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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctgttttcatctccggcttatacttctgttctaaatatattgaaggtaaatgtttattactagttgtgacagacgtatctggtatctgaattgtgcagGAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTCAAGGTTCAGGCATGAAGGTCTCAATTCGCCAGTTGGGACCGAACATGATTCAGCAG

Basic information

species Physcomitrella patens
transcript PP1S174_37V6.1
intron # 3
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|162153711|gb|FC329114.1|FC329114
EST:     TCTAAGAAGCTGTCATTGTCTCGGAATGTACTTTGCTCCAAATGTAAAGG                         GAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTCAAGGTTC
genomic: TCTAAGAAGCTGTCATTGTCTCGGAATGTACTTTGCTCCAAATGTAAAGGgtaagctatt ... aattgtgcagGAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTCAAGGTTC
EST: gi|162197042|gb|FC375241.1|FC375241
EST:     TCTAAGAAGCTGTCATTGTCTCGGAATGTACTTTGCTCCAAATGTAAAGG                         GAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTC
genomic: TCTAAGAAGCTGTCATTGTCTCGGAATGTACTTTGCTCCAAATGTAAAGGgtaagctatt ... aattgtgcagGAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTC
EST: gi|162180092|gb|FC356657.1|FC356657
EST:     TCTAAGAAGCTGTCATTGTCTCGGAATGTACTTTGCTCCAAATGTAAAGG                         GAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTCAAGGTTC
genomic: TCTAAGAAGCTGTCATTGTCTCGGAATGTACTTTGCTCCAAATGTAAAGGgtaagctatt ... aattgtgcagGAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTCAAGGTTC
EST: gi|100431293|gb|BY960124.1|BY960124
EST:     TCTAAGAAGCTGTCATTGTCTCGGAATGTACTTTGCTCCAAATGTAAAGG                         GAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTCAAGGTTC
genomic: TCTAAGAAGCTGTCATTGTCTCGGAATGTACTTTGCTCCAAATGTAAAGGgtaagctatt ... aattgtgcagGAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTCAAGGTTC
EST: gi|162151466|gb|FC326971.1|FC326971
EST:     TCTAAGAAGCTGTCATTGTCTCGGAATGTACTTTGCTCCAAATGTAAAGG                         GAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTCAAGGTTC
genomic: TCTAAGAAGCTGTCATTGTCTCGGAATGTACTTTGCTCCAAATGTAAAGGgtaagctatt ... aattgtgcagGAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTCAAGGTTC
EST: gi|162173994|gb|FC350509.1|FC350509
EST:     TCTAAGAAGCTGTCATTGTCTCGGAATGTACTTTGCTCCAAATGTAAAGG                         GAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTCAAGGTTC
genomic: TCTAAGAAGCTGTCATTGTCTCGGAATGTACTTTGCTCCAAATGTAAAGGgtaagctatt ... aattgtgcagGAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTCAAGGTTC
EST: gi|162263312|gb|FC439094.1|FC439094
EST:     TCTAAGAAGCTGTCATTGTCTCGGAATGTACTTTGCTCCAAATGTAAAGG                         GAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTCAAGGTTC
genomic: TCTAAGAAGCTGTCATTGTCTCGGAATGTACTTTGCTCCAAATGTAAAGGgtaagctatt ... aattgtgcagGAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTCAAGGTTC
EST: gi|100441389|gb|BY962678.1|BY962678
EST:     GGAATGTACTTTGCTCCAAATGTAAAGG                         GAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTCAAGGTTC
genomic: GGAATGTACTTTGCTCCAAATGTAAAGGgtaagctatt ... aattgtgcagGAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTCAAGGTTC
EST: gi|162166513|gb|FC343210.1|FC343210
EST:     TCTAAGAAGCTGTCATTGTCTCGGAATGTACTTTGCTCCAAATGTAAAGG                         GAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTCAAGGTTC
genomic: TCTAAGAAGCTGTCATTGTCTCGGAATGTACTTTGCTCCAAATGTAAAGGgtaagctatt ... aattgtgcagGAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTCAAGGTTC
EST: gi|161979173|gb|EE296304.1|EE296304
EST:     ACTTTGCTCCAAATGTAAAGG                         GAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTCAAGGTTC
genomic: ACTTTGCTCCAAATGTAAAGGgtaagctatt ... aattgtgcagGAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTCAAGGTTC
EST: gi|100384322|gb|BY969453.1|BY969453
EST:     TCTAAGAAGCTGTCATTGTCTCGGAATGTACTTTGCTCCAAATGTAAAGG                         GAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTCAAGGTTC
genomic: TCTAAGAAGCTGTCATTGTCTCGGAATGTACTTTGCTCCAAATGTAAAGGgtaagctatt ... aattgtgcagGAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTCAAGGTTC
EST: gi|100396849|gb|BY953858.1|BY953858
EST:     CNTA-GAAGCTGTCATTGTCTCGGAATGTACTTTGCTCCAAATGTAAAGG                         GAAAGGATCGA
genomic: C-TAAGAAGCTGTCATTGTCTCGGAATGTACTTTGCTCCAAATGTAAAGGgtaagctatt ... aattgtgcagGAAAGGATCGA

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: 109

ATGTAGTTCATCCTTTGAAGGTTTCATTGGAAGATCTTTACAATGGCACTTCTAAGAAGCTGTCATTGTCTCGGAATGTACTTTGCTCCAAATGTAAAGGgtaagctatt ... aattgtgcagGAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTCAAGGTTCAGGCATGAAGGTCTCAATTCGCCAGTTGGGACCGAACATGATTCAGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggtaaatgtttattactagttgtgacagacgtatctggtatctgaattgtgcagGAAAGGATCGAAGACTGGTGCATCTAGTCGGTGCGCAGGATGTCAAGGTTCAGGCATGAAGGTCTCAATTCGCCAGTTGGGACCGAACATGATTCAGCAG
     aatgtttattacta  TA-rich tract