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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagaatgtttttgtaattcctttctatttgtgtacaatgtaatttgattttgtagttgggaagacttgtgttcaaattttgctgagcgttttttttcagGCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCAATGAAGGCTACTCTATCTGGTTTACCAGAGAAGACTTTTATGAAGATAA

Basic information

species Physcomitrella patens
transcript PP1S13_127V6.2
intron # 9
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|37848097|gb|BJ606105.1|BJ606105
EST:     CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACANTGAAGAACAG                         GCAGTGGAAAAATTTGGCGANGTAGATGTTTACACTTCGNCCTTTAGGCCA
genomic: CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAGgtgtgtgctt ... tttttttcagGCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
EST: gi|37844512|gb|BJ602520.1|BJ602520
EST:     CGGTGTTCACTCANCCTCCTATCGGAACAGTCGGTTACACTGAAGAACAG                         GCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
genomic: CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAGgtgtgtgctt ... tttttttcagGCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
EST: gi|162220508|gb|FC396045.1|FC396045
EST:     CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAG                         GCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
genomic: CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAGgtgtgtgctt ... tttttttcagGCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
EST: gi|162220509|gb|FC396046.1|FC396046
EST:     CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAG                         GCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
genomic: CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAGgtgtgtgctt ... tttttttcagGCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
EST: gi|162226395|gb|FC403311.1|FC403311
EST:     CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAG                         GCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
genomic: CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAGgtgtgtgctt ... tttttttcagGCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
EST: gi|37843971|gb|BJ601979.1|BJ601979
EST:     CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAG                         GCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
genomic: CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAGgtgtgtgctt ... tttttttcagGCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
EST: gi|37827821|gb|BJ585833.1|BJ585833
EST:     CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAG                         GCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
genomic: CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAGgtgtgtgctt ... tttttttcagGCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
EST: gi|37830683|gb|BJ588695.1|BJ588695
EST:     CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAG                         GCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
genomic: CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAGgtgtgtgctt ... tttttttcagGCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
EST: gi|37826872|gb|BJ584884.1|BJ584884
EST:     CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAG                         GCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
genomic: CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAGgtgtgtgctt ... tttttttcagGCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
EST: gi|208393557|gb|DC949719.1|DC949719
EST:     CAGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAG                         GCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
genomic: CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAGgtgtgtgctt ... tttttttcagGCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
EST: gi|162256496|gb|FC432527.1|FC432527
EST:     CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAG                         GCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
genomic: CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAGgtgtgtgctt ... tttttttcagGCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
EST: gi|37825350|gb|BJ583416.1|BJ583416
EST:     CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAG                         GCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
genomic: CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAGgtgtgtgctt ... tttttttcagGCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
EST: gi|67697363|gb|BJ957596.1|BJ957596
EST:     CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAG                         GCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
genomic: CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAGgtgtgtgctt ... tttttttcagGCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
EST: gi|208392896|gb|DC928582.1|DC928582
EST:     CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAG                         GCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
genomic: CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAGgtgtgtgctt ... tttttttcagGCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
EST: gi|37852204|gb|BJ610212.1|BJ610212
EST:     CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAG                         GCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA
genomic: CGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAGgtgtgtgctt ... tttttttcagGCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCA

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: 22 (upstream exon), 33 (downstream exon)
Score: 13

ATTTATTGCTTCAGCGGTGTTCACTCAACCTCCTATCGGAACAGTCGGTTACACTGAAGAACAGgtgtgtgctt ... tttttttcagGCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCAATGAAGGCTACTCTATCTGGTTTACCAGAGAAGACTTTTATGAAGATAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattttgtagttgggaagacttgtgttcaaattttgctgagcgttttttttcagGCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCAATGAAGGCTACTCTATCTGGTTTACCAGAGAAGACTTTTATGAAGATAA
 atttgat  putative branch site (score: 13)
                                          cgttttttttc  putative PPT
                          ttcaaatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagaatgtttttgtaattcctttctatttgtgtacaatgtaatttgattttgtagttgggaagacttgtgttcaaattttgctgagcgttttttttcagGCAGTGGAAAAATTTGGCGACGTAGATGTTTACACTTCGACCTTTAGGCCAATGAAGGCTACTCTATCTGGTTTACCAGAGAAGACTTTTATGAAGATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA