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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgactcaaggtttcccatcgcttcacggtactacccagataggacactgaagggataaaaaacttatgttcaactcagccacagccaatttgagttgctaataaatgatagattgttccttagtctcatgcttcattaacattaaatgacattggtcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAGTTGAATCGGTACATTCCCACTGCAGCTGCCTTTGGAGGTATCTGTATTG

Basic information

species Physcomitrella patens
transcript PP1S114_48V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S114_48V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA12G35990.1 (Glycine max), 3'ss of exon 6
gtatgtgactcaaggtttcccatcgcttcacggtactacccagataggacactgaagggataaaaaacttatgttcaactcagccacagccaatttgagttgctaataaatgatagattgttccttagtctcatgcttcattaa-cattaaatgacattggtcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAGTTGAATCGGTACATTCCCACTGCAGCTGCCTTTGGAGGTATCTGTATTG
                                                                    | || |  || |           ||  |      | ||||||   ||  |  |    |  |  ||   ||  ||   ||    |     |||  |||   ||||| ||||||||| | ||||| || |||||||| || ||| | ||||  ||| ||||||| |||||||||||||| || || |||||||| ||||||||||
--------------------------------------------------------------------tcatatggaaattcatatgtattaagatatcagacaaataaactgtatctc-tattatgttggcaaattttgttggtcacggtacatttttgaactt--gcagGAACAACAAATGGTAATGCCCGGACACCGTGAGTCAAACTTGCAGAAAGAGCTGAATCGATACATTCCCACTGCCGCAGCATTTGGAGGCATCTGTATTG

upper sequence: PP1S114_48V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ11193 (Selaginella moellendorffii), 3'ss of exon 5
gtatgtgactcaaggtttcccatcgcttcacggtactacccagataggacactgaagggataaaaaacttatgttcaactcagccacagccaatttgagttgctaataaatgatagattgttccttagtctcatgcttcattaacattaaatgacattggtcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAGTTGAATCGGTACATTCCCACTGCAGCTGCCTTTGGAGGTATCTGTATTG
                                                                                                  ||    || || |  ||| | ||  ||   |||      | | |    |     |  ||||        ||||||||||||||| ||||||| || ||||| ||| | ||||||||||||||  | ||||| |||||||| || || || |||||||| ||||| ||||| |
--------------------------------------------------------------------------------------------------gtaagcaagaacttttagctcgtaactcgatctt---tctgacttctctccccgggaattg--------cagGAGCAACAAATGGTCATGCCCGGACACCGAGAAGCCAACCTCCAGAGGGAACTCAATCGCTACATTCCAACCGCGGCGGCCTTTGGTGGTATTTGTATCG

upper sequence: PP1S114_48V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: EFJ15673 (Selaginella moellendorffii), 3'ss of exon 5
gtatgtgactcaaggtttcccatcgcttcacggtactacccagataggacactgaagggataaaaaacttatgttcaactcagccacagccaatttgagttgctaataaatgatagattgttccttagtctcatgcttcattaacattaaatgacattggtcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAGTTGAATCGGTACATTCCCACTGCAGCTGCCTTTGGAGGTATCTGTATTG
                                                                                                          |||   | |  ||   |      |||   |||   | || |    |  |   ||   |   ||||||||||||||| | ||||| || ||||| ||| | ||||||||||||||  | ||||| |||||||| || || || |||||||| ||||| ||||| |
---------------------------------------------------------------------------------------------------------gtaagcaagaactttagctcgtaactcgatcttttctgacttc---tctccccgggaatt-gcagGAGCAACAAATGGTGATGCCCGGACACCGAGAAGCCAACCTCCAGAGGGAACTCAATCGCTACATTCCAACCGCGGCCGCCTTTGGTGGTATTTGTATCG

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|162172636|gb|FC348017.1|FC348017
EST:     GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|162180347|gb|FC355352.1|FC355352
EST:     GTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|162262091|gb|FC437379.1|FC437379
EST:     GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|37839616|gb|BJ597624.1|BJ597624
EST:     GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|37827136|gb|BJ585148.1|BJ585148
EST:     GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|37844270|gb|BJ602278.1|BJ602278
EST:     GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|37821807|gb|BJ579873.1|BJ579873
EST:     GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|208368248|gb|DC951514.1|DC951514
EST:     GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|37828143|gb|BJ586155.1|BJ586155
EST:     GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|18334363|gb|BJ166380.1|BJ166380
EST:     CGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: CGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|162245019|gb|FC424977.1|FC424977
EST:     GGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|37839617|gb|BJ597625.1|BJ597625
EST:     GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|18337271|gb|BJ169295.1|BJ169295
EST:     GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|37850899|gb|BJ608907.1|BJ608907
EST:     GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|37835924|gb|BJ593936.1|BJ593936
EST:     GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|162179031|gb|FC356432.1|FC356432
EST:     GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|18338761|gb|BJ170785.1|BJ170785
EST:     GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|208373135|gb|DC945117.1|DC945117
EST:     GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|162262090|gb|FC437378.1|FC437378
EST:     GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|162166590|gb|FC343482.1|FC343482
EST:     GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|208375228|gb|DC948753.1|DC948753
EST:     GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|37822103|gb|BJ580169.1|BJ580169
EST:     GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|208388528|gb|DC957082.1|DC957082
EST:     GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|37826369|gb|BJ584381.1|BJ584381
EST:     GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|162245018|gb|FC424976.1|FC424976
EST:     GGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|37835855|gb|BJ593867.1|BJ593867
EST:     GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
EST: gi|37827084|gb|BJ585096.1|BJ585096
EST:     GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAG                         GAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG
genomic: GGATCGAAGTGTCAGGATCGTCTGCACGAGACGTTGCCAAGCAGCTCAAGgtatgtgact ... tcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattgttccttagtctcatgcttcattaacattaaatgacattggtcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAGTTGAATCGGTACATTCCCACTGCAGCTGCCTTTGGAGGTATCTGTATTG
                       cattaac  putative branch site (score: 2)
                                             tcttccac  putative PPT
                     ttcattaacattaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgactcaaggtttcccatcgcttcacggtactacccagataggacactgaagggataaaaaacttatgttcaactcagccacagccaatttgagttgctaataaatgatagattgttccttagtctcatgcttcattaacattaaatgacattggtcttccacagGAGCAACAAATGTTCATGCCAGGGCACCGTGAATCTAACCTCCAGAGGGAGTTGAATCGGTACATTCCCACTGCAGCTGCCTTTGGAGGTATCTGTATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG