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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttttctacgcttgccagttcacaatacaggagtgatatgtcaaagaccgattaatggagtatgtgaatgataaacttgtggttagtaaatggtgcagGATTTTCGACTACGGAACACAAAGACGTATGAAGAGTGGTACAATGGACCCCATCGTGCTCCTAAGCTACAG

Basic information

species Physcomitrella patens
transcript PP1S101_184V6.1
intron # 5
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|162261824|gb|FC438348.1|FC438348
EST:     AGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG                         GATTTTCGACTACGGAACACAAAGACGTATGAAGAGTGGTACAATGGACCC
genomic: AGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCGgtaagcaata ... aatggtgcagGATTTTCGACTACGGAACACAAAGACGTATGAAGAGTGGTACAATGGACCC
EST: gi|162265711|gb|FC443117.1|FC443117
EST:     AGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG                         GATTTTCGACTACGGAACACAAAGACGTATGAAGAGTGGTACAATGGACCC
genomic: AGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCGgtaagcaata ... aatggtgcagGATTTTCGACTACGGAACACAAAGACGTATGAAGAGTGGTACAATGGACCC
EST: gi|100427283|gb|BY959068.1|BY959068
EST:     AGATAATTGCAGCTCTTCCGGACTACTTGAAGGGTGTAGATCTTTCAGCG                         GAATTTCGACTACGGAAACACAA-GACGTATGAA
genomic: AGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCGgtaagcaata ... aatggtgcagGATTTTCGACTACGGAA-CACAAAGACGTATGAA
EST: gi|100365102|gb|BY966811.1|BY966811
EST:     AGATAATTGCAGCTCTTCCGGACTACTTGAAGGGTGTAGATCTTTCAGCG                         GATTTTCGACTACGGAACACAAAGACGTATGAAGAGTGGTACAATGGACCC
genomic: AGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCGgtaagcaata ... aatggtgcagGATTTTCGACTACGGAACACAAAGACGTATGAAGAGTGGTACAATGGACCC
EST: gi|162179978|gb|FC356049.1|FC356049
EST:     AGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG                         GATTTTCGACTACGGAACACAAAGACGTATGAAGAGTGGTACAATGGACCC
genomic: AGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCGgtaagcaata ... aatggtgcagGATTTTCGACTACGGAACACAAAGACGTATGAAGAGTGGTACAATGGACCC
EST: gi|162168515|gb|FC344452.1|FC344452
EST:     AGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG                         GATTTTCGACTACGGAACACANAGACGTATGAAGAGTGGTACAATGGACCC
genomic: AGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCGgtaagcaata ... aatggtgcagGATTTTCGACTACGGAACACAAAGACGTATGAAGAGTGGTACAATGGACCC
EST: gi|100431865|gb|BY978545.1|BY978545
EST:     GATAATTGCAGCTCTTCCGGACTACTTGAAGGNNTGTAGATCTT-CAGCG                         GATTTTCGACTACGGAACACAAAGACGTATGAAGAGT
genomic: GATAATTGCAGCTCTTCCGGACTACTTGAAGGT-TGTAGATCTTTCAGCGgtaagcaata ... aatggtgcagGATTTTCGACTACGGAACACAAAGACGTATGAAGAGT
EST: gi|67508394|gb|BJ941261.1|BJ941261
EST:     AGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG                         GATTTTCGACTACGGAACACAAAGACGTATGAAGA
genomic: AGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCGgtaagcaata ... aatggtgcagGATTTTCGACTACGGAACACAAAGACGTATGAAGA
EST: gi|100379495|gb|BY949797.1|BY949797
EST:     GATAATTGCAGCTCTTCCGGACTACTTTGA-GGTTGTAGATCTTTCAGCG                         GATTTTCGACTACGGAACACAAAGACGTATGAAGAGTGGNTACA-TGGACC
genomic: GATAATTGCAGCTCTTCCGGACTACTT-GAAGGTTGTAGATCTTTCAGCGgtaagcaata ... aatggtgcagGATTTTCGACTACGGAACACAAAGACGTATGAAGAGTGG-TACAATGGACC
EST: gi|162234961|gb|FC411748.1|FC411748
EST:     AGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG                         GATTTTCGACTACGGAACACAAAGACGTATGAAGAGTGGTACAATGGACCC
genomic: AGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCGgtaagcaata ... aatggtgcagGATTTTCGACTACGGAACACAAAGACGTATGAAGAGTGGTACAATGGACCC
EST: gi|162261823|gb|FC438347.1|FC438347
EST:     CTAC-TGAAGGGTNGTAGATCTTTCAGCG                         GATTTTCGACTACGGAACACAAAGACGTATGAAGAGTGGTACAATGGACCC
genomic: CTACTTGAA-GGTTGTAGATCTTTCAGCGgtaagcaata ... aatggtgcagGATTTTCGACTACGGAACACAAAGACGTATGAAGAGTGGTACAATGGACCC
EST: gi|100449342|gb|CJ973641.1|CJ973641
EST:     AGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCANCG                         GATTT-CGACTACGGAACACAAAGACNTATGAA
genomic: AGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCGgtaagcaata ... aatggtgcagGATTTTCGACTACGGAACACAAAGACGTATGAA
EST: gi|100389059|gb|BY952263.1|BY952263
EST:     AGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCG                         GATTTTCGACTACGGAACACAAAGACGTATGAGGAGTGGTACAATGGACCC
genomic: AGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCGgtaagcaata ... aatggtgcagGATTTTCGACTACGGAACACAAAGACGTATGAAGAGTGGTACAATGGACCC

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), 24 (downstream exon)
Score: 13

GAGATAATTGCAGCTCTTCCGGACTACTTGAAGGTTGTAGATCTTTCAGCGgtaagcaata ... aatggtgcagGATTTTCGACTACGGAACACAAAGACGTATGAAGAGTGGTACAATGGACCCCATCGTGCTCCTAAGCTACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaccgattaatggagtatgtgaatgataaacttgtggttagtaaatggtgcagGATTTTCGACTACGGAACACAAAGACGTATGAAGAGTGGTACAATGGACCCCATCGTGCTCCTAAGCTACAG
      gattaat  putative branch site (score: 13)
                       aatgataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgttttctacgcttgccagttcacaatacaggagtgatatgtcaaagaccgattaatggagtatgtgaatgataaacttgtggttagtaaatggtgcagGATTTTCGACTACGGAACACAAAGACGTATGAAGAGTGGTACAATGGACCCCATCGTGCTCCTAAGCTACAG

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