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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctgaacaaactgaattagcaaaacatttgaggaaatctgatgataacagagtcaaaacatgcctagattaatgggggtgagtggtggaaatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGCAGGAGACGGCCGGAGATGTGCGTCTGACGGACACCCGGCAGGATGAGGC

Basic information

species Physcomitrella patens
transcript PP1S431_2V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S431_2V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g52470.1 (Oryza sativa), 3'ss of exon 2
-----------------------------atctgaacaaactgaattagcaaaacatttgaggaaatctga-tgataacagagtcaaaacatgcctagattaatg----ggggtgagtggtggaaatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGCAGGAGACGGCCGGAGATGTGCGTCTGACGGACACCCGGCAGGATGAGGC
                             ||  || | | |||   | ||     || |  |    | ||| ||      |  |   ||  ||  | |||    |    |||||| | | ||||| | || ||||||||||||| || || || ||||||||||| || || || || |||||||||||   |||||| || |||||  |||||||||| ||   ||| |||||
gtgagtgtttttcatcaagcaaaatttggattcgatcgatctg---tcgctttggatctctgtgtgtgtgagtgggggatggatagtaatgtggatcgatgtgcgttttggggtgggggttggaattctg-cagGGAAGTCGACGCTCACTGACTCGCTGGTGGCGGCGGCCGGCATCATCGCGCAGGACGTGGCCGGCGACGTGCGGATGACGGACACGCGCGCGGACGAGGC

upper sequence: PP1S431_2V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ20382 (Selaginella moellendorffii), 3'ss of exon 2
atctgaacaaactgaattagcaaaacatttgaggaaatctgatgataacagagtcaaaacatgcctagattaatgggggtgagtggtggaaatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGCAGGAGACGGCCGGAGATGTGCGTCTGACGGACACCCGGCAGGATGAGGC
                                |  | | |  |    | |   || |  ||| |      ||| |   ||   |     |  |  | |||| || || || ||||||||||| ||||| || || || ||||||||||| ||||||  ||| ||||| || ||  |||| ||||| || |||||||||||
--------------------------------gtgagtttctt--ctagattttccatccattcagtagctaaagctcgtcgatctgaaattttcgccagGAAAATCCACCCTGACGGATTCCCTGGTTGCGGCCGCTGGGATTATCGCCCAGGAGGTGGCTGGAGACGTCCGGATGACCGACACACGCCAGGATGAGGC
















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|18353882|gb|BJ185937.1|BJ185937
EST:     CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACGgtacgtatca ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|67703285|gb|BJ963518.1|BJ963518
EST:     CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACGgtacgtatca ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|100394266|gb|BY972010.1|BY972010
EST:     CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACGgtacgtatca ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|100402757|gb|BY973341.1|BY973341
EST:     CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACGgtacgtatca ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|100387850|gb|BY970595.1|BY970595
EST:     CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACGgtacgtatca ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|100440627|gb|BY962314.1|BY962314
EST:     CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACGgtacgtatca ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|100391100|gb|BY953110.1|BY953110
EST:     CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACGgtacgtatca ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|100385060|gb|BY987523.1|BY987523
EST:     CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACGgtacgtatca ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|18374280|gb|BJ205858.1|BJ205858
EST:     CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACGgtacgtatca ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|18343269|gb|BJ175307.1|BJ175307
EST:     CAAGAAGCACAATATTCGNAACATGTCTGTCATTGCCCACGTTGACCACG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACGgtacgtatca ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|100403457|gb|BY991209.1|BY991209
EST:     CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACGgtacgtatca ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|67571224|gb|BJ944048.1|BJ944048
EST:     CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACGgtacgtatca ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|100394044|gb|BY971930.1|BY971930
EST:     CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACGgtacgtatca ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|67702942|gb|BJ963175.1|BJ963175
EST:     CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACGgtacgtatca ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|100361752|gb|BY947805.1|BY947805
EST:     CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACGgtacgtatca ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|100386849|gb|BY988118.1|BY988118
EST:     CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAATATTCGTAACATGTCTGTCATTGCCCACGTTGACCACGgtacgtatca ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacagagtcaaaacatgcctagattaatgggggtgagtggtggaaatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGCAGGAGACGGCCGGAGATGTGCGTCTGACGGACACCCGGCAGGATGAGGC
                    tagattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctgaacaaactgaattagcaaaacatttgaggaaatctgatgataacagagtcaaaacatgcctagattaatgggggtgagtggtggaaatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGCAGGAGACGGCCGGAGATGTGCGTCTGACGGACACCCGGCAGGATGAGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG