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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGAAATCGATGTGCCTAACCTCCAGGTTATCAAGCTCATGCAGAGCTTCAAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtgtcgttttccctttaagcgccttgggatacgtgacatagttctggagcgttgtagtttcttttctttcttgtggttgtggtttggtcatct...

Basic information

species Physcomitrella patens
transcript PP1S18_236V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S18_236V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: AC209215.4_FGT006 (Zea mays), 5'ss of exon 3
--------------------------------------------CCG-AAATCGATGTGCCTAACCTCC--------AGGTTATCAAGCTCATGCAGAGCTTCAAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtgtcgttttccctttaagcgccttgggatacgtgacatagttctggagcgttgtagtttcttttctttcttgtggttgtggtttggtcatct
                                            ||| | ||||||||||| |||||||        |||| |||||||||||||||||||| ||||| |||||||| || | ||||| |||| ||||||   |||||||||  ||  |         |  ||    |  || |||                                                                   
AGGGCGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCCAACCTCCAGGACTCTAGgtgatcaagctcatgcagagctttaagtccaaggagtatgttagggagaccttctcctggcagtactactactactagtac-------ctcaccaacgatggcattg-------------------------------------------------------------------

upper sequence: PP1S18_236V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EDP00807 (Chlamydomonas reinhardtii), 5'ss of exon 2
CCGAAATCGATGTGCCTAACCTCCAGGTTATCAAGCTCATGCAGAGCTTCAAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtgtcgttttccctttaagcgccttgggatacgtgacatagttc-tggagcgttgtagtttcttttc-------tttcttgtggttgtggtttggtcatct--------------------------------------------------------------------------------------------
       ||  ||||| ||||| ||||| || |||||||||||||||||||||||  |||||   || |  |||  |||| ||||||||||||||||||||| ||  | |  |    | |     | |||  |||    |   |  ||  |  || ||  |||| |  |    |          |         |  | | ||| | |                                                                                            
AGATCCCCGGCGTGCCCAACCTGCAGGTCATTAAGCTCATGCAGAGCTTCAAGTCCCAGGAGCTGGTGACTGAGCGCTTCTCCTGGCGCCACTACTACTGgtgag-cgcgcggcacacacacacggggccgggggggggggcgccgagcgcgcggggcaatgtactaaccacgcagggcgacgccgcacacacattctctcgtcgtgtcccgcccagcatctaccgtcgcatccccactccccctcccgtccgcacaagcaccgacacacacgtatggtgttacatatctgcacatgtag
















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|18349905|gb|BJ181956.1|BJ181956
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|67725310|gb|BJ975569.1|BJ975569
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|208375780|gb|DC936720.1|DC936720
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|208371112|gb|DC931572.1|DC931572
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|18372406|gb|BJ204008.1|BJ204008
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|162272760|gb|FC448776.1|FC448776
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|18331191|gb|BJ163200.1|BJ163200
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|208376282|gb|DC902663.1|DC902663
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|37828875|gb|BJ586887.1|BJ586887
EST:     AAGTNTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTTACCTCAACCTTC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGAC-TTACCTCAACCTTC
EST: gi|67716791|gb|BJ967050.1|BJ967050
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|162243269|gb|FC415621.1|FC415621
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|67576412|gb|BJ949236.1|BJ949236
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|37848123|gb|BJ606131.1|BJ606131
EST:     AAGTNTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|67576638|gb|BJ949462.1|BJ949462
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|162251258|gb|FC428537.1|FC428537
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|37835544|gb|BJ593556.1|BJ593556
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|67703185|gb|BJ963418.1|BJ963418
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|56082280|gb|BJ199700.2|BJ199700
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|7147651|gb|AW509573.1|AW509573
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|162217304|gb|FC392044.1|FC392044
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|162272761|gb|FC448777.1|FC448777
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|67702781|gb|BJ963014.1|BJ963014
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|19776201|gb|BQ039045.1|BQ039045
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGATCTCCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|162251257|gb|FC428536.1|FC428536
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|162243268|gb|FC415620.1|FC415620
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|19776068|gb|BQ039029.1|BQ039029
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|208359824|gb|DC934853.1|DC934853
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|18352113|gb|BJ184167.1|BJ184167
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|37831800|gb|BJ589812.1|BJ589812
EST:     AAGTNTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
EST: gi|208388277|gb|DC956999.1|DC956999
EST:     AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTG                         GTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC
genomic: AAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCC

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), 31 (downstream exon)
Score: 37

CCGAAATCGATGTGCCTAACCTCCAGGTTATCAAGCTCATGCAGAGCTTCAAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtg ... tctttggcagGTACTTGACCAATGACGGCATTGAGCACCTCCGGACTTACCTCAACCTTCCATCTGAGATTGTCCCCGCTACTTTGAAGAAGTCTACTCGTCCCCCAAGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGAAATCGATGTGCCTAACCTCCAGGTTATCAAGCTCATGCAGAGCTTCAAGTCTAAGGAGTACGTCAAGGAGAACTTCGCCTGGCGCCACTACTACTGgtaagatgtgtcgttttccctttaagcgccttgggatacgtgacatagttctggagcgttgtagtttcttttctttcttgtggttgtggtttggtcatct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA