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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaaaccaggatgagtaatcgaaagcttcgtctgcttgaatttgtggtcacaattgtgcatagacactatgattgagttcaactcctgcgaattttgtagGATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGGTGCCTGTTGCGCAAGGCAACACACACAGTTGACTACGCTTGGCCTTACG

Basic information

species Physcomitrella patens
transcript PP1S91_80V6.1
intron # 3
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|19782263|gb|BQ039833.1|BQ039833
EST:     AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAG                         GATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
genomic: AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAGgtgcattata ... aattttgtagGATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
EST: gi|162201001|gb|FC378132.1|FC378132
EST:     AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAG                         GATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
genomic: AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAGgtgcattata ... aattttgtagGATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
EST: gi|162274752|gb|FC450506.1|FC450506
EST:     AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAG                         GATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
genomic: AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAGgtgcattata ... aattttgtagGATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
EST: gi|7148124|gb|AW510046.1|AW510046
EST:     TTAACAAACTGAAG                         GATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
genomic: TTAACAAACTGAAGgtgcattata ... aattttgtagGATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
EST: gi|208377551|gb|DC922654.1|DC922654
EST:     AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAG                         GATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
genomic: AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAGgtgcattata ... aattttgtagGATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
EST: gi|37830150|gb|BJ588162.1|BJ588162
EST:     AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAG                         GATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
genomic: AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAGgtgcattata ... aattttgtagGATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
EST: gi|208392838|gb|DC957105.1|DC957105
EST:     AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAG                         GATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
genomic: AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAGgtgcattata ... aattttgtagGATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
EST: gi|162274753|gb|FC450507.1|FC450507
EST:     AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAG                         GATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
genomic: AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAGgtgcattata ... aattttgtagGATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
EST: gi|208377095|gb|DC936827.1|DC936827
EST:     AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAG                         GATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
genomic: AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAGgtgcattata ... aattttgtagGATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
EST: gi|208395875|gb|DC920325.1|DC920325
EST:     AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAG                         GATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
genomic: AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAGgtgcattata ... aattttgtagGATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
EST: gi|19790325|gb|BQ041812.1|BQ041812
EST:     AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAG                         GATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
genomic: AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAGgtgcattata ... aattttgtagGATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
EST: gi|208399601|gb|DC908782.1|DC908782
EST:     ACCAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTANCAAACTGAAG                         GATNCTGTTGACCTCCTGACGTCCG
genomic: AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAGgtgcattata ... aattttgtagGATTCTGTTGACCTCCTGACGTCCG
EST: gi|162165178|gb|FC341160.1|FC341160
EST:     AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAG                         GATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
genomic: AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAGgtgcattata ... aattttgtagGATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
EST: gi|162201002|gb|FC378133.1|FC378133
EST:     AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAG                         GATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
genomic: AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAGgtgcattata ... aattttgtagGATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
EST: gi|208362982|gb|DC946893.1|DC946893
EST:     AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAG                         GATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG
genomic: AACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAGgtgcattata ... aattttgtagGATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGG

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), 28 (downstream exon)
Score: 8

ATTGTCAAAGCATATCAAGAGCGATGTGCGGAAGTGCGGCAACAAAATTTGGGGGAATCCGAAGCTCAGGAGATCCTTAACAAACTGAAGgtgcattata ... aattttgtagGATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGGTGCCTGTTGCGCAAGGCAACACACACAGTTGACTACGCTTGGCCTTACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtcacaattgtgcatagacactatgattgagttcaactcctgcgaattttgtagGATTCTGTTGACCTCCTGACGTCCGAAGAAGAACGGCGGCTGTATGACTGGTGCCTGTTGCGCAAGGCAACACACACAGTTGACTACGCTTGGCCTTACG
                                             aattttgta  TA-rich tract