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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagaatggccaaggaatggcaaaggattttgtggagattaaagtatgcagactgtatgaatttctgaaacgggtggtttgtgtggtgttcgattggaaagCCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGACACGGACTCTCCGATGAAGTACGTGGACATTGCTATCCCTGCGAACAACA

Basic information

species Physcomitrella patens
transcript PP1S59_133V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S59_133V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G092719_T01 (Zea mays), 3'ss of exon 2
--gagaatggccaaggaatggcaaaggattttgtggagattaaagtatgcagactgta-tgaatttctgaaacgggtggtttgtgtggtgttcgattggaaagCCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGACACGGACTCTCCGATGAAGTACGTGGACATTGCTATCCCTGCGAACAACA
  || ||| |     |  |  |||||  || ||  |   |||  |  || |  ||| | ||   |  ||||     || | ||  ||||  ||| ||| |  |||||||| |||| |||||||||| ||||| ||   ||| || ||||||||||| |||||||| |||  |||||| || || |  ||||| ||||||||||
gtgacaatagtttcagttt--caaag--ttctgaagtacttactgagtggaccctgcagtgtgatggtgaactaattgttatgc-tggtaatcgtttgca--gCCAATCAAGGAGTCTGCTCTGGGGAACATCCCAACCATTGCCTTCTGTGACACTGACTCTCCCATGCGGTACGTCGATATCGGCATCCCAGCGAACAACA

upper sequence: PP1S59_133V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G72370.2 (Arabidopsis thaliana), 3'ss of exon 2
gagaatggccaaggaatggcaaaggattttgtggagattaaagtatgcagactg--tatgaatttctgaaacgggtggtttgtgtggtgttcgattggaaagCCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGACACGGACTCTCCGATGAAGTACGTGGACATTGCTATCCCTGCGAACAACA
                  | |||    ||  |     | | |   |   || ||  ||   |||| ||  |  | |   | || | ||||  | |     |||| |||| ||| | |||| |||||||||||||  |||| || ||||||||||| |||||||| ||||  |  || ||||||| |||||| || |||||||
------------------gtaaact-cttcatatgattcatatactagtgattgattaatgatttttgttattgataaat-gtcttgtgtgtgtt---gcagCCTATCAAGGAAGGTGCTTTGGGAAACATTCCAATCATTGCTTTCTGTGACACAGACTCTCCAATGAGATTTGTTGACATTGGTATCCCAGCCAACAACA

upper sequence: PP1S59_133V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ32709 (Selaginella moellendorffii), 3'ss of exon 2
gagaatggccaaggaatggcaaaggattttgtggagattaaagtatgcagactgtatgaatt--tctgaaacgggtggtttgtgtggtgttcgattggaaagCCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGACACGGACTCTCCGATGAAGTACGTGGACATTGCTATCCCTGCGAACAACA
                      | | ||    |     |  || | |     | |    |||  | |    |   || |||||||| |||  | |     |||| || | |||||| || || |||||||| || || ||||| ||||| ||||||||||| || |||||||||||||||||||||||||| || |||||||
--------------------gtaagtttgctcgctcgatctagcacgacttttttcctcattggtttccttcttttgttttgtgtg-tgtgtgttcttccagCCGATTAAGGAGGCCGCGCTTGGAAACATCCCTGTGATCGCCTTCTGCGACACGGACTCGCCCATGAAGTACGTGGACATTGCTATCCCGGCCAACAACA

upper sequence: PP1S59_133V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: EFJ20712 (Selaginella moellendorffii), 3'ss of exon 2
gagaatggccaaggaatggcaaaggattttgtggagattaaagtatgcagactgtatgaatt--tctgaaacgggtggtttgtgtggtgttcgattggaaagCCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGACACGGACTCTCCGATGAAGTACGTGGACATTGCTATCCCTGCGAACAACA
                      | | ||    |     |  || | |     | |    |||  | |    |   || |||||||  |||  | |     |||| || | |||||| || || |||||||| ||||| ||||| ||||| ||||||||||| || |||||||||||||||||||||||||| || |||||||
--------------------gtaagtttgctcgctcgatctagcacgacttttttcctcattggtttccttcttttgttttgtgtc-tgtgtgttcttccagCCGATTAAGGAGGCCGCGCTTGGAAACATCCCCGTGATCGCCTTCTGCGACACGGACTCGCCCATGAAGTACGTGGACATTGCTATCCCGGCCAACAACA

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|208379664|gb|DC903719.1|DC903719
EST:     TCAGCGAGCCCAGGCTTCTAATTTTGACGGATCCTCGAACTGATCACCAG                         CCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCGTTCTGTGAC
genomic: TCAGCGAGCCCAGGCTTCTAATTTTGACGGATCCTCGAACTGATCACCAGgttagggttt ... gattggaaagCCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGAC
EST: gi|100429439|gb|BY959564.1|BY959564
EST:     TCAGCGAGCCCAGGCTTCTAATTTTGACGGATCCTCGAACTGATCACCAG                         CCAATCATGGAGGCTGCTCTNGGAAACATTCCCGTCATCGCATTCTGTGAC
genomic: TCAGCGAGCCCAGGCTTCTAATTTTGACGGATCCTCGAACTGATCACCAGgttagggttt ... gattggaaagCCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGAC
EST: gi|18329684|gb|BJ161690.1|BJ161690
EST:     TCAGCGAGCCCAGGCTTCTAATTTTGACGGATCCTCGAACTGATCACCAG                         CCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGAC
genomic: TCAGCGAGCCCAGGCTTCTAATTTTGACGGATCCTCGAACTGATCACCAGgttagggttt ... gattggaaagCCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGAC
EST: gi|100403042|gb|BY973478.1|BY973478
EST:     TCAGCGAGCCCAGGCTTCTAATTTTGACGGATCCTCGAACTGATCACCAG                         CCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGAC
genomic: TCAGCGAGCCCAGGCTTCTAATTTTGACGGATCCTCGAACTGATCACCAGgttagggttt ... gattggaaagCCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGAC
EST: gi|100439438|gb|BY961933.1|BY961933
EST:     TCAGCGAGCCCAGGCTTCTAATTTTGACGGATCCTCGAACTGATCACCAG                         CCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGAC
genomic: TCAGCGAGCCCAGGCTTCTAATTTTGACGGATCCTCGAACTGATCACCAGgttagggttt ... gattggaaagCCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGAC
EST: gi|67716287|gb|BJ966547.1|BJ966547
EST:     TCAGCGAGCCCAGGCTTCTAATTTTGACGGATCCTCGAACTGATCACCAG                         CCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGAC
genomic: TCAGCGAGCCCAGGCTTCTAATTTTGACGGATCCTCGAACTGATCACCAGgttagggttt ... gattggaaagCCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGAC
EST: gi|162160077|gb|FC335947.1|FC335947
EST:     TCAGCGAGCCCAGGCTTCTAATTTTGACGGATCCTCGAACTGATCACCAG                         CCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGAC
genomic: TCAGCGAGCCCAGGCTTCTAATTTTGACGGATCCTCGAACTGATCACCAGgttagggttt ... gattggaaagCCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGAC
EST: gi|208399572|gb|DC908753.1|DC908753
EST:     TCAGCGAGCCCAGGCTTCTAATTTTGACGGATCCTCGAACTGATCACCAG                         CCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGAC
genomic: TCAGCGAGCCCAGGCTTCTAATTTTGACGGATCCTCGAACTGATCACCAGgttagggttt ... gattggaaagCCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGAC
EST: gi|162248750|gb|FC422822.1|FC422822
EST:     TCAGCGAGCCCAGGCTTCTAATTTTGACGGATCCTCGAACTGATCACCAG                         CCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGAC
genomic: TCAGCGAGCCCAGGCTTCTAATTTTGACGGATCCTCGAACTGATCACCAGgttagggttt ... gattggaaagCCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGAC
EST: gi|67569851|gb|BJ942675.1|BJ942675
EST:     TCAGCGAGCCCAGGCTTCTAATTTTGACGGATCCTCGAACTGATCACCAG                         CCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGAC
genomic: TCAGCGAGCCCAGGCTTCTAATTTTGACGGATCCTCGAACTGATCACCAGgttagggttt ... gattggaaagCCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGAC
EST: gi|18324853|gb|BJ156848.1|BJ156848
EST:     TCAGCGAGCCCAGGCTTCTAATTTTGACGGATCCTCGAACTGATCACCAG                         CCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGAC
genomic: TCAGCGAGCCCAGGCTTCTAATTTTGACGGATCCTCGAACTGATCACCAGgttagggttt ... gattggaaagCCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcagactgtatgaatttctgaaacgggtggtttgtgtggtgttcgattggaaagCCAATCATGGAGGCTGCTCTGGGAAACATTCCCGTCATCGCATTCTGTGACACGGACTCTCCGATGAAGTACGTGGACATTGCTATCCCTGCGAACAACA
         tatgaattt  TA-rich tract