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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGTACGATGCGACGTGTCGAATGCATCTGATGTTGCTGCCTTGGCTTCTTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTGgtaatttttgatcttgtccaagttgtcctcctttagtgtccgccctagctcaagatattaatcatttctactcactcattggcttctaagtaactcatacacattcatctcatgatgtagttgcacatagctatgttatctaacctcatgagttcggatgtttgtag

Basic information

species Physcomitrella patens
transcript PP1S100_87V6.1
intron # 2
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|162193967|gb|FC371780.1|FC371780
EST:     TTTCGCAGCTGAGAAACTGGGAACCATTCACTTCTGGATTAACAATGCTG                         GAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
genomic: TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTGgtaatttttg ... atgtttgtagGAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
EST: gi|162175019|gb|FC351126.1|FC351126
EST:     TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTG                         GAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
genomic: TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTGgtaatttttg ... atgtttgtagGAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
EST: gi|208357676|gb|DC934128.1|DC934128
EST:     TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTG                         GAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
genomic: TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTGgtaatttttg ... atgtttgtagGAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
EST: gi|162165461|gb|FC340572.1|FC340572
EST:     TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTG                         GAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
genomic: TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTGgtaatttttg ... atgtttgtagGAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
EST: gi|67508113|gb|BJ940984.1|BJ940984
EST:     TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTG                         GAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
genomic: TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTGgtaatttttg ... atgtttgtagGAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
EST: gi|208354101|gb|DC902399.1|DC902399
EST:     TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTG                         GAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
genomic: TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTGgtaatttttg ... atgtttgtagGAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
EST: gi|162177445|gb|FC353706.1|FC353706
EST:     TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTG                         GAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
genomic: TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTGgtaatttttg ... atgtttgtagGAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
EST: gi|37850620|gb|BJ608628.1|BJ608628
EST:     TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTG                         GAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
genomic: TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTGgtaatttttg ... atgtttgtagGAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
EST: gi|208396220|gb|DC924014.1|DC924014
EST:     TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTG                         GAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
genomic: TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTGgtaatttttg ... atgtttgtagGAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
EST: gi|100393457|gb|BY953408.1|BY953408
EST:     TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTG                         GAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
genomic: TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTGgtaatttttg ... atgtttgtagGAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
EST: gi|208376855|gb|DC906824.1|DC906824
EST:     TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTG                         GAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
genomic: TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTGgtaatttttg ... atgtttgtagGAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
EST: gi|162193968|gb|FC371781.1|FC371781
EST:     TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTG                         GAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
genomic: TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTGgtaatttttg ... atgtttgtagGAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
EST: gi|208353205|gb|DC910172.1|DC910172
EST:     TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTG                         GAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG
genomic: TTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTGgtaatttttg ... atgtttgtagGAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTG

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: 31 (upstream exon), 18 (downstream exon)
Score: 5

GGAGTACGATGCGACGTGTCGAATGCATCTGATGTTGCTGCCTTGGCTTCTTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTGgtaatttttg ... atgtttgtagGAGAAGTGACAGGCAAGAAACTCCTGGCAGATGTGGATGCTGAGGAAATTGTTAGGGTAAGCGGAACAAACGTGGTGGGGTCGTTGTTGTGCTGCAGAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGTACGATGCGACGTGTCGAATGCATCTGATGTTGCTGCCTTGGCTTCTTTCGCAGCTGAGAAACTTGGAACCATTCACTTCTGGATTAACAATGCTGgtaatttttgatcttgtccaagttgtcctcctttagtgtccgccctagctcaagatattaatcatttctactcactcattggcttctaagtaactcatacacattcatctcatgatgtagttgcacatagctatgttatctaacctcatgagttcggatgtttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG