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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgatcatgaaaattcagccatgagtcattgatcaacttcgctatgttgccctgattacgacgaaggtttcaacataatgaaactattgtttaatggcagAGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAAGCATCGCTGAATCGCAAGGATCTGGGTCTTCTTACAT

Basic information

species Physcomitrella patens
transcript PP1S110_13V6.1
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|162166028|gb|FC340424.1|FC340424
EST:     AGGTTCTAGGTCGGAGGGTATTGTGGCAGCTGCTCGGAAGTCCACCCCAG                         AGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAA
genomic: AGGTTCTAGGTCGGAGGGTATTGTGGCAGCTGCTCGGAAGTCCACCCCAGgtcagtgtca ... ttaatggcagAGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAA
EST: gi|100451985|gb|CJ975042.1|CJ975042
EST:     AGGTTCTAGGTCGGAGGGTATTGTGGCAGCTGCTCGGAAGTCCACCCCAG                         AGCAAGAGGAGTACGTTGATACCAAGAATGATTCGAATGAGTACATTGAAA
genomic: AGGTTCTAGGTCGGAGGGTATTGTGGCAGCTGCTCGGAAGTCCACCCCAGgtcagtgtca ... ttaatggcagAGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAA
EST: gi|208352398|gb|DC906181.1|DC906181
EST:     AGGTTCTAGGTCGGAGGGTATTGTGGCAGCTGCTCGGAAGTCCACCCCAG                         AGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAA
genomic: AGGTTCTAGGTCGGAGGGTATTGTGGCAGCTGCTCGGAAGTCCACCCCAGgtcagtgtca ... ttaatggcagAGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAA
EST: gi|18372257|gb|BJ203859.1|BJ203859
EST:     GGTTCTAGGTCGGAGGGTATTGTGGCAGCTGCTTCGGAAGTCCACCCCAG                         AGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAA
genomic: GGTTCTAGGTCGGAGGGTATTGTGGCAGCTGCT-CGGAAGTCCACCCCAGgtcagtgtca ... ttaatggcagAGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAA
EST: gi|100429860|gb|BY978125.1|BY978125
EST:     AGGTTCTAGGTCGGAGGGTATTGTGGCAGCTGCTCGGAAGTCCACCCCAG                         AGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAA
genomic: AGGTTCTAGGTCGGAGGGTATTGTGGCAGCTGCTCGGAAGTCCACCCCAGgtcagtgtca ... ttaatggcagAGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAA
EST: gi|100440859|gb|BY962347.1|BY962347
EST:     AGGTTCTAGGTCGGAGGGTATTGTGGCAGCTGCTCGGAAGTCCACCCCAG                         AGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAA
genomic: AGGTTCTAGGTCGGAGGGTATTGTGGCAGCTGCTCGGAAGTCCACCCCAGgtcagtgtca ... ttaatggcagAGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAA
EST: gi|100442213|gb|BY963106.1|BY963106
EST:     AGGTTCTAGGTCGGAGGGTATTGTGGCAGCTGCTCGGAAGTCCACCCCAG                         AGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAA
genomic: AGGTTCTAGGTCGGAGGGTATTGTGGCAGCTGCTCGGAAGTCCACCCCAGgtcagtgtca ... ttaatggcagAGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAA
EST: gi|18356867|gb|BJ188926.1|BJ188926
EST:     GGTTCTAGGTCGGAGGGTATTGTGGCAGCCTGCTCGGAAGTCCACCCCAG                         AGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAA
genomic: GGTTCTAGGTCGGAGGGTATTGTGGCAGC-TGCTCGGAAGTCCACCCCAGgtcagtgtca ... ttaatggcagAGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAA
EST: gi|208357241|gb|DC910652.1|DC910652
EST:     AGGTTCTAGGTCGGAGGGTATTGTGGCAGCTGCTCGGAAGTCCACCCCAG                         AGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAA
genomic: AGGTTCTAGGTCGGAGGGTATTGTGGCAGCTGCTCGGAAGTCCACCCCAGgtcagtgtca ... ttaatggcagAGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAA
EST: gi|162176403|gb|FC353588.1|FC353588
EST:     AGGTTCTAGGTCGGAGGGTATTGTGGCAGCTGCTCGGAAGTCCACCCCAG                         AGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAA
genomic: AGGTTCTAGGTCGGAGGGTATTGTGGCAGCTGCTCGGAAGTCCACCCCAGgtcagtgtca ... ttaatggcagAGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAA
EST: gi|162184458|gb|FC359204.1|FC359204
EST:     AGGTTCTAGGTCGGAGGGTATTGTGGCAGCTGCTCGGAAGTCCACCCCAG                         AGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAA
genomic: AGGTTCTAGGTCGGAGGGTATTGTGGCAGCTGCTCGGAAGTCCACCCCAGgtcagtgtca ... ttaatggcagAGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAA

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), 27 (downstream exon)
Score: 20

GGCGCCAAGCTGCGGGACGTGGGGATTGAGTGTGGGAGATGCGGGAAGAAAGGTTCTAGGTCGGAGGGTATTGTGGCAGCTGCTCGGAAGTCCACCCCAGgtcagtgtca ... ttaatggcagAGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAAGCATCGCTGAATCGCAAGGATCTGGGTCTTCTTACAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgccctgattacgacgaaggtttcaacataatgaaactattgtttaatggcagAGCAAGAGGAGTACGTTGTTACCAAGAATGATTCGAATGAGTACATTGAAAGCATCGCTGAATCGCAAGGATCTGGGTCTTCTTACAT
                                           gtttaat  putative branch site (score: 20)
                             ataatgaaactattgt  TA-rich tract