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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catctcttcattagtgttctggttcacatcaccatatgtgtatcagaaatatttactcaagctcgtaccatgtcctcaattttcatgctgtcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCTCGCTATCAACGAG

Basic information

species Physcomitrella patens
transcript PP1S74_193V6.2
intron # 2
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|162253736|gb|FC429850.1|FC429850
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|37835110|gb|BJ593122.1|BJ593122
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|162200202|gb|FC376074.1|FC376074
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|162275357|gb|FC451541.1|FC451541
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|67727870|gb|BJ978129.1|BJ978129
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|37828224|gb|BJ586236.1|BJ586236
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|162232758|gb|FC408165.1|FC408165
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|162236236|gb|FC412005.1|FC412005
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|162259564|gb|FC435491.1|FC435491
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|22492309|gb|BU052232.1|BU052232
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|162209172|gb|FC385391.1|FC385391
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|162259565|gb|FC435492.1|FC435492
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|162274918|gb|FC450569.1|FC450569
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|37843558|gb|BJ601566.1|BJ601566
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|162271402|gb|FC446975.1|FC446975
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|162212767|gb|FC388567.1|FC388567
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|18349284|gb|BJ181333.1|BJ181333
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|22132063|gb|BQ826960.1|BQ826960
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|162238997|gb|FC418463.1|FC418463
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|67719603|gb|BJ969862.1|BJ969862
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|162213098|gb|FC389522.1|FC389522
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|162200201|gb|FC376073.1|FC376073
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|67727046|gb|BJ977305.1|BJ977305
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|162277946|gb|FC454077.1|FC454077
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
EST: gi|162253737|gb|FC429851.1|FC429851
EST:     CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTG                         GTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT
genomic: CGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCT

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), 35 (downstream exon)
Score: 109

TGGTTGGGCGGGCCCTTCCTACCGCGACCAATGAGACACCTAAGGCTTACCGCATGAAGCTCTGGGCCACCAACGAAGTGCGCGCCAAGTCTAAGTTCTGgtatggtgtt ... tcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCTCGCTATCAACGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaatatttactcaagctcgtaccatgtcctcaattttcatgctgtcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCTCGCTATCAACGAG
                                          ctgtctt  CT-rich tract
                                aattttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catctcttcattagtgttctggttcacatcaccatatgtgtatcagaaatatttactcaagctcgtaccatgtcctcaattttcatgctgtcttgtgcagGTATTTCCTCAGGAAGTTGCAGAAAGTCAAGAAGGCCCACGGTCAACTTCTCGCTATCAACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG