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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agacacgtgagcgggaagactttattttatgacgacaacaaaattcaaacaaacatatgacgcatgagtttaatgggggtgagtggtgggaatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGCAGGAGACGGCCGGAGATGTGCGTCTGACGGACACCCGGCAGGATGAGGC

Basic information

species Physcomitrella patens
transcript PP1S431_6V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S431_6V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g52470.1 (Oryza sativa), 3'ss of exon 2
---------------------------agacacgtgagcgggaagacttta---ttttatg-acgacaacaaaattcaaacaaacatatg-acgcatgagtttaatgggggtgagtggtgggaatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGCAGGAGACGGCCGGAGATGTGCGTCTGACGGACACCCGGCAGGATGAGGC
                            ||  ||   |        ||||     | | ||   |  |           | |   || || |   ||| |  |  ||||| || | ||| |||||   |||||||||||||| || || || ||||||||||| || || || || |||||||||||   |||||| || |||||  |||||||||| ||   ||| |||||
gtgagtgtttttcatcaagcaaaatttggattcgatcgatctgtcgctttggatctctgtgtgtgtgagtgggggatggatagtaatgtggatcgatgtgcgttttgggg-tggg-ggttggaattctgcagGGAAGTCGACGCTCACTGACTCGCTGGTGGCGGCGGCCGGCATCATCGCGCAGGACGTGGCCGGCGACGTGCGGATGACGGACACGCGCGCGGACGAGGC

upper sequence: PP1S431_6V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ20382 (Selaginella moellendorffii), 3'ss of exon 2
agacacgtgagcgggaagactttattttatgacgacaacaaaattcaaacaaacatatgacgcatgagtttaatgggggtgagtggtgggaa---tgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGCAGGAGACGGCCGGAGATGTGCGTCTGACGGACACCCGGCAGGATGAGGC
                                        |  |||    | |  |   |  |||    |   |   | |    | |  |||   |  | |||| || || || ||||||||||| ||||| || || || ||||||||||| ||||||  ||| ||||| || ||  |||| ||||| || |||||||||||
-------------------------------------gtgagtttcttctagattttccatccattcagtagctaaagctcgtcgatctgaaattttcgccagGAAAATCCACCCTGACGGATTCCCTGGTTGCGGCCGCTGGGATTATCGCCCAGGAGGTGGCTGGAGACGTCCGGATGACCGACACACGCCAGGATGAGGC
















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|18324872|gb|BJ156867.1|BJ156867
EST:     CAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATGgtaagtggat ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|18327863|gb|BJ159867.1|BJ159867
EST:     CAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATGgtaagtggat ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|100419640|gb|BY957660.1|BY957660
EST:     CAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATGgtaagtggat ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|18356348|gb|BJ188407.1|BJ188407
EST:     CAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATGgtaagtggat ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|100446089|gb|CJ970388.1|CJ970388
EST:     CAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATG                         GGAAGTCNACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATGgtaagtggat ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|18327383|gb|BJ159385.1|BJ159385
EST:     CAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATGgtaagtggat ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|18357878|gb|BJ189937.1|BJ189937
EST:     CAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATGgtaagtggat ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|100450013|gb|CJ974050.1|CJ974050
EST:     CAAGAAGCACAACATCAGAAATATGTCCGTTATTGCCCACGTCGATCACG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATGgtaagtggat ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|18326615|gb|BJ158614.1|BJ158614
EST:     CAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATGgtaagtggat ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
EST: gi|18365797|gb|BJ197875.1|BJ197875
EST:     CAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATG                         GGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC
genomic: CAAGAAGCACAACATCAGGAACATGTCCGTTATCGCCCATGTGGATCATGgtaagtggat ... aatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaacaaacatatgacgcatgagtttaatgggggtgagtggtgggaatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGCAGGAGACGGCCGGAGATGTGCGTCTGACGGACACCCGGCAGGATGAGGC
                      gtttaat  putative branch site (score: 4)
     aaacatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agacacgtgagcgggaagactttattttatgacgacaacaaaattcaaacaaacatatgacgcatgagtttaatgggggtgagtggtgggaatgtggcagGGAAGTCGACACTGACGGATTCGCTGGTGGCTGCTGCGGGGATTATCGCGCAGGAGACGGCCGGAGATGTGCGTCTGACGGACACCCGGCAGGATGAGGC

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