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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cggtggtgcagaagcttttaagagggacatagatagaaatgtccacaagaaatggtcatttgtattggaatgttcatgaaagcaatatttgggggtgcagGAAGCGTTGGAGGAGCACGATGGAGTGAGCAAAGGAAAGTACACTATTGGTCTTGGACAAGACCGGCTTGCCTTCTGCACCGATCTTGAGGACGTTATTT

Basic information

species Physcomitrella patens
transcript PP1S154_103V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S154_103V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os08g43170.1 (Oryza sativa), 3'ss of exon 1
-cggtggtgcagaagcttttaagagggacatagatagaaatgtcc---acaagaaatggt--catttgtattggaatgttcatgaaagcaatatttgggggtgcagGAAGCGTTGGAGGAGCACGATGGAGTGAGCAAAGGAAAGTACACTATTGGTCTTGGACAAGACCGGCTTGCCTTCTGCACCGATCTTGAGGACGTTATTT
    || ||     | | |    ||     ||||    | |  ||   |||  |  | ||  || ||  | | |||||||||||     || |  | |   ||||||||||| |||| | |||||||||||  ||||| || |||||||| ||||||||||| || ||| |  | ||||  |||| |||  | || || ||||| |
tttatgctgtgttggttct----agttttttagagcagattacccttgacagaattttgttacacttagagttgaatgttcatgtgtttaacaaattgc--tgcagGAAGCGCTGGAAGCGCACGATGGAGCCAGCAAGGGTAAGTACACAATTGGTCTTGGGCAGGACTGCATGGCCTATTGCAGCGAGGTGGAAGATGTTATCT

upper sequence: PP1S154_103V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os03g02710.1 (Oryza sativa), 3'ss of exon 1
-cggtggtgc--agaagcttttaagagggacatagatagaaatgtccacaagaaatggtcatttgtattggaatgttcatgaaagcaatatttgggggtgcagGAAGCGTTGGAGGAGCACGATGGAGTGAGCAAAGGAAAGTACACTATTGGTCTTGGACAAGACCGGCTTGCCTTCTGCACCGATCTTGAGGACGTTATTT
  ||   |      | ||| |  |    | |     ||  ||| |  |       |      | ||||| || ||   ||| | |  || ||||    | ||||| | | ||||| | || ||||| ||||||||||| |||||||| ||||| |||||||| ||  |  | ||||| ||||| ||  | || || |||||||
ttggcaatatctcaatgctgtacatcatgtcgatattaataatctttatttcgtgtttcacctagtattagactgcaaatgcatgtgatgtttgc---tacagGACGAGCTGGAGAATCATGATGGCGTGAGCAAAGGGAAGTACACCATTGGGCTTGGACAGGATAGCATGGCCTTTTGCACTGAAGTGGAAGATGTTATTT

upper sequence: PP1S154_103V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA09G27380.1 (Glycine max), 3'ss of exon 1
-----------------------------cggtggtgcagaagcttttaagagggacatagatagaaatgtccacaagaaatggtcatt-tgtattggaatgt-tcatgaaagcaatatttgggggt---gcagGAAGCGTTGGAGGAGCACGATGGAGTGAGCAAAGGAAAGTACACTATTGGTCTTGGACAAGACCGGCTTGCCTTCTGCACCGATCTTGAGGACGTTATTT
                             |  ||      |  ||||      |   ||   | |   |||  |   |  ||  | ||| | | || |  | | |  ||       | ||   ||||   ||||||||| |||||||  || ||||| ||||||||||| || ||||||||||| |||||||| ||  |  | ||||||||| | ||  |||| || ||||| |
gtctcaatttgtgtttttttctcataaagctctgacttttatactttctttttgt-tatgttttgttttgtaaagctgtgatttttattctttgtttggttatgttgtgtgttttgttttgatgggttctgcagGAAGCTTTGGAGGGTCATGATGGGGTGAGCAAAGGGAAATACACTATTGGGCTTGGACAGGATTGCATGGCCTTCTGCTCTGAGGTTGAAGATGTTATCT

upper sequence: PP1S154_103V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA16G32480.1 (Glycine max), 3'ss of exon 1
----------------------------cggtggtgcagaagcttttaagagggacatagatagaaatgt-ccacaagaaatggtcatttgta---ttggaatgttcatgaaa--------gcaatatttgggggtgcagGAAGCGTTGGAGGAGCACGATGGAGTGAGCAAAGGAAAGTACACTATTGGTCTTGGACAAGACCGGCTTGCCTTCTGCACCGATCTTGAGGACGTTATTT
                            |  || |    |  ||||       |  ||   | |   | |        ||   |  |||| ||   ||||  || | |||           |   |  | ||  |||||||| || |||||||  || ||||| ||||||||||| || || |||||||| |||||||| ||  |  | ||||||||| | ||  |||| || ||||| |
gtctcaatttgtggtttttctcataaagctctgatttttatactttcttttttgttatgttttgtgttttgttttgtaaagctgcgatttttattcttggtttggttatgttgtgttttttgttttgatgggttgtgcagGATGCTTTGGAGGGTCATGATGGGGTGAGCAAAGGGAAATATACTATTGGGCTTGGACAGGATTGCATGGCCTTCTGCTCTGAGGTTGAAGATGTTATCT

upper sequence: PP1S154_103V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv16s0100g00160.t01 (Vitis vinifera), 3'ss of exon 1
cggtggtgcagaagcttttaagagggacatagatagaaatgtccacaa--gaaatggtcatttgtattggaatgttcatgaaagcaatatt--tgggggtgcagGAAGCGTTGGAGGAGCACGATGGAGTGAGCAAAGGAAAGTACACTATTGGTCTTGGACAAGACCGGCTTGCCTTCTGCACCGATCTTGAGGACGTTATTT
      |  | |  || |   |   |    | ||  || |  | |  |  ||  | |||||||||     | |  |    | |   || ||  |||   |  ||||||| |||||||  || ||||| |  ||||||||||| ||||||||||| |||||||||||  |    || || || || ||  | || || || || |
-aactatatatatactgt---gcatgcttcaaatttaatttcctattatggactttgtcatttgttcctcatttgttcctataatgatcttgatggacatatagGAAGCTTTGGAGGCTCATGATGGTGCCAGCAAAGGAAAATACACTATTGGGCTTGGACAAGATTGCACGGCATTTTGTACAGAGGTGGAAGATGTCATCT

upper sequence: PP1S154_103V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv02s0025g04580.t01 (Vitis vinifera), 3'ss of exon 1
-cggtggtgcagaagcttttaagagggacatagatagaaatgtccacaagaaatggtcatttgtattggaatgttcatgaaagcaatatttgggggtgcagGAAGCGTTGGAGGAGCACGATGGAGTGAGCAAAGGAAAGTACACTATTGGTCTTGGACAAGACCGGCTTGCCTTCTGCACCGATCTTGAGGACGTTATTT
    |  |  |  || |||  | |      || |   |    |  |  | | ||   | |||| |||    ||||  ||       |   ||       |||||||  |||| |  || ||||| |  || || ||||||||||||||||| |||||||||||| |  | || |||||  | ||  | || || || || |
attctattatattagatttgcaaaatcttgtaaaccaatcacttaatcacacattaccttttgaatttatctgtttctgtttcttttgaatgcaaa-atagGAAGCTCTGGAAGTTCATGATGGTGCAAGTAAGGGAAAGTACACTATTGGACTTGGACAAGACTGTATGGCATTCTGTTCGGAGGTGGAAGATGTCATCT

upper sequence: PP1S154_103V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv16s0022g01310.t01 (Vitis vinifera), 3'ss of exon 1
cggtggtgcagaagcttttaagag---ggacatagatagaaatgt--ccacaagaaatggtcatttgtattggaatgttcatgaaagcaatatt--tgggggtgcagGAAGCGTTGGAGGAGCACGATGGAGTGAGCAAAGGAAAGTACACTATTGGTCTTGGACAAGACCGGCTTGCCTTCTGCACCGATCTTGAGGACGTTATTT
  | ||  |  || || |  | |    |  |||  ||  |||| |     |     |||| | ||   |||    ||||| |  ||   || ||  |||   |  ||||| | |||||||  || ||||| |  | ||||||||| ||||||||||| |||||||||||  |  | || || || || ||  | || || || || |
--gaggaactaaaactatagatatactgtgcatgcattcaaatttaatttcctattatggactttgtcatt----tgttcctataa-tgatcttgatggacatatagGAAACCTTGGAGGCTCATGATGGTGCCACCAAAGGAAAATACACTATTGGGCTTGGACAAGATTGCATGGCATTTTGTACAGAGGTGGAAGATGTCATCT

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|18353183|gb|BJ185238.1|BJ185238
EST:     TGGGCATTTTGGCCATGGACGTATACTTCCCAGCGAGTTACGTGCATCAG                         GAAGCGTTGGAGGAGCACGATGGAGTGAGCAAAGGAAAGTACACTATTGGT
genomic: TGGGCATTTTGGCCATGGACGTATACTTCCCAGCGAGTTACGTGCATCAGgtatgcattc ... gggggtgcagGAAGCGTTGGAGGAGCACGATGGAGTGAGCAAAGGAAAGTACACTATTGGT
EST: gi|208373795|gb|DC936580.1|DC936580
EST:     TGGGCATTTTGGCCATGGACGTATACTTCCCAGCGAGTTACGTGCATCAG                         GAAGCGTTGGAGGAGCACGATGGAGTGAGCAAAGGAAAGTACACTATTGGT
genomic: TGGGCATTTTGGCCATGGACGTATACTTCCCAGCGAGTTACGTGCATCAGgtatgcattc ... gggggtgcagGAAGCGTTGGAGGAGCACGATGGAGTGAGCAAAGGAAAGTACACTATTGGT
EST: gi|162176267|gb|FC352724.1|FC352724
EST:     TGGGCATTTTGGCCATGGACGTATACTTCCCAGCGAGTTACGTGCATCAG                         GAAGCGTTGGAGGAGCACGATGGAGTGAGCAAAGGAAAGTACACTATTGGT
genomic: TGGGCATTTTGGCCATGGACGTATACTTCCCAGCGAGTTACGTGCATCAGgtatgcattc ... gggggtgcagGAAGCGTTGGAGGAGCACGATGGAGTGAGCAAAGGAAAGTACACTATTGGT
EST: gi|100431625|gb|BY960292.1|BY960292
EST:     TGGGCATTTTGGCCATGGACGTATACTTCCCAGCGAGTTACGTGCATCAG                         GAAGCGTTGGAGGAGCACGATGGAGTGAGCAAAGGAAAGTACACTATTGGT
genomic: TGGGCATTTTGGCCATGGACGTATACTTCCCAGCGAGTTACGTGCATCAGgtatgcattc ... gggggtgcagGAAGCGTTGGAGGAGCACGATGGAGTGAGCAAAGGAAAGTACACTATTGGT
EST: gi|67508264|gb|BJ941133.1|BJ941133
EST:     TGGGCATTTTGGCCATGGACGTATACTTCCCAGCGAGTTACGTGCATCAG                         GAAGCGTTGGAGGAGCACGATGGAGTGAGCAAAGGAAAGTACACTATTGGT
genomic: TGGGCATTTTGGCCATGGACGTATACTTCCCAGCGAGTTACGTGCATCAGgtatgcattc ... gggggtgcagGAAGCGTTGGAGGAGCACGATGGAGTGAGCAAAGGAAAGTACACTATTGGT
EST: gi|208346757|gb|DC913038.1|DC913038
EST:     TGGGCATTTTGGCCATGGACGTATACTTCCCAGCGAGTTACGTGCATCAG                         GAAGCGTTGGAGGAGCACGATGGAGTGAGCAAAGGAAAGTACACTATTGGT
genomic: TGGGCATTTTGGCCATGGACGTATACTTCCCAGCGAGTTACGTGCATCAGgtatgcattc ... gggggtgcagGAAGCGTTGGAGGAGCACGATGGAGTGAGCAAAGGAAAGTACACTATTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagaaatggtcatttgtattggaatgttcatgaaagcaatatttgggggtgcagGAAGCGTTGGAGGAGCACGATGGAGTGAGCAAAGGAAAGTACACTATTGGTCTTGGACAAGACCGGCTTGCCTTCTGCACCGATCTTGAGGACGTTATTT
            atttgtatt  TA-rich tract