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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataaatacttctgtttgttaatgatagcactttgtgaacgggtcacatttcaattgctgtgaactcccgcatatcctgcaactcctgcttatggcttagtttcgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTGTACTTGAAG

Basic information

species Physcomitrella patens
transcript PP1S396_19V6.1
intron # 3
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|13250572|gb|BG361475.1|BG361475
EST:     TTTAATAACTACAG                         GCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGCTTTTGGTACTG
genomic: TTTAATAACTACAGgtataaatac ... cgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
EST: gi|67700053|gb|BJ960286.1|BJ960286
EST:     GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAG                         GCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
genomic: GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAGgtataaatac ... cgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
EST: gi|37848806|gb|BJ606814.1|BJ606814
EST:     GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAG                         GCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
genomic: GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAGgtataaatac ... cgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
EST: gi|208382420|gb|DC927954.1|DC927954
EST:     GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAG                         GCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
genomic: GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAGgtataaatac ... cgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
EST: gi|162168540|gb|FC344464.1|FC344464
EST:     GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAG                         GCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
genomic: GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAGgtataaatac ... cgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
EST: gi|18338396|gb|BJ170420.1|BJ170420
EST:     AACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTNCAG                         GCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
genomic: AACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAGgtataaatac ... cgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
EST: gi|18338416|gb|BJ170440.1|BJ170440
EST:     GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAG                         GCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
genomic: GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAGgtataaatac ... cgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
EST: gi|208376481|gb|DC918926.1|DC918926
EST:     GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAG                         GCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
genomic: GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAGgtataaatac ... cgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
EST: gi|208367432|gb|DC951322.1|DC951322
EST:     GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAG                         GCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
genomic: GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAGgtataaatac ... cgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
EST: gi|162171130|gb|FC347744.1|FC347744
EST:     GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAG                         GCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
genomic: GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAGgtataaatac ... cgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
EST: gi|208399882|gb|DC925178.1|DC925178
EST:     GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAG                         GCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
genomic: GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAGgtataaatac ... cgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
EST: gi|67695658|gb|BJ955891.1|BJ955891
EST:     GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAG                         GCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
genomic: GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAGgtataaatac ... cgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
EST: gi|162171129|gb|FC347743.1|FC347743
EST:     GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAG                         GCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
genomic: GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAGgtataaatac ... cgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
EST: gi|37848739|gb|BJ606747.1|BJ606747
EST:     GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAG                         GCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
genomic: GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAGgtataaatac ... cgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
EST: gi|37851042|gb|BJ609050.1|BJ609050
EST:     GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAG                         GCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
genomic: GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAGgtataaatac ... cgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
EST: gi|162178738|gb|FC353981.1|FC353981
EST:     GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAG                         GCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
genomic: GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAGgtataaatac ... cgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
EST: gi|67696672|gb|BJ956905.1|BJ956905
EST:     GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAG                         GCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
genomic: GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAGgtataaatac ... cgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
EST: gi|162254580|gb|FC429430.1|FC429430
EST:     GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAG                         GCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
genomic: GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAGgtataaatac ... cgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
EST: gi|162178739|gb|FC353982.1|FC353982
EST:     GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAG                         GCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
genomic: GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAGgtataaatac ... cgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
EST: gi|208362717|gb|DC947180.1|DC947180
EST:     GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAG                         GCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
genomic: GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAGgtataaatac ... cgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
EST: gi|37844953|gb|BJ602961.1|BJ602961
EST:     GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAG                         GCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
genomic: GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAGgtataaatac ... cgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
EST: gi|208356943|gb|DC922279.1|DC922279
EST:     GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAG                         GCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG
genomic: GATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAGgtataaatac ... cgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTG

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-Seq library.


Block sizes: 20 (upstream exon), 34 (downstream exon)
Score: 6

AGACCTGGCACGGTCTCCCTTTGCCTATCAGAAAATGACGACGAAGAAGCGATCAAACTTAATACAGACTACCGGAACGTGGAGTTTTTAATAACTACAGgtataaatac ... cgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTGTACTTGAAG































 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgaactcccgcatatcctgcaactcctgcttatggcttagtttcgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTGTACTTGAAG
                                      ttagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtataaatacttctgtttgttaatgatagcactttgtgaacgggtcacatttcaattgctgtgaactcccgcatatcctgcaactcctgcttatggcttagtttcgggtgtcagGCCCCGGACCTGCCCCTCAGCTGGACAACGGGAACATCGTTTTTGGTACTGTACTTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG