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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgattaatttacttttttcgttgggtagggatcgtagatggttaaaccgtaatttagagatctgataattaatgacttgcgtgggattccgcatgcagGTAGTTGAGGATGGTTATGAATTCTTCGCCAAGCGCCAGCTGGTTACTATTTTCTCTGCACCGAATTACTGTGGTGAATTTGATAATGCGGGTGCCATGA

Basic information

species Physcomitrella patens
transcript PP1S283_48V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os06g06880.1 (Oryza sativa), 3'ss of exon 2
attgattaatttacttttttcgt--tgggtagggatcgtagatggttaaaccgtaatttagagatctgataattaatgacttgcg-tgggat-tccgcatgcagGTAGTTGAGGATGGTTATGAATTCTTCGCCAAGCGCCAGCTGGTTACTATTTTCTCTGCACCGAATTACTGTGGTGAATTTGATAATGCGGGTGCCATGA
 ||  | | |  |  | |   ||  ||       || ||  ||  || | |  |  | |  |  | |   | | | ||  ||| | |||||| | | |   ||||| || |||||||| ||||||||||| || ||||||||||| || || || ||||||||||| || || ||||| || ||||| |||||||| || ||||
-tttctcagtgaatctctgctgtagtgaactattattgtt-attattgagcgattgtcttta--tttaccactcactgctttgtgctgggatcttctctgacagGTTGTGGAGGATGGCTATGAATTCTTTGCTAAGCGCCAGCTTGTAACCATATTCTCTGCACCCAACTATTGTGGCGAGTTTGACAATGCGGGGGCGATGA

upper sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os02g57450.2 (Oryza sativa), 3'ss of exon 2
attgattaatttacttttttcgttgggtagggatcgtagatggttaaaccgtaatttagagatctgataattaatgacttgcgtgggattccgcatgcagGTAGTTGAGGATGGTTATGAATTCTTCGCCAAGCGCCAGCTGGTTACTATTTTCTCTGCACCGAATTACTGTGGTGAATTTGATAATGCGGGTGCCATGA
      |     |   |     ||   |     |  ||  |   | | |   | |  |  ||| |   | ||| |  ||||| | |   |  | || ||||| || || ||||| || || ||||| || || ||||| || || || || ||||| || || ||||||||||| |||||||||||||| ||||||||||
-----gtgccccatgctcacaattacctgacctttttatttttcttacca--agtgaattgatttatcagttatt--cttgccttg---ttggaattcagGTTGTCGAAGATGGGTACGAGTTCTTTGCTAACCGCCAACTTGTAACAATATTCTCGGCCCCTAATTACTGTGGAGAATTTGATAATGCTGGTGCCATGA

upper sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G016930_T01 (Zea mays), 3'ss of exon 2
-attgattaatttacttttttcgttgggta-gggatcgtagatggttaaaccgtaatttagagatctgataattaatgacttgcgtgggattccgcatgcagGTAGTTGAGGATGGTTATGAATTCTTCGCCAAGCGCCAGCTGGTTACTATTTTCTCTGCACCGAATTACTGTGGTGAATTTGATAATGCGGGTGCCATGA
 |     ||   | ||  | |  |  | |  |  ||  ||  | | |    | |    | ||   |   | | |  |  |||     | ||        ||||| || ||||||||||||||||| ||||| || |||||||| || || || ||||| |||||||| |||||||| || || || ||||| |||||  |||
aaacatctagagtgctcatctgttgagctgtgaaatactattttggttgtgcattgccttgattaccattgacttct--cttcaactgaatctacttcacagGTCGTAGAGGATGGTTATGAATTTTTCGCAAAACGCCAGCTTGTAACAATATTCTCAGCACCGAACTACTGTGGAGAGTTCGACAATGCTGGTGCACTGA

upper sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G160237_T02 (Zea mays), 3'ss of exon 3
attgattaatttacttttttcgttgggtagggatcgtagatggttaaaccgtaattta--gagatctgataattaatgacttgcgtgggattccgcatgcagGTAGTTGAGGATGGTTATGAATTCTTCGCCAAGCGCCAGCTGGTTACTATTTTCTCTGCACCGAATTACTGTGGTGAATTTGATAATGCGGGTGCCATGA
    |     |||   |||      | |   | |   |  |  |||   |  | || |  |  |  |||   |   |   |||| || |||      | ||||| || |||||||| |||||||| || ||  |  | ||||| || || || ||||| || || ||||| |||||||||||||||||||| ||||| ||||
--gtaccgccttagcatttagtgcagcttctgttttgatctttttatttcacagttaactggaaattgaaggtgtttatattgcatgcgatgtgatgt-cagGTTGTCGAGGATGGGTATGAATTTTTTGCTGACAGACAGCTTGTCACCATATTCTCGGCCCCCAATTATTGTGGTGAATTTGATAATGCTGGTGCAATGA

upper sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA05G37370.1 (Glycine max), 3'ss of exon 2
---attgattaatt---tacttttttcgttgggtagggatcgtagatggttaaaccgtaatttagagatctgataattaatgacttgcgtgggattccgcatgcagGTAGTTGAGGATGGTTATGAATTCTTCGCCAAGCGCCAGCTGGTTACTATTTTCTCTGCACCGAATTACTGTGGTGAATTTGATAATGCGGGTGCCATGA
     ||||  |||    | ||  || | |    ||   |  |  || | |||| | |  ||||  | | |  |  || |  | ||   |||| ||     | ||||| || |||||||| ||||| || || |||||||| |||||||| || || ||||| ||||| |||||||| ||||||||||||||||| ||||| ||||
tatgctgatgtattgggcatttgcttggctcatcagtcttaatccattggtaaatc-tggtttaatgttttcct--tttaaaattt---tgggctttgtgtttcagGTTGTAGAGGATGGATATGAGTTTTTTGCCAAGCGTCAGCTGGTGACGATATTCTCCGCACCAAATTACTGCGGTGAATTTGATAATGCTGGTGCTATGA

upper sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA08G02180.1 (Glycine max), 3'ss of exon 2
attgattaatttacttttttcgttgggtagggatcgtagatggttaaaccgtaatttagagatctgataattaatgacttgcgtgggattccg-----catgcagGTAGTTGAGGATGGTTATGAATTCTTCGCCAAGCGCCAGCTGGTTACTATTTTCTCTGCACCGAATTACTGTGGTGAATTTGATAATGCGGGTGCCATGA
    ||  |||     ||| | | |   |    || ||     ||  |  | ||||     ||||| |  |   |        |   |||  |       |  |||| || |||||||| || || || || |||||||| ||||| || ||||| ||||| ||||| || ||||||||||||||||||||||| ||||| ||||
----atgtattgggcatttgcttggctcatcagtcttaatccattttaatg-aattggtgaatctggttttatgttttccttctaaaattttgggctttgtatagGTTGTAGAGGATGGATACGAGTTTTTTGCCAAGCGTCAGCTAGTGACTATATTCTCCGCACCAAACTACTGTGGTGAATTTGATAATGCTGGTGCTATGA

upper sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT3G46820.1 (Arabidopsis thaliana), 3'ss of exon 2
attgattaatttacttttttcgttgggtagggatcgtagatggttaaaccgtaatttagagatctgataattaatgacttgcgtgggattccgcatgcagGTAGTTGAGGATGGTTATGAATTCTTCGCCAAGCGCCAGCTGGTTACTATTTTCTCTGCACCGAATTACTGTGGTGAATTTGATAATGCGGGTGCCATGA
          ||| |   ||   |   |        ||| |  ||     |  |  | || ||||| |  | ||  || |       | | | |   ||||| || |||||||| ||||| ||||| ||  |  | ||||| || ||||| || ||||| || || ||||||||||||||||| |||||||||||  |||
---------gttagtacattgtataaatgtttcctctagtttttttgtttgggaaatcga-atctgctgctcaagaacctat-----aatgctcccacagGTTGTAGAGGATGGGTATGAGTTCTTTGCTGATAGACAGCTTGTGACTATGTTTTCTGCTCCAAACTACTGTGGTGAATTTGACAATGCGGGTGCATTGA

upper sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT5G59160.2 (Arabidopsis thaliana), 3'ss of exon 2
attgattaatt-tacttttttcgttgggtagggatcgtagatggttaaaccgtaatttagagatctgataattaatgacttgcgtgggattccgcatgcagGTAGTTGAGGATGGTTATGAATTCTTCGCCAAGCGCCAGCTGGTTACTATTTTCTCTGCACCGAATTACTGTGGTGAATTTGATAATGCGGGTGCCATGA
 ||  |    |  ||  | ||||||        |    |||||         |  | || | || | |   ||  ||  || |      ||   |    |||| || |||||||| ||||| || |||||| |  | ||||| ||||| || || ||||| || || ||||||||||||||||| ||||| ||||| ||||
gttcgtcgtctacacactgttcgtttctattttactaaagatgtcacggaacttctataaaaatataactgttg-tgtttttc------tttttctaaaagGTTGTAGAGGATGGATATGAGTTTTTCGCCGATAGACAGCTTGTTACGATATTTTCTGCTCCCAACTACTGTGGTGAATTTGACAATGCTGGTGCTATGA

upper sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT2G39840.1 (Arabidopsis thaliana), 3'ss of exon 2
attgattaatttacttttttcgttgggtagggatcgtagatggttaaaccgtaatttagagatctgataattaatgacttgcgtgggattccgcatg-cagGTAGTTGAGGATGGTTATGAATTCTTCGCCAAGCGCCAGCTGGTTACTATTTTCTCTGCACCGAATTACTGTGGTGAATTTGATAATGCGGGTGCCATGA
         |  |  ||||||  |    | |  || | |||  |   || |   ||| | ||| |  |||  |  || |||     ||||    ||| ||||| || |||||||| ||||| ||||| ||  |  | || || || ||  | || || || || || ||||||||||||||||||||||| ||||| ||||
--------gtagatatttttcaat---catgtctctttgatact---actgc--ttttgtgatgt--taacaagggagttg-----gattttttatggcagGTCGTGGAGGATGGGTATGAGTTCTTTGCTGATAGACAACTTGTGACGGTGTTTTCAGCTCCTAACTACTGTGGTGAATTTGATAATGCTGGTGCGATGA

upper sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv05s0049g00890.t01 (Vitis vinifera), 3'ss of exon 2
attgattaatttacttttttcgttgggtagggatcgtagatggttaaaccgtaatttagagatctgata-attaatgacttgcgtgggattccgc----atgcagGTAGTTGAGGATGGTTATGAATTCTTCGCCAAGCGCCAGCTGGTTACTATTTTCTCTGCACCGAATTACTGTGGTGAATTTGATAATGCGGGTGCCATGA
   | || |  | || |||| | |   |     |  |   |||| |  ||    |||| |  ||| |   |||  |  ||| |     ||| |       ||||||| || || ||||| || || || || || ||  | || || || || || || || ||||| |||||||||||||| ||||||||||||||||||||||
---gtttcagct-ctgttttagctttttgcattttttttttggtca--cc----tttaaacctctcaggcatttttctcttactacatatttccttgttgtgcagGTTGTGGAAGATGGATACGAGTTTTTTGCTAATAGACAACTTGTAACCATATTTTCAGCACCTAATTACTGTGGTGAGTTTGATAATGCGGGTGCCATGA

upper sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv14s0036g00370.t01 (Vitis vinifera), 3'ss of exon 2
attgattaatttacttttttcgttgggtagggatcgtagatggttaaaccgtaat-ttagagatctgataattaatgacttgcgtgggattccgcatgcagGTAGTTGAGGATGGTTATGAATTCTTCGCCAAGCGCCAGCTGGTTACTATTTTCTCTGCACCGAATTACTGTGGTGAATTTGATAATGCGGGTGCCATGA
    |  | || ||| |  | | || |  | | |  |   |  |||  |  ||    |  |  | | |||     |    |  |    | |     ||||||| || |||||||||||||||||||| || || || || || || || || || || || || ||||| ||||| || ||||||||||| ||||||||||
-cataagatttgactgtaatggatgtgaggagcttattacttattactcattaggacttcaattttcatagaggtttttctaagataaaattaatttgcagGTTGTAGAGGATGGTTATGAATTCTTTGCAAACCGGCAACTTGTAACCATATTTTCGGCGCCTAATTATTGTGGGGAGTTTGATAATGCTGGTGCCATGA

upper sequence: PP1S283_48V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv13s0019g02410.t01 (Vitis vinifera), 3'ss of exon 2
attgattaatttacttttttcgttgggtagggatcgtagatggttaaaccgtaatttagagatctgataattaatgacttgcgtgggattccgcatgcagGTAGTTGAGGATGGTTATGAATTCTTCGCCAAGCGCCAGCTGGTTACTATTTTCTCTGCACCGAATTACTGTGGTGAATTTGATAATGCGGGTGCCATGA
                          ||      | |   | |||    | |  | ||     || ||  | ||  |||    |     |     |  |||| || |||||||| ||||||||||| ||| |  | || || |||||  | ||||| || || || ||||||||||||||||||||||| ||||| ||||
--------------------------gttattggcatttttagttttctcttgttctattttactcatgctgaa-aactgaaattcttcttttggtctagGTTGTGGAGGATGGATATGAATTCTTTGCCGATAGGCAACTTGTTACCGTATTCTCAGCTCCCAACTACTGTGGTGAATTTGATAATGCTGGTGCAATGA

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|37852534|gb|BJ610542.1|BJ610542
EST:     CAGAGTTTCTACAAAAGCATGACTTGGATCTTATCTGCCGAGCCCATCAA                         GTAGTTGAGGATGGTTATGAATTCTTCGCCAAGCGCCAGCTGGTTACTATT
genomic: CAGAGTTTCTACAAAAGCATGACTTGGATCTTATCTGCCGAGCCCATCAAgtactgtgat ... ccgcatgcagGTAGTTGAGGATGGTTATGAATTCTTCGCCAAGCGCCAGCTGGTTACTATT
EST: gi|37841068|gb|BJ599076.1|BJ599076
EST:     CAGAGTTTCTACAAAAGCATGACTTGGATCTTATCTGCCGAGCCCATCAA                         GTAGTTGAGGATGGTTATGAATTCTTCGCCAAGCGCCAGCTGGTTACTATT
genomic: CAGAGTTTCTACAAAAGCATGACTTGGATCTTATCTGCCGAGCCCATCAAgtactgtgat ... ccgcatgcagGTAGTTGAGGATGGTTATGAATTCTTCGCCAAGCGCCAGCTGGTTACTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaccgtaatttagagatctgataattaatgacttgcgtgggattccgcatgcagGTAGTTGAGGATGGTTATGAATTCTTCGCCAAGCGCCAGCTGGTTACTATTTTCTCTGCACCGAATTACTGTGGTGAATTTGATAATGCGGGTGCCATGA
                       aattaat  putative branch site (score: 3)
                atctgataattaat  TA-rich tract