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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaggaaaagtttctacaattaagagcggctttagggtggtaatttggcctttgctctatctgatgaatacttaactctggtactgcaatggattttcagATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTCGAGTGTGGAAATTACTCTGGTGCATCTGATTATCTGTATCAGTATCGGA

Basic information

species Physcomitrella patens
transcript PP1S9_109V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S9_109V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA10G16090.1 (Glycine max), 3'ss of exon 2
acaggaaaagtttctacaattaagagcggctttagggt-ggtaatttggcctttgctctatctgatgaatacttaactctggtactgcaatggattttc------agATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTCGAGTGTGGAAATTACTCTGGTGCATCTGATTATCTGTATCAGTATCGGA
 | |    |||   |  ||  ||||     | ||   | || | ||||   ||||   |||  ||    |   | ||| ||  |   |||||  | | |      |||||||  |||  || ||||| ||  | || || |||||||| || ||||| ||||||||||| |||||||||||  |||| ||||| ||||||||  |  
-ctgttttagtggttttaa--aagaattattctacttttggaagtttgaattttgtggtat--gagtcctgtctgactatgtaa--acaatgattctgctgaaacagATTGGTCCTGCACAGATAGAAGCGTTGTACCAATATGCCAAATTCCAGTTTGAGTGTGGAAACTACTCTGGTGCTGCTGACTATCTTTATCAGTACAGAG

upper sequence: PP1S9_109V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv00s0252g00070.t01 (Vitis vinifera), 3'ss of exon 2
acaggaaaagtttctacaatta-agagcggctt-tagggtggtaatttggccttt--gctctatctgatgaatacttaactctggtactgcaatggatttt---cagATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTCGAGTGTGGAAATTACTCTGGTGCATCTGATTATCTGTATCAGTATCGGA
         |||| |    ||  |  |  |||  |  |   | | | | |  |||  | ||||| ||     |||  || | |    ||    |   || |   ||||||||    ||||| ||||||||  | ||||| |||||||| |||||||| || |||||||| |||||||||||  ||||||| |||||||||||  || 
-----tcctgtttttgttgttgtattgttgctaatttgacagaattctaggtttttgggtctatttggct--tacaaaattatatcccttttttcttttctgaccagATTGGCCAGGAGCAGATAGAGGCATTATATCAGTATGCCAAATTTCAGTTTGAATGTGGAAACTACTCTGGTGCTGCTGATTACCTGTATCAGTACAGGG
















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|100398534|gb|BY972660.1|BY972660
EST:     TACGATCTGATAAGCATTACAACCTCCAAATGTTACAGGAACGACACCAG                         ATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
genomic: TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAGgttaggtttt ... ggattttcagATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
EST: gi|19790100|gb|BQ041695.1|BQ041695
EST:     TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAG                         ATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
genomic: TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAGgttaggtttt ... ggattttcagATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
EST: gi|208396897|gb|DC908189.1|DC908189
EST:     TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAG                         ATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
genomic: TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAGgttaggtttt ... ggattttcagATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
EST: gi|208354961|gb|DC914225.1|DC914225
EST:     TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAG                         ATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
genomic: TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAGgttaggtttt ... ggattttcagATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
EST: gi|67717505|gb|BJ967764.1|BJ967764
EST:     TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAG                         ATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
genomic: TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAGgttaggtttt ... ggattttcagATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
EST: gi|100414960|gb|BY956947.1|BY956947
EST:     TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAG                         ATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
genomic: TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAGgttaggtttt ... ggattttcagATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
EST: gi|162171468|gb|FC346743.1|FC346743
EST:     TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAG                         ATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
genomic: TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAGgttaggtttt ... ggattttcagATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
EST: gi|208348620|gb|DC905857.1|DC905857
EST:     TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAG                         ATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
genomic: TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAGgttaggtttt ... ggattttcagATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
EST: gi|208368174|gb|DC931428.1|DC931428
EST:     TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAG                         ATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
genomic: TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAGgttaggtttt ... ggattttcagATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
EST: gi|100402664|gb|BY954948.1|BY954948
EST:     TACGATCTGATAAGCGTTACAACCTCCAAATGTTGCAGGAACGACACCAG                         ATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
genomic: TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAGgttaggtttt ... ggattttcagATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
EST: gi|18363928|gb|BJ196000.1|BJ196000
EST:     TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAG                         ATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
genomic: TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAGgttaggtttt ... ggattttcagATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
EST: gi|100394165|gb|BY971971.1|BY971971
EST:     TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAG                         ATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
genomic: TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAGgttaggtttt ... ggattttcagATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
EST: gi|67508674|gb|BJ941535.1|BJ941535
EST:     TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAG                         ATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC
genomic: TACGATCTGATAAGCATTACAACCTCCAAATGTTGCAGGAACGACACCAGgttaggtttt ... ggattttcagATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcctttgctctatctgatgaatacttaactctggtactgcaatggattttcagATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTCGAGTGTGGAAATTACTCTGGTGCATCTGATTATCTGTATCAGTATCGGA
                        acttaac  putative branch site (score: 3)
                                                ttttc  putative PPT
                     aatacttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaggaaaagtttctacaattaagagcggctttagggtggtaatttggcctttgctctatctgatgaatacttaactctggtactgcaatggattttcagATTGGGTCTGAGCAAATAGAGGCCCTCTATCATTATGCCAAGTTTCAGTTCGAGTGTGGAAATTACTCTGGTGCATCTGATTATCTGTATCAGTATCGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tactgca