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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgcttgctgcaatgcatcaatttctcattctctcgtgttaattattcttgtgttttgttcttctctttgttctcagttcacaatgtaacgttgccataagaaggtattttggagaaaaagggttgacgtatcattggtggttattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCTTCATGAAAGGCAGGTTGTACCTTCATTTTACAGTTGAAGTCCCTGAGAG

Basic information

species Physcomitrella patens
transcript PP1S100_36V6.1
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|162167267|gb|FC342832.1|FC342832
EST:     GATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: GATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|208364176|gb|DC947280.1|DC947280
EST:     TGGGCGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACGTCACCTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|162175063|gb|FC351144.1|FC351144
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|162221417|gb|FC397226.1|FC397226
EST:     GGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: -GGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|162257999|gb|FC434093.1|FC434093
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|162258000|gb|FC434094.1|FC434094
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|37840042|gb|BJ598050.1|BJ598050
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|162167363|gb|FC343066.1|FC343066
EST:     AACTTCTGATTTAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: AACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|162180148|gb|FC356713.1|FC356713
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|162163669|gb|FC340281.1|FC340281
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|162185304|gb|FC360878.1|FC360878
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|162221418|gb|FC397227.1|FC397227
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAAATTCA-GGCTATNCA-TGACGAGGGCATGCCACATCACCTAAGGCC
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAA-TTCAAGGCTAT-CAATGACGAGGGCATGCCACATCACCTAAGGCC
EST: gi|162194543|gb|FC370766.1|FC370766
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|162185305|gb|FC360879.1|FC360879
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|162167364|gb|FC343067.1|FC343067
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|162258184|gb|FC433966.1|FC433966
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|208361192|gb|DC954298.1|DC954298
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|208387126|gb|DC941298.1|DC941298
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|162152659|gb|FC328326.1|FC328326
EST:     CAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: CAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|162180862|gb|FC358363.1|FC358363
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|162152282|gb|FC328469.1|FC328469
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|18340870|gb|BJ172901.1|BJ172901
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|100400617|gb|BY954563.1|BY954563
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|162167268|gb|FC342833.1|FC342833
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|162258183|gb|FC433965.1|FC433965
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|162184180|gb|FC360460.1|FC360460
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|37844413|gb|BJ602421.1|BJ602421
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACNTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|37853531|gb|BJ611539.1|BJ611539
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|162194542|gb|FC370765.1|FC370765
EST:     TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: TGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
EST: gi|162180861|gb|FC358362.1|FC358362
EST:     GCCCCCGGGGAGATTATCAAGCCAG                         GTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT
genomic: GCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCT

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), 34 (downstream exon)
Score: 36

AGCCTCACAGAAGCTTTGTGTGGTTTCCAATTCCCACTCACACACCTTGATGGACGGCAACTTCTGATTAAGTCAGCCCCCGGGGAGATTATCAAGCCAGgtatttgctt ... tattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCTTCATGAAAGGCAGGTTGTACCTTCATTTTACAGTTGAAGTCCCTGAGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagaaggtattttggagaaaaagggttgacgtatcattggtggttattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCTTCATGAAAGGCAGGTTGTACCTTCATTTTACAGTTGAAGTCCCTGAGAG
                        ggttgac  putative branch site (score: 36)
                                            ttattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgcttgctgcaatgcatcaatttctcattctctcgtgttaattattcttgtgttttgttcttctctttgttctcagttcacaatgtaacgttgccataagaaggtattttggagaaaaagggttgacgtatcattggtggttattgttcagGTCAATTCAAGGCTATCAATGACGAGGGCATGCCACATCACCTAAGGCCCTTCATGAAAGGCAGGTTGTACCTTCATTTTACAGTTGAAGTCCCTGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG