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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taggtctttttgtactgtatcaagtccaaaaaactgcttcttacactacccgacaggagtttgaacagttctagccataattgggtcatcccttttgcagGCCCTGAGGCAGTATTCTATTCCTTCCACGACAAATGTTTCGAGTTGAAAGTACAAAA

Basic information

species Physcomitrella patens
transcript PP1S92_53V6.1
intron # 8
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|162157910|gb|FC334896.1|FC334896
EST:     TGTTCAACATCAAATTTCAGAGTTGGAGTCTAAACTGAAAGAAGACTTCG                         GCCCTGAGGCAGTATTCTATTCCTTCCACGACAAATGTTTCGAGTTGAAAG
genomic: TGTTCAACATCAAATTTCAGAGTTGGAGTCTAAACTGAAAGAAGACTTCGgtatgtccaa ... ccttttgcagGCCCTGAGGCAGTATTCTATTCCTTCCACGACAAATGTTTCGAGTTGAAAG
EST: gi|37829259|gb|BJ587271.1|BJ587271
EST:     TGTTCAACATCAAATTTCAGAGTTGGAGTCTAAACTGGAAGAAGACTTCG                         GCCCTGAGGCAGTATTCTATTCCTTCCACGACAAATGTTTCGAGTTGAAAG
genomic: TGTTCAACATCAAATTTCAGAGTTGGAGTCTAAACTGAAAGAAGACTTCGgtatgtccaa ... ccttttgcagGCCCTGAGGCAGTATTCTATTCCTTCCACGACAAATGTTTCGAGTTGAAAG
EST: gi|19784441|gb|BQ040174.1|BQ040174
EST:     TGTTCAACATCAAATTTCAGAGTTGGAGTTTAAACTGAAAGAAGACTTCG                         GCCCTGAGGCAGTATTCTATTCCTTCCACGACAAATGTTTCGAGTTGAAAG
genomic: TGTTCAACATCAAATTTCAGAGTTGGAGTCTAAACTGAAAGAAGACTTCGgtatgtccaa ... ccttttgcagGCCCTGAGGCAGTATTCTATTCCTTCCACGACAAATGTTTCGAGTTGAAAG
EST: gi|162157909|gb|FC334895.1|FC334895
EST:     TGTTCAACATCAAATTTCAGAGTTGGAGTCTAAACTGAAAGAAGACTTCG                         GCCCTGAGGCAGTATTCTATTCCTTCCACGACAAATGTTTCGAGTTGAAAG
genomic: TGTTCAACATCAAATTTCAGAGTTGGAGTCTAAACTGAAAGAAGACTTCGgtatgtccaa ... ccttttgcagGCCCTGAGGCAGTATTCTATTCCTTCCACGACAAATGTTTCGAGTTGAAAG
EST: gi|162196285|gb|FC375394.1|FC375394
EST:     TGTTCAACATCAAATTTCAGAGTTGGAGTCTAAACTGAAAGAAGACTTCG                         GCCCTGAGGCAGTATTCTATTCCTTCCACGACAAATGTTTCGAGTTGAAAG
genomic: TGTTCAACATCAAATTTCAGAGTTGGAGTCTAAACTGAAAGAAGACTTCGgtatgtccaa ... ccttttgcagGCCCTGAGGCAGTATTCTATTCCTTCCACGACAAATGTTTCGAGTTGAAAG

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: 28 (upstream exon), 22 (downstream exon)
Score: 4

GCAGAGCGGATTAGGAACCAGTACTCTGAAGCAACAACTCAATTGGCCACTGTTCAACATCAAATTTCAGAGTTGGAGTCTAAACTGAAAGAAGACTTCGgtatgtccaa ... ccttttgcagGCCCTGAGGCAGTATTCTATTCCTTCCACGACAAATGTTTCGAGTTGAAAGTACAAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacccgacaggagtttgaacagttctagccataattgggtcatcccttttgcagGCCCTGAGGCAGTATTCTATTCCTTCCACGACAAATGTTTCGAGTTGAAAGTACAAAA
                                        tcatccctttt  CT-rich tract
                               ataatt  TA-rich tract