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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccaccatgttcatgttgtggctttgatgctcttcttcaccgtctgtattcgctctcctgttcagctagtctgctggcaaccagtgtaagaagagctaactgtcagtatcatgcatttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACTATGGAAGATATCCTTGTGGAGCTCAAGAAGCAGATGGCAAGCCCGGCTA

Basic information

species Physcomitrella patens
transcript PP1S490_20V6.2
intron # 5
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|208363724|gb|DC954695.1|DC954695
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|162260754|gb|FC435406.1|FC435406
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|208365088|gb|DC947324.1|DC947324
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|37821329|gb|BJ579395.1|BJ579395
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|67698924|gb|BJ959157.1|BJ959157
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|37843398|gb|BJ601406.1|BJ601406
EST:     CGGATCAACATGACTCATGTGAACTCGGAGACGGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATAC
genomic: CGGATCAACATGACTCATGTGAACTCGGAGAC-GGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATAC
EST: gi|162248627|gb|FC424480.1|FC424480
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|162211664|gb|FC387952.1|FC387952
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|67573475|gb|BJ946299.1|BJ946299
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|162277404|gb|FC453210.1|FC453210
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|37840937|gb|BJ598945.1|BJ598945
EST:     GATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|162224431|gb|FC399807.1|FC399807
EST:     ATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: ATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|162277403|gb|FC453209.1|FC453209
EST:     AGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: AGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|100446255|gb|CJ970554.1|CJ970554
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|162176507|gb|FC352976.1|FC352976
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|208388041|gb|DC941694.1|DC941694
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|162248628|gb|FC424481.1|FC424481
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|67696855|gb|BJ957088.1|BJ957088
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|18348930|gb|BJ180979.1|BJ180979
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|37835895|gb|BJ593907.1|BJ593907
EST:     ATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATAC
genomic: ATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGAC-GGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATAC
EST: gi|37834644|gb|BJ592656.1|BJ592656
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|15320319|gb|BI488125.1|BI488125
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|18355140|gb|BJ187199.1|BJ187199
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|37832091|gb|BJ590103.1|BJ590103
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|100447101|gb|CJ971400.1|CJ971400
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|162245980|gb|FC424378.1|FC424378
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
EST: gi|67575457|gb|BJ948281.1|BJ948281
EST:     GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTG                         GTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT
genomic: GATTCCATTCTCGGATCAACATGACTCATGTGAACTCGGAGACGGGATTGgtaaccacca ... catttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctgctggcaaccagtgtaagaagagctaactgtcagtatcatgcatttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACTATGGAAGATATCCTTGTGGAGCTCAAGAAGCAGATGGCAAGCCCGGCTA
                         agctaac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaccaccatgttcatgttgtggctttgatgctcttcttcaccgtctgtattcgctctcctgttcagctagtctgctggcaaccagtgtaagaagagctaactgtcagtatcatgcatttcgtagGTTGATCCAAGATATTTTCCTTTGCTGGCAAATTGGCGCCGTAACCATACTATGGAAGATATCCTTGTGGAGCTCAAGAAGCAGATGGCAAGCCCGGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG