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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgggtttacttgagattgtttgtcaattaccttagtattcatcatgacatttgctacgaacaagtgatgatacggagaaggtagtgattaatgtgggggtaccttgaacgccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTTGATGAGAAGAAAGCAGTACTGGAGTCTTTGTTGTCTATAAGGCGAGCTG

Basic information

species Physcomitrella patens
transcript PP1S450_21V6.2
intron # 11
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|208357191|gb|DC926538.1|DC926538
EST:     TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAG                         GTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
genomic: TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
EST: gi|7583276|gb|AW699440.1|AW699440
EST:     TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAG                         GTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
genomic: TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
EST: gi|162218487|gb|FC395064.1|FC395064
EST:     TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAG                         GTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
genomic: TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
EST: gi|208353431|gb|DC918487.1|DC918487
EST:     TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAG                         GTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
genomic: TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
EST: gi|162234869|gb|FC410642.1|FC410642
EST:     TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAG                         GTCTCAGGAGAGTATTCTATGATTAAAGCAGCTGCTGCTGCAGGCATGCTT
genomic: TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
EST: gi|37828958|gb|BJ586970.1|BJ586970
EST:     TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAG                         GTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
genomic: TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
EST: gi|162219726|gb|FC395930.1|FC395930
EST:     TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAG                         GTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
genomic: TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
EST: gi|162185929|gb|FC361029.1|FC361029
EST:     TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAG                         GTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
genomic: TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
EST: gi|37852710|gb|BJ610718.1|BJ610718
EST:     TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAG                         GTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
genomic: TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
EST: gi|162268622|gb|FC443676.1|FC443676
EST:     TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAG                         GTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
genomic: TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
EST: gi|162232564|gb|FC408400.1|FC408400
EST:     TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAG                         GTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
genomic: TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
EST: gi|162184165|gb|FC359639.1|FC359639
EST:     TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAG                         GTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
genomic: TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
EST: gi|162176322|gb|FC353507.1|FC353507
EST:     TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATTTCAGCCTATCAG                         GTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
genomic: TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
EST: gi|208397366|gb|DC916320.1|DC916320
EST:     TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAG                         GTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
genomic: TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
EST: gi|37827165|gb|BJ585177.1|BJ585177
EST:     TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAG                         GTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
genomic: TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
EST: gi|37822149|gb|BJ580215.1|BJ580215
EST:     TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAG                         GTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
genomic: TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
EST: gi|208380828|gb|DC923310.1|DC923310
EST:     TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAG                         GTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
genomic: TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
EST: gi|67727441|gb|BJ977700.1|BJ977700
EST:     TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAG                         GTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
genomic: TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
EST: gi|162265940|gb|FC442943.1|FC442943
EST:     TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAG                         GTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
genomic: TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
EST: gi|208388243|gb|DC945575.1|DC945575
EST:     TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAG                         GTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
genomic: TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
EST: gi|162232563|gb|FC408399.1|FC408399
EST:     TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATTTCAGCCTATCAG                         GTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
genomic: TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
EST: gi|37821562|gb|BJ579628.1|BJ579628
EST:     TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAG                         GTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
genomic: TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
EST: gi|162227004|gb|FC403361.1|FC403361
EST:     TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATTTCAGCCTATCAG                         GTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT
genomic: TCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTT

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: 11 (upstream exon), 33 (downstream exon)
Score: 4

GTTAAGCCTGCCATGCCCTACCTGGACGTCATCAGGCTTTTGCGCGACAACACCGCATTGCCTATCTCAGCCTATCAGgtatgtgggt ... gccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTTGATGAGAAGAAAGCAGTACTGGAGTCTTTGTTGTCTATAAGGCGAGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgatacggagaaggtagtgattaatgtgggggtaccttgaacgccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTTGATGAGAAGAAAGCAGTACTGGAGTCTTTGTTGTCTATAAGGCGAGCTG
                     gattaat  putative branch site (score: 4)
                                              ccttgcc  putative PPT
                    tgattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgggtttacttgagattgtttgtcaattaccttagtattcatcatgacatttgctacgaacaagtgatgatacggagaaggtagtgattaatgtgggggtaccttgaacgccttgccagGTCTCAGGAGAGTATTCTATGATCAAAGCAGCTGCTGCTGCAGGCATGCTTGATGAGAAGAAAGCAGTACTGGAGTCTTTGTTGTCTATAAGGCGAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA