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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaagtattttgttggctacttttacatgctaaagtacctttccgttagaacagtatcatcttattgcggttgaaaaaattgaagtaagcactg...

Basic information

species Physcomitrella patens
transcript PP1S44_102V6.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 17
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 17
--CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaagtattttgttggctacttttacatgctaaagtacctttccgttagaacagtatca-tcttattgcggttgaaaaaattgaagtaagcactg---
  |||||||| || ||||| ||||||||||| ||||||||||| |||||   ||| || |||||| | ||||||||| | ||||| || |||||||   ||| |||  || |    |||     | ||  ||    |   |||    | |   | | |  | | | | ||  |     |  | || ||  |  |  || ||   
AGCTTGTTGGAAAGGATGCTTTGGCAGAAACGGATAAAATTACACTGGAGACTGCAAAGCTCTTGAGGGAGGACTATCTTGCTCAAAATGCTTTCACACCgtaagtggaaat----tgtacttaatttagaccccgtttggtagtgattctaaaaagcgtttttaatatttctaatacttgataatttttatcattcaatggta
















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|37836831|gb|BJ594839.1|BJ594839
EST:     GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC                         TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
genomic: GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
EST: gi|37838710|gb|BJ596718.1|BJ596718
EST:     GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC                         TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
genomic: GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
EST: gi|162276207|gb|FC452899.1|FC452899
EST:     GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC                         TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
genomic: GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
EST: gi|37845049|gb|BJ603057.1|BJ603057
EST:     GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC                         TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
genomic: GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
EST: gi|37838267|gb|BJ596275.1|BJ596275
EST:     GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC                         TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
genomic: GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
EST: gi|22131932|gb|BQ826891.1|BQ826891
EST:     GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC                         TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
genomic: GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
EST: gi|18337399|gb|BJ169423.1|BJ169423
EST:     GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC                         TTATGATAAATTNTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACA
genomic: GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATT-TTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACA
EST: gi|37852823|gb|BJ610831.1|BJ610831
EST:     GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC                         TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
genomic: GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
EST: gi|15327219|gb|BI487765.1|BI487765
EST:     GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC                         TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
genomic: GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
EST: gi|37848114|gb|BJ606122.1|BJ606122
EST:     GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC                         TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
genomic: GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
EST: gi|162276206|gb|FC452898.1|FC452898
EST:     GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC                         TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
genomic: GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
EST: gi|67578993|gb|BJ951144.1|BJ951144
EST:     GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC                         TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
genomic: GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
EST: gi|37834888|gb|BJ592900.1|BJ592900
EST:     GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC                         TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
genomic: GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
EST: gi|162186096|gb|FC361300.1|FC361300
EST:     GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC                         TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
genomic: GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
EST: gi|37846602|gb|BJ604610.1|BJ604610
EST:     GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC                         TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
genomic: GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
EST: gi|162258844|gb|FC434851.1|FC434851
EST:     GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC                         TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
genomic: GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
EST: gi|37853133|gb|BJ611141.1|BJ611141
EST:     GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC                         TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
genomic: GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
EST: gi|37822114|gb|BJ580180.1|BJ580180
EST:     GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC                         TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
genomic: GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
EST: gi|37834988|gb|BJ593000.1|BJ593000
EST:     GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC                         TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
genomic: GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
EST: gi|162239653|gb|FC418014.1|FC418014
EST:     GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC                         TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
genomic: GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
EST: gi|37848974|gb|BJ606982.1|BJ606982
EST:     GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC                         TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
genomic: GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
EST: gi|37850336|gb|BJ608344.1|BJ608344
EST:     GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC                         TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
genomic: GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
EST: gi|162179502|gb|FC356542.1|FC356542
EST:     GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCAC                         TTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT
genomic: GTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACAT

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: 31 (upstream exon), 34 (downstream exon)
Score: 12

CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaa ... tgggtggcagTTATGATAAATTTTGCCCATTTTATAAGTCGGTGTGGATGATGCGCAACATTGTCCACTTCAACACTCTTGCCAATCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGTTGGTAAAGATGCCTTGGCAGAAACAGATAAAATTACTCTGGAAGTTGCTAAACTCTTGCGTGAGGACTATTTGGCTCAGAACGCTTTCAGCACgtgagtttaagtattttgttggctacttttacatgctaaagtacctttccgttagaacagtatcatcttattgcggttgaaaaaattgaagtaagcactg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaaaaaa