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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggattgattgttctgaagcataggtaataattgttgggagtagcgggataaggattgttatgtgtgagaatttcactcatctcgtggtgttctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAATCCCAGTGATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGA

Basic information

species Physcomitrella patens
transcript PP1S209_114V6.2
intron # 2
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|67575443|gb|BJ948267.1|BJ948267
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         AGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
EST: gi|162233637|gb|FC409396.1|FC409396
EST:     G-TGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         AGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
EST: gi|162225361|gb|FC401165.1|FC401165
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         AGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
EST: gi|100416767|gb|BY993077.1|BY993077
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         AGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
EST: gi|162238593|gb|FC418163.1|FC418163
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         AGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
EST: gi|67698910|gb|BJ959143.1|BJ959143
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         AGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
EST: gi|100386838|gb|BY988107.1|BY988107
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGCAG                       
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCT-G--Ggtaagagtgt ... tctctagc
EST: gi|162200693|gb|FC377876.1|FC377876
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         AGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
EST: gi|162215669|gb|FC391709.1|FC391709
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         AGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
EST: gi|162264864|gb|FC440639.1|FC440639
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         AGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
EST: gi|162225362|gb|FC401166.1|FC401166
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         AGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
EST: gi|162246388|gb|FC422420.1|FC422420
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         AGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
EST: gi|162200692|gb|FC377875.1|FC377875
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         AGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
EST: gi|162246361|gb|FC422419.1|FC422419
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         AGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
EST: gi|162173286|gb|FC350068.1|FC350068
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         AGAAAAGGCAGGCGGAGGCTTCAAGGATTCCTGACAAATATCCCGACAGAA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
EST: gi|162262384|gb|FC437711.1|FC437711
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         AGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
EST: gi|162233638|gb|FC409397.1|FC409397
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         AGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
EST: gi|162215670|gb|FC391710.1|FC391710
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         AGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
EST: gi|162270438|gb|FC447554.1|FC447554
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         AGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
EST: gi|6102504|gb|AW126974.1|AW126974
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         C
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcag-
EST: gi|6102504|gb|AW126974.1|AW126974
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         C
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcag-
EST: gi|18350954|gb|BJ183005.1|BJ183005
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         AGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
EST: gi|162238594|gb|FC418164.1|FC418164
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         AGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
EST: gi|162216854|gb|FC393036.1|FC393036
EST:     GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGG                         AGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA
genomic: GTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAA

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), 35 (downstream exon)
Score: 31

GTGTAAAGGCGATCGTGGTGTTGGGGAAGTTTTGAAGGTATAGGTGTGGCGTTGGAGGGGACGATGGCGAAGAGTTCGTTCAAGCAGGAACATCCTCTGGgtaagagtgt ... tctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAATCCCAGTGATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggataaggattgttatgtgtgagaatttcactcatctcgtggtgttctctagcagAGAAAAGGCAGGCGGAGGCTTCAAGGATTCGTGACAAATATCCCGACAGAATCCCAGTGATTGTGGAAAAGGCAGAGAAAAGCGACATACCAGACATCGA
                                          tgttctct  CT-rich tract
        attgttat  TA-rich tract