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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catcaagattgacggcttgtagattccaacataggtttttgtttcataatccagtaaattatgaagtttaagtttgagacattgctcgtatgaattgcagAAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCTACCTATCCTGATTCGTGAGTGTAGCGGCGTGCAGCCTCGCATTTGGGCC

Basic information

species Physcomitrella patens
transcript PP1S9_379V6.1
intron # 1
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|67712906|gb|BJ966355.1|BJ966355
EST:     GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAG                         AAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCGACGCT
genomic: GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAGgtgttactag ... tgaattgcagAAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT
EST: gi|19789252|gb|BQ041195.1|BQ041195
EST:     GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAG                         AAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT
genomic: GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAGgtgttactag ... tgaattgcagAAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT
EST: gi|18359342|gb|BJ191403.1|BJ191403
EST:     GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAG                         AAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT
genomic: GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAGgtgttactag ... tgaattgcagAAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT
EST: gi|162220060|gb|FC395380.1|FC395380
EST:     GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAG                         AAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT
genomic: GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAGgtgttactag ... tgaattgcagAAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT
EST: gi|18332637|gb|BJ164650.1|BJ164650
EST:     GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAG                         AAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT
genomic: GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAGgtgttactag ... tgaattgcagAAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT
EST: gi|18366488|gb|BJ198567.1|BJ198567
EST:     GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAG                         AAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT
genomic: GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAGgtgttactag ... tgaattgcagAAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT
EST: gi|18329199|gb|BJ161205.1|BJ161205
EST:     GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAG                         AAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT
genomic: GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAGgtgttactag ... tgaattgcagAAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT
EST: gi|37846870|gb|BJ604878.1|BJ604878
EST:     GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAG                         AAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT
genomic: GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAGgtgttactag ... tgaattgcagAAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT
EST: gi|18328788|gb|BJ160793.1|BJ160793
EST:     GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAG                         AAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT
genomic: GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAGgtgttactag ... tgaattgcagAAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT
EST: gi|18337000|gb|BJ169023.1|BJ169023
EST:     GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAG                         AAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT
genomic: GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAGgtgttactag ... tgaattgcagAAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT
EST: gi|18361077|gb|BJ193141.1|BJ193141
EST:     GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAG                         AAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT
genomic: GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAGgtgttactag ... tgaattgcagAAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT
EST: gi|67724615|gb|BJ974874.1|BJ974874
EST:     GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAG                         AAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCGACGCT
genomic: GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAGgtgttactag ... tgaattgcagAAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT
EST: gi|37838969|gb|BJ596977.1|BJ596977
EST:     GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAG                         AAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT
genomic: GAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAGgtgttactag ... tgaattgcagAAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCT

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: 33 (upstream exon), 28 (downstream exon)
Score: 23

AGAGAGCAGACATCATGTCGTGGCGAGGGAAGCTGTCGCAGGTGGTGCAGGAACTTCGGATCCATTGCTGCCAGACTTCGCCTGCGTCCACTGTCACCAGgtgttactag ... tgaattgcagAAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCTACCTATCCTGATTCGTGAGTGTAGCGGCGTGCAGCCTCGCATTTGGGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataatccagtaaattatgaagtttaagtttgagacattgctcgtatgaattgcagAAATTTTATTCAGAGGAACTATGCTGACTTGAAAGCTCTGAACCCAACGCTACCTATCCTGATTCGTGAGTGTAGCGGCGTGCAGCCTCGCATTTGGGCC
         taaattatgaagttta  TA-rich tract