATCCCGAC
EST: gi|162173286|gb|FC350068.1|FC350068
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCT-G                         --GAGAAAAGGCAGGCGGAGGCTTCAAGGATTCCTGACAAATATCCCGACA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tgttctctagCAGAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
EST: gi|162215669|gb|FC391709.1|FC391709
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCT-G                         --GAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tgttctctagCAGAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
EST: gi|18350954|gb|BJ183005.1|BJ183005
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCT-G                         --GAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tgttctctagCAGAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
EST: gi|162233637|gb|FC409396.1|FC409396
EST:     G-TGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCT-G                         --GAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tgttctctagCAGAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
EST: gi|162225362|gb|FC401166.1|FC401166
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCT-G                         --GAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tgttctctagCAGAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
EST: gi|100386838|gb|BY988107.1|BY988107
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         CAGAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tgttctctagCAGAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTAAAGGCGATCGTGGTGTTGGGGAAGTTTTGAAGGTATAGGTGTGGCGTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgttgtttgtattgaattgtggttgatgacttcccaagcaatgcatgcgtcgtcgcttcagttgtagcatttttcgtttcggaacgccctcct

- - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA