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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtgtctggaacattaacgcccccccgtttttcacctttctgctcttgttttcaaacgtgctctttcacatcgcagaattttgccctgtctctgtgtgaggagcgtcattgtagtaagtttttatctgatttgtgggaacgattcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGAATCCCACCGAAGCTGAGCTACAGGACATGATCAACGAAGTTGATGCCGA

Basic information

species Physcomitrella patens
transcript PP1S79_158V6.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S79_158V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv05s0020g04420.t01 (Vitis vinifera), 3'ss of exon 1
gtaatgtgtctggaacattaacgcccccccgtttttcacctttctgctcttgttttcaaacgtgctctttcacatcgcagaattttgccctgtctctgtgtgaggagcgtcattgtagtaagtttttatctgatttgtgggaacgattcaata---acagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGAATCCCACCGAAGCTGAGCTACAGGACATGATCAACGAAGTTGATGCCGA
                                            ||   ||  |||         || |   | | | | |  ||||     |||   || |       || ||||  | | || |   |  |||  ||  |  | || |||      |||  |||| ||     | ||  |||  || ||||| |||||||||| ||||||||||||||| |  ||||| ||||||||||| |  ||||| ||||| ||
-------------------------------------------gtgagttttctttttgggtcattcctaggcct-gtatatctttggttcctcttactggg-------tctttgttattatttctgggcatattcatga-agtggttgaatgtgtgtagGCTGCATTACCGTAGAAGAATTGGCGACGGTGATTCGGTCGTTGGATCAGAATCCCACCGAGGAAGAGCTTCAGGACATGATAAGAGAAGTGGATGCTGA
















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|162279550|gb|FC455328.1|FC455328
EST:     GAGGCGTTTAGC-TGTTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GAGGCGTTTAGCTTG-TTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|19789534|gb|BQ041364.1|BQ041364
EST:     GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|67692513|gb|BJ952746.1|BJ952746
EST:     GATTGCCGAG-TTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|67694904|gb|BJ955137.1|BJ955137
EST:     TTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: TTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|67698628|gb|BJ958861.1|BJ958861
EST:     GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|162227831|gb|FC403639.1|FC403639
EST:     TTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: TTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|208374214|gb|DC945260.1|DC945260
EST:     GANTGCCGAG-TTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|162249136|gb|FC420387.1|FC420387
EST:     GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|67569257|gb|BJ942081.1|BJ942081
EST:     GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|208385346|gb|DC915146.1|DC915146
EST:     GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|18343887|gb|BJ175925.1|BJ175925
EST:     GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|162256969|gb|FC433279.1|FC433279
EST:     GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|208397052|gb|DC928895.1|DC928895
EST:     GANTGCCGAG-TTAAGGAGGCGTTTAGCNTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|162279223|gb|FC455770.1|FC455770
EST:     GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|208375983|gb|DC906974.1|DC906974
EST:     GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|208372675|gb|DC944640.1|DC944640
EST:     GCGTTTAGCNTG-TTGACAAGGATGGCGACG                         GTAGCATCACTACCNAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|162152778|gb|FC329784.1|FC329784
EST:     GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|162256968|gb|FC433278.1|FC433278
EST:     ATTG-CGNAGTTTAAGGAGGCGTTTAGCTT-TTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: ATTGCCG-AGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|162227832|gb|FC403640.1|FC403640
EST:     GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|162249065|gb|FC421187.1|FC421187
EST:     GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|162279222|gb|FC455769.1|FC455769
EST:     ATTGCCGAGTTTAAGGAGGCGTTTAGC-TGTTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: ATTGCCGAGTTTAAGGAGGCGTTTAGCTTG-TTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|162235070|gb|FC411205.1|FC411205
EST:     CGTTTAGCTTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: CGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|162279551|gb|FC455329.1|FC455329
EST:     GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|208352946|gb|DC926053.1|DC926053
EST:     GGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|67697386|gb|BJ957619.1|BJ957619
EST:     GAGTTTAAGGAGGCGTTTAGCNTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|162257078|gb|FC432817.1|FC432817
EST:     GATTGCCGAGTTTAAGGAGGCGTTTAGCTT-TTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|162277269|gb|FC453699.1|FC453699
EST:     GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|208397191|gb|DC920848.1|DC920848
EST:     CGAG-TTAAGGAGGCG-TTAGC-TGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: CGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|37842115|gb|BJ600123.1|BJ600123
EST:     GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|162270506|gb|FC447601.1|FC447601
EST:     GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|67699019|gb|BJ959252.1|BJ959252
EST:     GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
EST: gi|162262741|gb|FC439017.1|FC439017
EST:     GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACG                         GTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA
genomic: GATTGCCGAGTTTAAGGAGGCGTTTAGCTTGTTTGACAAGGATGGCGACGgtaatgtgtc ... tcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggagcgtcattgtagtaagtttttatctgatttgtgggaacgattcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGAATCCCACCGAAGCTGAGCTACAGGACATGATCAACGAAGTTGATGCCGA
                         atctgat  putative branch site (score: 4)
             tagtaagtttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtgtctggaacattaacgcccccccgtttttcacctttctgctcttgttttcaaacgtgctctttcacatcgcagaattttgccctgtctctgtgtgaggagcgtcattgtagtaagtttttatctgatttgtgggaacgattcaataacagGTAGCATCACTACCAAGGAGCTGGGAACAGTGATGCGGTCGTTGGGTCAGAATCCCACCGAAGCTGAGCTACAGGACATGATCAACGAAGTTGATGCCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA