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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttgtggtgcctacttggtttcttggctatgtgcattctcggatgatatgcggatctatgtgctaagtattggattgattcatggtgatgatattccagGCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCGGTGTTGTGTGGGCACAAACAAATGGCACTG

Basic information

species Physcomitrella patens
transcript PP1S4_215V6.1
intron # 4
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|22491814|gb|BU051737.1|BU051737
EST:     TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAG                         GCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
genomic: TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAGgtagtgttag ... gatattccagGCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
EST: gi|162264332|gb|FC440498.1|FC440498
EST:     TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAG                         GCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
genomic: TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAGgtagtgttag ... gatattccagGCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
EST: gi|18333863|gb|BJ165879.1|BJ165879
EST:     TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAG                         GCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
genomic: TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAGgtagtgttag ... gatattccagGCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
EST: gi|18332708|gb|BJ164721.1|BJ164721
EST:     TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAG                         GCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
genomic: TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAGgtagtgttag ... gatattccagGCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
EST: gi|162245009|gb|FC424967.1|FC424967
EST:     AGGTTACGTACAG                         GCAGTCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGC
genomic: AGGTTACGTACAGgtagtgttag ... gatattccagGCAG-CTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGC
EST: gi|162238939|gb|FC417703.1|FC417703
EST:     TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAG                         GCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCANACTGGTGCG
genomic: TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAGgtagtgttag ... gatattccagGCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
EST: gi|208371352|gb|DC944516.1|DC944516
EST:     TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAG                         GCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
genomic: TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAGgtagtgttag ... gatattccagGCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
EST: gi|162245008|gb|FC424966.1|FC424966
EST:     AGGTTACGTACAG                         GCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
genomic: AGGTTACGTACAGgtagtgttag ... gatattccagGCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
EST: gi|67696462|gb|BJ956695.1|BJ956695
EST:     TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAG                         GCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
genomic: TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAGgtagtgttag ... gatattccagGCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
EST: gi|162238938|gb|FC417702.1|FC417702
EST:     TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAG                         GCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
genomic: TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAGgtagtgttag ... gatattccagGCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
EST: gi|162179827|gb|FC356418.1|FC356418
EST:     TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAG                         GCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
genomic: TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAGgtagtgttag ... gatattccagGCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
EST: gi|162264333|gb|FC440499.1|FC440499
EST:     TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAG                         GCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
genomic: TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAGgtagtgttag ... gatattccagGCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
EST: gi|162235909|gb|FC411652.1|FC411652
EST:     TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAG                         GCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
genomic: TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAGgtagtgttag ... gatattccagGCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
EST: gi|162199674|gb|FC375913.1|FC375913
EST:     TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAG                         GCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG
genomic: TATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAGgtagtgttag ... gatattccagGCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCG

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: 35 (upstream exon), 33 (downstream exon)
Score: 18

GATAGATTTAAGGACTGGGAAGCATCAGGTGTTCAAGTAATCCCTGTATTGTCTCAGCCTACCGGCCCCTGGAATGGGGCTCAAGGTTACGTACAGgtagtgttag ... gatattccagGCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCGGTGTTGTGTGGGCACAAACAAATGGCACTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatatgcggatctatgtgctaagtattggattgattcatggtgatgatattccagGCAGCTTTCTCCAATGACAAGGGAAGCATAGTTGGGTCGCAAACTGGTGCGGTGTTGTGTGGGCACAAACAAATGGCACTG
                            gattgat  putative branch site (score: 18)
                   taagtatt  TA-rich tract