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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatgctgtggttgtttgtcattgacaaagggggacccggttagggttgtactgctttcgagtggtgattgatctttcatgcaatggattttttggcgcagCTTTCATTGATCTTACGAGGAGTTTTGACTTGGGGACAAGGATTGGTAGTATTGCAACTTGAAAAGATTGTGGGGGGTCTGTTTTTGAATTGGGCTTTAC

Basic information

species Physcomitrella patens
transcript PP1S6_409V6.2
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|67575683|gb|BJ948507.1|BJ948507
EST:     CGCATTGGGCTTGCGCATGCTGCTGCATCGACAGCTCGGAGAGTTCCACG                         CTTTCATTGATCTTACGAGGAGTTTTGACTTGGGGACAAGGATTGGTAGTA
genomic: CGCATT-GGCTTGCGCATGCTGCTGCATCGACAGCTCGGAGAGTTCCACGgtgcgctcct ... tttggcgcagCTTTCATTGATCTTACGAGGAGTTTTGACTTGGGGACAAGGATTGGTAGTA
EST: gi|208348042|gb|DC905365.1|DC905365
EST:     GCATGCTGCTGCATCGACAGCTCGGAGAGTTCCACG                         CTTTCATTGATCTTACGAGGAGTTTTGACTTGGGGACAAGGATTGGTAGTA
genomic: GCATGCTGCTGCATCGACAGCTCGGAGAGTTCCACGgtgcgctcct ... tttggcgcagCTTTCATTGATCTTACGAGGAGTTTTGACTTGGGGACAAGGATTGGTAGTA
EST: gi|100430815|gb|BY978411.1|BY978411
EST:     TCGCATTGGCTTGCGCATGCTGCTGCATCGACAGCTCGGAGAGTTCCACG                         CTTTCATTGATCTTACGAGGAGTTTTGACTTGGGGACAAGGATTGGTAGTA
genomic: TCGCATTGGCTTGCGCATGCTGCTGCATCGACAGCTCGGAGAGTTCCACGgtgcgctcct ... tttggcgcagCTTTCATTGATCTTACGAGGAGTTTTGACTTGGGGACAAGGATTGGTAGTA
EST: gi|208391260|gb|DC933521.1|DC933521
EST:     TCGCATTGGCTTGCGCATGCTGCTGCATCGACAGCTCGGAGAGTTCCACG                         CTTTCATTGATCTTACGAGGAGTTTTGACTTGGGGACAAGGATTGGTAGTA
genomic: TCGCATTGGCTTGCGCATGCTGCTGCATCGACAGCTCGGAGAGTTCCACGgtgcgctcct ... tttggcgcagCTTTCATTGATCTTACGAGGAGTTTTGACTTGGGGACAAGGATTGGTAGTA
EST: gi|208373818|gb|DC936589.1|DC936589
EST:     ATGCTGCTGCATCGACAGCTCGGAGAGTTCCACG                         CTTTCATTGATCTTACGAGGAGTTTTGACTTGGGGACAAGGATTGGTAGTA
genomic: ATGCTGCTGCATCGACAGCTCGGAGAGTTCCACGgtgcgctcct ... tttggcgcagCTTTCATTGATCTTACGAGGAGTTTTGACTTGGGGACAAGGATTGGTAGTA
EST: gi|208360397|gb|DC930778.1|DC930778
EST:     TCGCATTGGCTTGCGCATGCTGCTGCATCGACAGCTCGGAGAGTTCCACG                         CTTTCATTGATCTTACGAGGAGTTTTGACTTGGGGACAAGGATTGGTAGTA
genomic: TCGCATTGGCTTGCGCATGCTGCTGCATCGACAGCTCGGAGAGTTCCACGgtgcgctcct ... tttggcgcagCTTTCATTGATCTTACGAGGAGTTTTGACTTGGGGACAAGGATTGGTAGTA
EST: gi|100379138|gb|BY986594.1|BY986594
EST:     TCGCATTGGCTTGCGCATGCTGCTGCATCGACAGCTCGGAGAGTTCCACG                         CTTTCATTGATCTTACGAGGAGTTTTGACTTGGGGACAAGGATTGGTAGTA
genomic: TCGCATTGGCTTGCGCATGCTGCTGCATCGACAGCTCGGAGAGTTCCACGgtgcgctcct ... tttggcgcagCTTTCATTGATCTTACGAGGAGTTTTGACTTGGGGACAAGGATTGGTAGTA
EST: gi|100416820|gb|BY993105.1|BY993105
EST:     TCGCATTGGCTTGCGCATGCTGCTGCATCGACAGCTCGGAGAGTTCCACG                         CTTTCATTGATCTTACGAGGAGTTTTGACTTGGGGACAAGGATTGGTAGTA
genomic: TCGCATTGGCTTGCGCATGCTGCTGCATCGACAGCTCGGAGAGTTCCACGgtgcgctcct ... tttggcgcagCTTTCATTGATCTTACGAGGAGTTTTGACTTGGGGACAAGGATTGGTAGTA
EST: gi|100417855|gb|BY975687.1|BY975687
EST:     GCATTGGCTTGCGCATGCTGCTGCATCGACAGCTCGGAGAGTTCCACG                         CTTTCATTGATCTTACGAGGAGTTTTGACTTGGGGACAAGGATTGGTAGTA
genomic: GCATTGGCTTGCGCATGCTGCTGCATCGACAGCTCGGAGAGTTCCACGgtgcgctcct ... tttggcgcagCTTTCATTGATCTTACGAGGAGTTTTGACTTGGGGACAAGGATTGGTAGTA
EST: gi|162203521|gb|FC380437.1|FC380437
EST:     GGCTTGCGCATGCTGCTGCATCGACAGCTCGGAGAGTTCCACG                         CTTTCATTGATCTTACGAGGAGTTTTGACTTGGGGACAAGGATTGGTAGTA
genomic: GGCTTGCGCATGCTGCTGCATCGACAGCTCGGAGAGTTCCACGgtgcgctcct ... tttggcgcagCTTTCATTGATCTTACGAGGAGTTTTGACTTGGGGACAAGGATTGGTAGTA

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), 35 (downstream exon)
Score: 10

CCCCTTCCACGCTTGCCTCAGGGTGATTGAGTCCATTCCTTCGCTTCCGCTCGCATTGGCTTGCGCATGCTGCTGCATCGACAGCTCGGAGAGTTCCACGgtgcgctcct ... tttggcgcagCTTTCATTGATCTTACGAGGAGTTTTGACTTGGGGACAAGGATTGGTAGTATTGCAACTTGAAAAGATTGTGGGGGGTCTGTTTTTGAATTGGGCTTTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtactgctttcgagtggtgattgatctttcatgcaatggattttttggcgcagCTTTCATTGATCTTACGAGGAGTTTTGACTTGGGGACAAGGATTGGTAGTATTGCAACTTGAAAAGATTGTGGGGGGTCTGTTTTTGAATTGGGCTTTAC
                    gattgat  putative branch site (score: 10)
                                          tttttt  putative PPT
                                         atttttt  TA-rich tract