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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgggagcattgtgcttttgaatttcctgttagctttctctcttctgttgtatccaaattgattattcaacggtcaatgctgttccaccgtgtttgcagATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAGCATGCTCTGCGTCGGTATCCTACCGGTGAAGAACGGTGCATTGCTTGCA

Basic information

species Physcomitrella patens
transcript PP1S83_83V6.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S83_83V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os03g56300.1 (Oryza sativa), 3'ss of exon 4
tgtgggagcattgtgcttttgaatttcctgttagctttctctcttctgttgtatccaaattgattattcaacggtcaatgctgttccaccgtgtttgcagATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAGCATGCTCTGCGTCGGTATCCTACCGGTGAAGAACGGTGCATTGCTTGCA
                  || | |      || |   |     |||  || ||    |||||  |  |      |   | ||  |||  | |  || |||||||| ||||| || ||||||||||||||||| ||||| ||| |||| |||||||||||  | || ||||| || || ||||| || ||||| || || |
-----------------gttaagtggtgaatttggcatactgtttcctttataatgtaattgcatgcttgtatttaccttcttatcctacctccttacagATCAACTATCCATTTGAGAAGGGTCCTTTGAGCCCTCGCTTCCGAGGAGAGCATGCTCTCAGACGCTATCCAACTGGAGAAGAGCGTTGCATCGCCTGTA

upper sequence: PP1S83_83V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA15G07790.2 (Glycine max), 3'ss of exon 4
tgtgggagcattgtgcttttgaatttcctgttagctttctctcttctgttgtatccaaattgattattcaacggtcaatgctgttccaccgtgtttgcagATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAGCATGCTCTGCGTCGGTATCCTACCGGTGAAGAACGGTGCATTGCTTGCA
       | |  |||  ||||||    ||||| |||  | |  | |||||| | |     |  | ||| || |   |||| | |  |  | |   |||||||||||||||| || ||||| || |||||||| || |||||| | || || ||||| || || || ||||| || || || ||||| |||||||||||||
-------gtaa-gtgtctttgaaaa--ctgtttgctggc-caatactgttgcagc-----ttctaattaaatgcataatg-tatgacttctttgatgcagATCAATTATCCATTTGAGAAAGGCCCTTTGAGCCCCCGTTTCCGGGGTGAACATGCACTCCGACGATATCCAACAGGAGAGGAACGCTGCATTGCTTGCA

upper sequence: PP1S83_83V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA13G31520.1 (Glycine max), 3'ss of exon 5
tgtgggagcattgtgcttttgaatttcctgttagctttctctcttctgttgtatccaaattgattattcaacggtcaatgctgttccaccgtgtttgcagATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAGCATGCTCTGCGTCGGTATCCTACCGGTGAAGAACGGTGCATTGCTTGCA
         | |||  | |  || |   || | ||     |  | |||||| | |     |  | ||| || | | |||||    |  |  || | ||||||||||||||| || ||||| || |||||||| ||||||||| | || || ||||| || || || ||||| || || || ||||| || ||||||||||
------gtaagtgtcttctaaaactgtttgctggc-----caatactgttgcagc-----ttctaattaaatgcttaatgcatgacttctttgat-gcagATCAATTATCCATTTGAGAAAGGCCCTTTGAGCCCTCGTTTCCGTGGTGAACATGCACTCCGGCGATATCCAACAGGGGAGGAACGTTGTATTGCTTGCA

upper sequence: PP1S83_83V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT1G79010.1 (Arabidopsis thaliana), 3'ss of exon 4
tgtgggagcattgtgcttttgaatttcctgttagctttctctcttctgttgtatccaaattgattattcaacg-gtcaatgctgttccaccgtgtttgcagATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAGCATGCTCTGCGTCGGTATCCTACCGGTGAAGAACGGTGCATTGCTTGCA
                        |   || || |||| |||  |||     |   | |||||         | || | ||  | ||   ||||| |||||||||||||||| || |||||||||||| |||| ||||| ||| | || || |||||||| ||  | ||||||||||| |||||||| |||||||| ||||
-----------------------gtgagtgatatcttt-tctagtcttccaaacttagattgaaagaaatctgtgttactgaagctctttcgtgtatgcagATCAATTATCCATTTGAGAAGGGTCCTCTGAGCCCTCGCTTCCGTGGTGAACATGCTCTTCGAAGATATCCTACCGGGGAAGAACGCTGCATTGCCTGCA

upper sequence: PP1S83_83V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT1G16700.1 (Arabidopsis thaliana), 3'ss of exon 5
tgtgggagcattgtgcttttgaatttcctgttagctttctctctt--ctgttgtatccaaattgattattcaacggtc-aatgct---gttccaccgtgtttgcagATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAGCATGCTCTGCGTCGGTATCCTACCGGTGAAGAACGGTGCATTGCTTGCA
                               | ||| |||| |||  || | |||   |   |||      ||   ||  || ||   |||  | | | | |||||||||||||||| || ||||||||||| ||||| ||||||||| | || || || ||||| ||  ||||||| || || |||||||| |||||||| ||||
--------------------------gtgagtggctgtctcccttgactctagtaattaggctgaaagaaaaatattctgattctcaagttttatcttttgtgcagATCAATTATCCTTTTGAGAAGGGTCCATTGAGCCCTCGTTTCCGTGGTGAACACGCTCTTCGAAGGTATCCAACTGGGGAAGAACGCTGCATTGCCTGCA

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|162226492|gb|FC402446.1|FC402446
EST:     CCAGAGGCATGGGTTTGGCACTCAAATATTTTTTCGAGAAGAAAGTCACA                         ATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAG
genomic: CCAGAGGCATGGGTTTGGCACTCAAATATTTTTTCGAGAAGAAAGTCACAgtatgatttt ... gtgtttgcagATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAG
EST: gi|67569163|gb|BJ941987.1|BJ941987
EST:     CCAGAGGCATGGGTTTGGCACTCAAATATTTTTTCGAGAAGAAAGTCACA                         ATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGNTTCAGAGGGGAG
genomic: CCAGAGGCATGGGTTTGGCACTCAAATATTTTTTCGAGAAGAAAGTCACAgtatgatttt ... gtgtttgcagATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAG
EST: gi|208365908|gb|DC951087.1|DC951087
EST:     CCAGAGGCATGGGTTTGGCACTCAAATATTTTTTCGAGAAGAAAGTCACA                         ATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAG
genomic: CCAGAGGCATGGGTTTGGCACTCAAATATTTTTTCGAGAAGAAAGTCACAgtatgatttt ... gtgtttgcagATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAG
EST: gi|100407453|gb|BY991709.1|BY991709
EST:     CCAGAGGCATGGGTTTGGCACTCAAATATTTTTTCGAGAAGAAAGTCACA                         ATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAG
genomic: CCAGAGGCATGGGTTTGGCACTCAAATATTTTTTCGAGAAGAAAGTCACAgtatgatttt ... gtgtttgcagATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAG
EST: gi|208391815|gb|DC937991.1|DC937991
EST:     CCAGAGGCATGGGTTTGGCACTCAAATATTTTTTCGAGAAGAAAGTCACA                         ATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAG
genomic: CCAGAGGCATGGGTTTGGCACTCAAATATTTTTTCGAGAAGAAAGTCACAgtatgatttt ... gtgtttgcagATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAG
EST: gi|208356711|gb|DC902543.1|DC902543
EST:     CCAGAGGCATGGGTTTGGCACTCAAATATTTTTTCGAGAAGAAAGTCACA                         ATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAG
genomic: CCAGAGGCATGGGTTTGGCACTCAAATATTTTTTCGAGAAGAAAGTCACAgtatgatttt ... gtgtttgcagATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAG
EST: gi|67719791|gb|BJ970050.1|BJ970050
EST:     CCAGAGGCATGGGTTTGGCACTCAAATATTTTTTCGAGAAGAAAGTCACA                         ATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAG
genomic: CCAGAGGCATGGGTTTGGCACTCAAATATTTTTTCGAGAAGAAAGTCACAgtatgatttt ... gtgtttgcagATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAG
EST: gi|208389974|gb|DC938029.1|DC938029
EST:     CCAGAGGCATGGGTTTGGCACTCAAATATTTTTTCGAGAAGAAAGTCACA                         ATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAG
genomic: CCAGAGGCATGGGTTTGGCACTCAAATATTTTTTCGAGAAGAAAGTCACAgtatgatttt ... gtgtttgcagATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAG
EST: gi|208398252|gb|DC916419.1|DC916419
EST:     CCAGAGGCATGGG-TTGGCACTCAAATA-TTTTTCGAGAAGAAAGTCACA                         ATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAG
genomic: CCAGAGGCATGGGTTTGGCACTCAAATATTTTTTCGAGAAGAAAGTCACAgtatgatttt ... gtgtttgcagATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAG
EST: gi|100407742|gb|BY955757.1|BY955757
EST:     CCAGAGGCATGGGTTTGGCACTCAAATATTTTTTCGAGAAGAAAGTCACA                         ATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAG
genomic: CCAGAGGCATGGGTTTGGCACTCAAATATTTTTTCGAGAAGAAAGTCACAgtatgatttt ... gtgtttgcagATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAG
EST: gi|208365816|gb|DC951051.1|DC951051
EST:     CCAGAGGCATGGGTTTGGCACTCAAATATTTTTTCGAGAAGAAAGTCACA                         ATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAG
genomic: CCAGAGGCATGGGTTTGGCACTCAAATATTTTTTCGAGAAGAAAGTCACAgtatgatttt ... gtgtttgcagATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttgtatccaaattgattattcaacggtcaatgctgttccaccgtgtttgcagATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAGCATGCTCTGCGTCGGTATCCTACCGGTGAAGAACGGTGCATTGCTTGCA
            aattgat  putative branch site (score: 4)
           aaattgattattcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgggagcattgtgcttttgaatttcctgttagctttctctcttctgttgtatccaaattgattattcaacggtcaatgctgttccaccgtgtttgcagATCAATTATCCCTTCGAGAAGGGTCCTTTGAGTCCTCGTTTCAGAGGGGAGCATGCTCTGCGTCGGTATCCTACCGGTGAAGAACGGTGCATTGCTTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC