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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGATCACCTCTTTTATGGATCGGTGTGGGAGTGGGTCTTTCAGCACTATTCTCTTTTgtgagtattgagtagtccaagcgcttttggggccaagctactgctactaaaacctctgacttcgtaataaagacgcttctcacaatttgtatggttattt...

Basic information

species Physcomitrella patens
transcript PP1S110_13V6.1
intron # 3
splice site 5'
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:     CTCTTTTATGGATCGGTGTGGGAGTGGGTCTTTCAGCACTATTCTCTTTT                         GGTGCTAACAGCGTGAAG
genomic: CTCTTTTATGGATCGGTGTGGGAGTGGGTCTTTCAGCACTATTCTCTTTTgtgagtattg ... tggctcgcagGGTGCTAACAGCGTGAAG
EST: gi|100451985|gb|CJ975042.1|CJ975042
EST:     CTCTTTTATGGATCGGTGTGGGAGTGGGTCTTTCAGCACTATTCTCTTTT                         GGTGCTAACAGCGTGAAG
genomic: CTCTTTTATGGATCGGTGTGGGAGTGGGTCTTTCAGCACTATTCTCTTTTgtgagtattg ... tggctcgcagGGTGCTAACAGCGTGAAG
EST: gi|208352398|gb|DC906181.1|DC906181
EST:     CTCTTTTATGGATCGGTGTGGGAGTGGGTCTTTCAGCACTATTCTCTTTT                         GGTGCTAACAGCGTGAAG
genomic: CTCTTTTATGGATCGGTGTGGGAGTGGGTCTTTCAGCACTATTCTCTTTTgtgagtattg ... tggctcgcagGGTGCTAACAGCGTGAAG
EST: gi|18372257|gb|BJ203859.1|BJ203859
EST:     CTTTTATGGATCGGTGTGGGAAGTGGGGTCTTTCAGCACTATTCTCTTTT                         GGTGCTAACAGCGTGAA
genomic: CTTTTATGGATCGGTGTGGGA-GTGGG-TCTTTCAGCACTATTCTCTTTTgtgagtattg ... tggctcgcagGGTGCTAACAGCGTGAA
EST: gi|100429860|gb|BY978125.1|BY978125
EST:     CTCTTTTATGGATCGGTGTGGGAGTGGGTCTTTCAGCACTATTCTCTTTT                         GGTGCTAACAGCGTGAAG
genomic: CTCTTTTATGGATCGGTGTGGGAGTGGGTCTTTCAGCACTATTCTCTTTTgtgagtattg ... tggctcgcagGGTGCTAACAGCGTGAAG
EST: gi|100440859|gb|BY962347.1|BY962347
EST:     CTCTTTTATGGATCGGTGTGGGAGTGGGTCTTTCAGCACTATTCTCTTTT                         GGTGCTAACAGCGTGAAG
genomic: CTCTTTTATGGATCGGTGTGGGAGTGGGTCTTTCAGCACTATTCTCTTTTgtgagtattg ... tggctcgcagGGTGCTAACAGCGTGAAG
EST: gi|100442213|gb|BY963106.1|BY963106
EST:     CTCTTTTATGGATCGGTGTGGGAGTGGGTCTTTCAGCACTATTCTCTTTT                         GGTGCTAACAGCGTGAAG
genomic: CTCTTTTATGGATCGGTGTGGGAGTGGGTCTTTCAGCACTATTCTCTTTTgtgagtattg ... tggctcgcagGGTGCTAACAGCGTGAAG
EST: gi|208357241|gb|DC910652.1|DC910652
EST:     CTCTTTTATGGATCGGTGTGGGAGTGGGTCTTTCAGCACTATTCTCTTTT                         GGTGCTAACAGCGTGAAG
genomic: CTCTTTTATGGATCGGTGTGGGAGTGGGTCTTTCAGCACTATTCTCTTTTgtgagtattg ... tggctcgcagGGTGCTAACAGCGTGAAG
EST: gi|162176403|gb|FC353588.1|FC353588
EST:     CTCTTTTATGGATCGGTGTGGGAGTGGGTCTTTCAGCACTATTCTCTTTT                         GGTGCTAACAGCGTGAAG
genomic: CTCTTTTATGGATCGGTGTGGGAGTGGGTCTTTCAGCACTATTCTCTTTTgtgagtattg ... tggctcgcagGGTGCTAACAGCGTGAAG
EST: gi|162184458|gb|FC359204.1|FC359204
EST:     CTCTTTTATGGATCGGTGTGGGAGTGGGTCTTTCAGCACTATTCTCTTTT                         GGTGCTAACAGCGTGAAG
genomic: CTCTTTTATGGATCGGTGTGGGAGTGGGTCTTTCAGCACTATTCTCTTTTgtgagtattg ... tggctcgcagGGTGCTAACAGCGTGAAG

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), 9 (downstream exon)
Score: 4

TGGATCACCTCTTTTATGGATCGGTGTGGGAGTGGGTCTTTCAGCACTATTCTCTTTTgtgagtattg ... tggctcgcagGGTGCTAACAGCGTGAAG




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