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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCGATTCAACTGTGGGAATTCATCCTACTGCAGCTGAAGAGCTCGTCACCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGGgtaagtgcatgcacttttgtttccttttagtgattttaactggcattataagctgggatttggggtctacgttattatgcattgtgatataatccgccgcaagttatggttatctaatgaagagaggataatcaagtcatcaatgctttaactttggcctcgacctttggcag

Basic information

species Physcomitrella patens
transcript PP1S13_127V6.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S13_127V6.2 (Physcomitrella patens), 5'ss of exon 11
lower sequence: Vv07s0141g00390.t01 (Vitis vinifera), 5'ss of exon 9
---GTTCGATTCAACTGTGGGAATTCATCCTACTGCAGCTGAAGAGCTCGTCACCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGGgtaagtg-catgcacttttgtttccttttagtgattttaactggcattataagctgggatttggggtctacgttattatgcattgtgatataatccgccgcaagttatggttatctaatgaagagaggataatcaagtcatcaatgctttaactttggcctcgacctttggcag
    || ||| | ||||||||||| || ||||||||||| || ||||| ||||| ||||| ||||| || ||||| ||  | || |  |||   | | | | |||  ||| ||  ||     |  || |||||  | || |       || |||  ||  |   ||     | |  |    |   ||  ||  | ||   || |          | | |||                                                        
AGACTTTGATGCCACTGTGGGAATCCACCCTACTGCAGCAGAGGAGCTTGTCACAATGAGGACTCCTACTCGGAAGATTCGAAACAGCTCT---CCACCCGAGgtttgtgtcagaca-----gaatctttttatcggttatt-----tatcatagacttagtcctg----ttgcactgacctat-ttaagaagtgatgaaccactgacc-----tgtttaaaa------------------------------------------------------
















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|37848097|gb|BJ606105.1|BJ606105
EST:     CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGG                         GGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
genomic: CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGGgtaagtgcat ... cctttggcagGGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
EST: gi|37844512|gb|BJ602520.1|BJ602520
EST:     CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTNTGAGCAAACTGGG                         GGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
genomic: CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGGgtaagtgcat ... cctttggcagGGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
EST: gi|162220508|gb|FC396045.1|FC396045
EST:     CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGG                         GGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
genomic: CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGGgtaagtgcat ... cctttggcagGGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
EST: gi|162220509|gb|FC396046.1|FC396046
EST:     CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGG                         GGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
genomic: CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGGgtaagtgcat ... cctttggcagGGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
EST: gi|162226395|gb|FC403311.1|FC403311
EST:     CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGG                         GGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
genomic: CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGGgtaagtgcat ... cctttggcagGGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
EST: gi|37843971|gb|BJ601979.1|BJ601979
EST:     CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGG                         GGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
genomic: CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGGgtaagtgcat ... cctttggcagGGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
EST: gi|37827821|gb|BJ585833.1|BJ585833
EST:     CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGG                         GGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
genomic: CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGGgtaagtgcat ... cctttggcagGGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
EST: gi|37830683|gb|BJ588695.1|BJ588695
EST:     CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGG                         GGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
genomic: CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGGgtaagtgcat ... cctttggcagGGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
EST: gi|37826872|gb|BJ584884.1|BJ584884
EST:     CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGG                         GGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
genomic: CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGGgtaagtgcat ... cctttggcagGGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
EST: gi|208393557|gb|DC949719.1|DC949719
EST:     CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGG                         GGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
genomic: CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGGgtaagtgcat ... cctttggcagGGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
EST: gi|67699357|gb|BJ959590.1|BJ959590
EST:     CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGG                         GGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
genomic: CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGGgtaagtgcat ... cctttggcagGGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
EST: gi|162256496|gb|FC432527.1|FC432527
EST:     CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGG                         GGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
genomic: CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGGgtaagtgcat ... cctttggcagGGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
EST: gi|37825350|gb|BJ583416.1|BJ583416
EST:     CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGG                         GGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
genomic: CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGGgtaagtgcat ... cctttggcagGGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
EST: gi|67697363|gb|BJ957596.1|BJ957596
EST:     CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGG                         GGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
genomic: CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGGgtaagtgcat ... cctttggcagGGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
EST: gi|7583130|gb|AW699294.1|AW699294
EST:     CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAACAAACTGGG                         GGAGATAAGGAANAGTCCGCTCCNGCGACATCAACGTATTAAATGATGGGC
genomic: CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGGgtaagtgcat ... cctttggcagGGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
EST: gi|208392896|gb|DC928582.1|DC928582
EST:     CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGG                         GGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
genomic: CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGGgtaagtgcat ... cctttggcagGGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
EST: gi|37852204|gb|BJ610212.1|BJ610212
EST:     CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGG                         GGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC
genomic: CCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGGgtaagtgcat ... cctttggcagGGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGC

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: 36

GTTCGATTCAACTGTGGGAATTCATCCTACTGCAGCTGAAGAGCTCGTCACCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGGgtaagtgcat ... cctttggcagGGAGATAAGGAAGAGTCCGCTCCGGCGACATCAGCGTATTAAATGATGGGCATTTGCCGTTTGTGTATTGATTCTCTCAATTAAATTAGATTTTTTTCCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCGATTCAACTGTGGGAATTCATCCTACTGCAGCTGAAGAGCTCGTCACCATGAGAACTCCCACACGGAAAATAAGGAAAAAGTCTGAGCAAACTGGGgtaagtgcatgcacttttgtttccttttagtgattttaactggcattataagctgggatttggggtctacgttattatgcattgtgatataatccgccgcaagttatggttatctaatgaagagaggataatcaagtcatcaatgctttaactttggcctcgacctttggcag

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