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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCTACAAAAAAAAGCCAAAAGGCGTTTGTGCATGTTGCCTCTGAGATTGGAGCCTACGAGGCCGAGGAAATTGgtgtgtattcactaccatcaaacgttttctgtgatcttccacattcagacctgaatgttgttaatttgaaataactgtctttatgtcagcgtcaatagaa...

Basic information

species Physcomitrella patens
transcript PP1S197_115V6.1
intron # 5
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|208351962|gb|DC925771.1|DC925771
EST:     GTTTGTGCATGTTGCCTCTGAGATTGGAGCCTACGAGGCCGAGGAAATTG                         GTGTGGAACATTTGTTAAGGGATGTGAAGGATGCGACCATCAGCACTCTTG
genomic: GTTTGTGCATGTTGCCTCTGAGATTGGAGCCTACGAGGCCGAGGAAATTGgtgtgtattc ... tcgtgtgcagGTGTGGAACATTTGTTAAGGGATGTGAAGGATGCGACCATCAGCACTCTTG
EST: gi|162212343|gb|FC388071.1|FC388071
EST:     GTTTGTGCATGTTGCCTCTGAGATTGGAGCCTACGAGGCCGAGGAAATTG                         GTGTGGAACATTTGTTAAGGGATGTGAAGGATGCGACCATCAGCACTCTTG
genomic: GTTTGTGCATGTTGCCTCTGAGATTGGAGCCTACGAGGCCGAGGAAATTGgtgtgtattc ... tcgtgtgcagGTGTGGAACATTTGTTAAGGGATGTGAAGGATGCGACCATCAGCACTCTTG
EST: gi|208368978|gb|DC955063.1|DC955063
EST:     GTTTGTGCATGTTGCCTCTGAGATTGGAGCCTACGAGGCCGAGGAAATTG                         GTGTGGAACATTTGTTAAGGGATGTGAAGGATGCGACCATCAGCACTCTTG
genomic: GTTTGTGCATGTTGCCTCTGAGATTGGAGCCTACGAGGCCGAGGAAATTGgtgtgtattc ... tcgtgtgcagGTGTGGAACATTTGTTAAGGGATGTGAAGGATGCGACCATCAGCACTCTTG
EST: gi|162212342|gb|FC388070.1|FC388070
EST:     GTTTGTGCATGTTGCCTCTGAGATTGGAGCCTACGAGGCCGAGGAAATTG                         GTGTGGAACATTTGTTAAGGGATGTGAAGGATGCGACCATCAGCACTCTTG
genomic: GTTTGTGCATGTTGCCTCTGAGATTGGAGCCTACGAGGCCGAGGAAATTGgtgtgtattc ... tcgtgtgcagGTGTGGAACATTTGTTAAGGGATGTGAAGGATGCGACCATCAGCACTCTTG
EST: gi|100398742|gb|BY990493.1|BY990493
EST:     GTTTGTGCATGTTGCCTCTGAGATTGGAGCCTACGAGGCCGAGGAAATTG                         GTGTGGAACATTTGTTAAGGG
genomic: GTTTGTGCATGTTGCCTCTGAGATTGGAGCCTACGAGGCCGAGGAAATTGgtgtgtattc ... tcgtgtgcagGTGTGGAACATTTGTTAAGGG
EST: gi|100362914|gb|BY947592.1|BY947592
EST:     TTTGTGCATGTTGCCTCTGAGATTGGAGCCTACGAGGCCCGAG-AAATTG                         GTGTGGAACATTTTGT-AAGGGATGTGA-GGNATGCGACCATCAGCACTCT
genomic: TTTGTGCATGTTGCCTCTGAGATTGGAGCCTACGAGGCC-GAGGAAATTGgtgtgtattc ... tcgtgtgcagGTGTGGAACATTT-GTTAAGGGATGTGAAGG-ATGCGACCATCAGCACTCT
EST: gi|208371459|gb|DC955795.1|DC955795
EST:     GTTTGTGCATGTTGCCTCTGAGATTGGAGCCTACGAGGCCGAGGAAATTG                         GTGTGGAACATTTGTTAAGGGATGTGAAGGATGCGACCATCAGCACTCTTG
genomic: GTTTGTGCATGTTGCCTCTGAGATTGGAGCCTACGAGGCCGAGGAAATTGgtgtgtattc ... tcgtgtgcagGTGTGGAACATTTGTTAAGGGATGTGAAGGATGCGACCATCAGCACTCTTG
EST: gi|37826136|gb|BJ584148.1|BJ584148
EST:     GTTTGTGCATGTTGCCTCTGAGATTGGAGCCTACGAGGCCGAGGAAATTG                         GTGTGGAACATTTGTTAAGGGATGTGAAGGATGCGACCATCAGCACTCTTG
genomic: GTTTGTGCATGTTGCCTCTGAGATTGGAGCCTACGAGGCCGAGGAAATTGgtgtgtattc ... tcgtgtgcagGTGTGGAACATTTGTTAAGGGATGTGAAGGATGCGACCATCAGCACTCTTG

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: 17

GATGCTACAAAAAAAAGCCAAAAGGCGTTTGTGCATGTTGCCTCTGAGATTGGAGCCTACGAGGCCGAGGAAATTGgtgtgtattc ... tcgtgtgcagGTGTGGAACATTTGTTAAGGGATGTGAAGGATGCGACCATCAGCACTCTTGCTACCGAG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGCTACAAAAAAAAGCCAAAAGGCGTTTGTGCATGTTGCCTCTGAGATTGGAGCCTACGAGGCCGAGGAAATTGgtgtgtattcactaccatcaaacgttttctgtgatcttccacattcagacctgaatgttgttaatttgaaataactgtctttatgtcagcgtcaatagaa

- - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG