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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggtgcttttgttgggtcaggactggggttttgcgcatgttgtgtctgcattgttgcccgcgtctcgtgcagtgggtttcgatcaagggagtttatgtccgatgcagtcacgatgcactcagcatcttaattcaaccctaaaatgtttcgggtctcctcactcttggttggaatgttgttttgagcagGCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAGGGACGCAACGTCGTGCTTGAAAGTAAGTACGGGTCCCCCAAGATTGTGA

Basic information

species Physcomitrella patens
transcript PP1S276_75V6.1
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|208357238|gb|DC910649.1|DC910649
EST:     CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAG                         GCTGGAGTAGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
genomic: CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAGgtgggtgctt ... ttttgagcagGCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
EST: gi|162187015|gb|FC363421.1|FC363421
EST:     CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAG                         GCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
genomic: CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAGgtgggtgctt ... ttttgagcagGCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
EST: gi|18355188|gb|BJ187247.1|BJ187247
EST:     CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAG                         GCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
genomic: CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAGgtgggtgctt ... ttttgagcagGCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
EST: gi|18349489|gb|BJ181538.1|BJ181538
EST:     CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAG                         GCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
genomic: CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAGgtgggtgctt ... ttttgagcagGCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
EST: gi|18343197|gb|BJ175235.1|BJ175235
EST:     CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAG                         GCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
genomic: CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAGgtgggtgctt ... ttttgagcagGCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
EST: gi|18354362|gb|BJ186418.1|BJ186418
EST:     CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAG                         GCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
genomic: CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAGgtgggtgctt ... ttttgagcagGCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
EST: gi|67572411|gb|BJ945235.1|BJ945235
EST:     CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAG                         GCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
genomic: CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAGgtgggtgctt ... ttttgagcagGCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
EST: gi|67569513|gb|BJ942337.1|BJ942337
EST:     CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAG                         GCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
genomic: CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAGgtgggtgctt ... ttttgagcagGCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
EST: gi|18369385|gb|BJ201471.1|BJ201471
EST:     CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAG                         GCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
genomic: CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAGgtgggtgctt ... ttttgagcagGCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
EST: gi|56082257|gb|BJ176717.2|BJ176717
EST:     CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAG                         GCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
genomic: CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAGgtgggtgctt ... ttttgagcagGCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
EST: gi|18344268|gb|BJ176308.1|BJ176308
EST:     CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAG                         GCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
genomic: CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAGgtgggtgctt ... ttttgagcagGCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
EST: gi|18372339|gb|BJ203941.1|BJ203941
EST:     CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAG                         GCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
genomic: CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAGgtgggtgctt ... ttttgagcagGCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
EST: gi|18355098|gb|BJ187157.1|BJ187157
EST:     CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAG                         GCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
genomic: CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAGgtgggtgctt ... ttttgagcagGCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
EST: gi|18372360|gb|BJ203962.1|BJ203962
EST:     CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAG                         GCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
genomic: CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAGgtgggtgctt ... ttttgagcagGCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
EST: gi|100363541|gb|BY966441.1|BY966441
EST:     CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAG                         GCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
genomic: CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAGgtgggtgctt ... ttttgagcagGCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
EST: gi|18366797|gb|BJ198876.1|BJ198876
EST:     CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAG                         GCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG
genomic: CGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAGgtgggtgctt ... ttttgagcagGCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAG

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: 24 (upstream exon), 34 (downstream exon)
Score: 6

CGCGAAGTTGCAGAGGCAGCGGGTGGCGCATCGCTTGCCGGTCAAGGCTGCGAAGGAGCTTCATTTCAACAAGGATGGCTCCGCTATCAAGAGGATGCAGgtgggtgctt ... ttttgagcagGCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAGGGACGCAACGTCGTGCTTGAAAGTAAGTACGGGTCCCCCAAGATTGTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccctaaaatgtttcgggtctcctcactcttggttggaatgttgttttgagcagGCTGGAGTTGACAAGCTTGCGGATCTAGTCGGTGTCACTTTGGGACCCAAGGGACGCAACGTCGTGCTTGAAAGTAAGTACGGGTCCCCCAAGATTGTGA
                     tcctcac  putative branch site (score: 6)
                                          ttgtttt  putative PPT
     taaaatgttt  TA-rich tract