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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcaggatggctggtcattactactgctatatcatatctttcgtttacataatcacaccgtacatattctcagtgaaaagcttgctctaccctgtgtagACTTGGAGAAAACATCACTAAACGCAGCAGTGCGGCTCTTTCAAACTAAATTTTTGGACCCACTCCAACGTGCGAACAAG

Basic information

species Physcomitrella patens
transcript PP1S90_95V6.1
intron # 15
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|208375020|gb|DC956416.1|DC956416
EST:     ATTGTATGATCTTAACAACGAAGGAGGTAAAGCGGGGCCAGAAGTGAAAG                         ACTTGGAGAAAACATCACTAAACGCAGCAGTGCGGCTCTTTCAAACTAAAT
genomic: ATTGTATGATCTTAACAACGAAGGAGGTAAAGCGGGGCCAGAAGTGAAAGgtagtatttc ... ccctgtgtagACTTGGAGAAAACATCACTAAACGCAGCAGTGCGGCTCTTTCAAACTAAAT
EST: gi|18341360|gb|BJ173395.1|BJ173395
EST:     ATTGTATGATCTTAACAACGAAGGAGGTAAAGCGGGGCCAGAAGTGAAAG                         ACTTGGAGAAAACATCACTAAACGCAGCAGTGCGGCTCTTTCAAACTAAAT
genomic: ATTGTATGATCTTAACAACGAAGGAGGTAAAGCGGGGCCAGAAGTGAAAGgtagtatttc ... ccctgtgtagACTTGGAGAAAACATCACTAAACGCAGCAGTGCGGCTCTTTCAAACTAAAT
EST: gi|18337995|gb|BJ170019.1|BJ170019
EST:     ATTGTATGATCTTAACAACGAAGGAGGTAAAGCGGGGCCAGAAGTGAAAG                         ACTTGGAGAAAACATCACTAAACGCAGCAGTGCGGCTCTTTCAAACTAAAT
genomic: ATTGTATGATCTTAACAACGAAGGAGGTAAAGCGGGGCCAGAAGTGAAAGgtagtatttc ... ccctgtgtagACTTGGAGAAAACATCACTAAACGCAGCAGTGCGGCTCTTTCAAACTAAAT
EST: gi|162191193|gb|FC367871.1|FC367871
EST:     ATTGTATGATCTTAACAACGAAGGAGGTAAAGCGGGGCCAGAAGTGAAAG                         ACTTGGAGAAAACATCACTAAATGCAGCAGTGCGGCTCTTTCAAACTAAAT
genomic: ATTGTATGATCTTAACAACGAAGGAGGTAAAGCGGGGCCAGAAGTGAAAGgtagtatttc ... ccctgtgtagACTTGGAGAAAACATCACTAAACGCAGCAGTGCGGCTCTTTCAAACTAAAT

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: 23 (upstream exon), 29 (downstream exon)
Score: 4

TTATTGTATGATCTTAACAACGAAGGAGGTAAAGCGGGGCCAGAAGTGAAAGgtagtatttc ... ccctgtgtagACTTGGAGAAAACATCACTAAACGCAGCAGTGCGGCTCTTTCAAACTAAATTTTTGGACCCACTCCAACGTGCGAACAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacataatcacaccgtacatattctcagtgaaaagcttgctctaccctgtgtagACTTGGAGAAAACATCACTAAACGCAGCAGTGCGGCTCTTTCAAACTAAATTTTTGGACCCACTCCAACGTGCGAACAAG
                                        ctctaccct  CT-rich tract
                tacatatt  TA-rich tract