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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaaacattgacaatctagcagctgtctgcagctgttgacgcaggccacaatcggctgtttttatctctttcattcgacatagttatctggtaattaccttcttcacacttaaccttttgttgtttgtctacagGGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATCAACAAG

Basic information

species Physcomitrella patens
transcript PP1S32_182V6.1
intron # 5
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|162246708|gb|FC424690.1|FC424690
EST:     ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAG                         GGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
genomic: ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAGgtataaaaca ... ttgtctacagGGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
EST: gi|162268251|gb|FC444540.1|FC444540
EST:     ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAG                         GGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
genomic: ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAGgtataaaaca ... ttgtctacagGGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
EST: gi|162158818|gb|FC335341.1|FC335341
EST:     ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAG                         GGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
genomic: ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAGgtataaaaca ... ttgtctacagGGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
EST: gi|162152941|gb|FC329243.1|FC329243
EST:     ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAG                         GGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
genomic: ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAGgtataaaaca ... ttgtctacagGGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
EST: gi|162172189|gb|FC348754.1|FC348754
EST:     ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAG                         GGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
genomic: ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAGgtataaaaca ... ttgtctacagGGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
EST: gi|162156021|gb|FC332188.1|FC332188
EST:     ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAG                         GGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
genomic: ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAGgtataaaaca ... ttgtctacagGGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
EST: gi|162197334|gb|FC372296.1|FC372296
EST:     ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAG                         GGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
genomic: ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAGgtataaaaca ... ttgtctacagGGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
EST: gi|162159618|gb|FC335796.1|FC335796
EST:     ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAG                         GGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
genomic: ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAGgtataaaaca ... ttgtctacagGGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
EST: gi|162162061|gb|FC338852.1|FC338852
EST:     ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAG                         GGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
genomic: ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAGgtataaaaca ... ttgtctacagGGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
EST: gi|162151213|gb|FC327693.1|FC327693
EST:     ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAG                         GGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
genomic: ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAGgtataaaaca ... ttgtctacagGGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
EST: gi|162164955|gb|FC342146.1|FC342146
EST:     ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAG                         GGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
genomic: ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAGgtataaaaca ... ttgtctacagGGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
EST: gi|162173783|gb|FC349959.1|FC349959
EST:     ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAG                         GGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
genomic: ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAGgtataaaaca ... ttgtctacagGGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
EST: gi|162151358|gb|FC327487.1|FC327487
EST:     ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAG                         GGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
genomic: ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAGgtataaaaca ... ttgtctacagGGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATC
EST: gi|162161280|gb|FC337343.1|FC337343
EST:     ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAG                         GGAAATGATGNCA-CTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCAT
genomic: ATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAGgtataaaaca ... ttgtctacagGGAAATGATG-CAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCAT

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), 34 (downstream exon)
Score: 74

AGAATTGTATTATGCTGGGAGTCATGGCATGGACATTCAGGGACCATCGAATATCTCTGATGGTTTTCGGGTGAAGGGAACCAAGTCCAGAGACAAGAAGgtataaaaca ... ttgtctacagGGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATCAACAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagttatctggtaattaccttcttcacacttaaccttttgttgtttgtctacagGGAAATGATGCAACTAACTTTCAGCCAGCCAGTGAATTTCTGCCGCTCATCAACAAG
                            acttaac  putative branch site (score: 74)
                                            tttgtct  putative PPT
            taatta  TA-rich tract