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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcttgtgaaaatcatgtttcttatgtgatcctgtgtatctaatggtttttaggtataagcattgctctgaatgaaattacttttgtttgacactgtagGATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAG

Basic information

species Physcomitrella patens
transcript PP1S84_76V6.1
intron # 6
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|37851942|gb|BJ609950.1|BJ609950
EST:     CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAG                         GATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
genomic: CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAGgtatgaatct ... gacactgtagGATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
EST: gi|208360945|gb|DC946634.1|DC946634
EST:     CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAG                         GATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
genomic: CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAGgtatgaatct ... gacactgtagGATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
EST: gi|162182473|gb|FC357448.1|FC357448
EST:     CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAG                         GATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
genomic: CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAGgtatgaatct ... gacactgtagGATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
EST: gi|18339266|gb|BJ171293.1|BJ171293
EST:     CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAG                         GATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
genomic: CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAGgtatgaatct ... gacactgtagGATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
EST: gi|162258880|gb|FC434887.1|FC434887
EST:     CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAG                         GATGATCTAGACAACGTCACTCGGTTTTTAATGCTCGCTCGAGAACCTATC
genomic: CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAGgtatgaatct ... gacactgtagGATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
EST: gi|208372438|gb|DC952282.1|DC952282
EST:     CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAG                         GATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
genomic: CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAGgtatgaatct ... gacactgtagGATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
EST: gi|37847781|gb|BJ605789.1|BJ605789
EST:     CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAG                         GATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
genomic: CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAGgtatgaatct ... gacactgtagGATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
EST: gi|208375291|gb|DC945018.1|DC945018
EST:     CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAG                         GATGATCTAGACAACGTCACTCGGTTTCTAACGCTCGCTCGAGAACCTATC
genomic: CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAGgtatgaatct ... gacactgtagGATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
EST: gi|18334585|gb|BJ166602.1|BJ166602
EST:     CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAG                         GATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
genomic: CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAGgtatgaatct ... gacactgtagGATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
EST: gi|208365784|gb|DC951047.1|DC951047
EST:     CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAG                         GATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
genomic: CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAGgtatgaatct ... gacactgtagGATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
EST: gi|18334591|gb|BJ166608.1|BJ166608
EST:     CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAG                         GATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
genomic: CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAGgtatgaatct ... gacactgtagGATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
EST: gi|18334132|gb|BJ166148.1|BJ166148
EST:     GATGGCTTACAG                         GATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
genomic: GATGGCTTACAGgtatgaatct ... gacactgtagGATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
EST: gi|208372580|gb|DC952357.1|DC952357
EST:     CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAG                         GATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
genomic: CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAGgtatgaatct ... gacactgtagGATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
EST: gi|18340558|gb|BJ172586.1|BJ172586
EST:     CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAG                         GATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
genomic: CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAGgtatgaatct ... gacactgtagGATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
EST: gi|15320383|gb|BI488392.1|BI488392
EST:     CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAG                         GATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
genomic: CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAGgtatgaatct ... gacactgtagGATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
EST: gi|162182472|gb|FC357447.1|FC357447
EST:     CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAG                         GATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
genomic: CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAGgtatgaatct ... gacactgtagGATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
EST: gi|162196646|gb|FC374936.1|FC374936
EST:     CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAG                         GATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
genomic: CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAGgtatgaatct ... gacactgtagGATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
EST: gi|208367467|gb|DC955675.1|DC955675
EST:     CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAG                         GATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
genomic: CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAGgtatgaatct ... gacactgtagGATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
EST: gi|37842276|gb|BJ600284.1|BJ600284
EST:     CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAG                         GATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC
genomic: CACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAGgtatgaatct ... gacactgtagGATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATC

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: 30 (upstream exon), 35 (downstream exon)
Score: 17

TTCATTGCCGCTCATAAATTGAAGGACACAGGAGCTGTTGCAAGTGCACGGGCTGCAGAAATATATGGGCTGGAAATCCTAGTGGATGGCTTACAGgtatgaatct ... gacactgtagGATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtttttaggtataagcattgctctgaatgaaattacttttgtttgacactgtagGATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAG
                                         gtttgac  putative branch site (score: 17)
                          aatgaaattactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attcttgtgaaaatcatgtttcttatgtgatcctgtgtatctaatggtttttaggtataagcattgctctgaatgaaattacttttgtttgacactgtagGATGATCTAGACAACGTCACTCGGTTTCTAATGCTCGCTCGAGAACCTATCATTCCAAGAACTGACAGACCATTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC