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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtagtacgatgaaacagagcatttttgaatttgagctagaattcggtggatttctcctccactgtgtgtggtctaaagacctttgtggggactgtgcagTGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGACTTTCCAGACACTACAAAATGAGTGTCAGGTTTCTCTCAACACTGTGGAC

Basic information

species Physcomitrella patens
transcript PP1S31_68V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S31_68V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os01g21940.1 (Oryza sativa), 3'ss of exon 1
cgtagtacgatgaaacagagcatttt--tgaatttgagctagaattcggtggatttctcctccactgtgtgtggtctaaagaccttt-----gtggggactgtg----cagTGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGACTTTCCAGACACTACAAAATGAGTGTCAGGTTTCTCTCAACACTGTGGAC
           ||| |    |  |    |    | | |||| |  |  |   |||  | | | |   ||   ||| | |     |||     |||  | |  ||    ||| ||  | |||||||||||||||||||| || ||||||||  |||||||||| |||||||| || || || ||||| ||||| || |||||||| || |||
-----------gaaccccccccctcccattgggtagtgctatagcttaggaaattattacgcaaggttgctaggtttgatagtgtttcttgcgtgatgtccatggatgcagCGTGGTGAAGATAGTGCTGCAGTTCTGCAAGGAGAACTCGCTGCAGCAGACGTTCCAGACGCTGCAGAACGAGTGCCAGGTCTCGCTCAACACCGTCGAC

upper sequence: PP1S31_68V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 1
--cgtagtacgatgaaacagagcatttttgaatttgagctagaattcggtggatttctcctccactgtgtgtggtctaaagacctttgtggggactgtgcagTGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGACTTTCCAGACACTACAAAATGAGTGTCAGGTTTCTCTCAACACTGTGGAC
    |  |   ||  | | ||| |       | |||   ||| ||| |     |     |  ||  |  | ||  |   |    ||| |   |  || |||| ||  |||||||||||||||||||||| || ||||| ||  |||||||||| |||||||| || ||||| ||||| ||||| || ||||||||||| |||
catcttattgaatctatccgagaaccgcctgacttgcagtagcattagtgtcttaaggtcgacaaaggatttgagcgcgatgttttttttttg--tgcgcagCGTGGTTAAGATAGTGCTGCAGTTCTGCAAGGAGAATTCGCTGCAGCAGACGTTCCAGACGCTGCAAAACGAGTGCCAGGTCTCCCTCAACACTGTTGAC

upper sequence: PP1S31_68V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 1
------------------------------------------------------------------------------cgtagtacgatgaaacagagcatttttgaa------tttgagctagaattcggtggatttctcctccactgtgtgtggtctaaagacctttgtggggactgtgcagTGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGACTTTCCAGACACTACAAAATGAGTGTCAGGTTTCTCTCAACACTGTGGAC
                                                                               ||   |||   ||    |||   ||| |       || |  | | |  ||  |    || |       | |||||  | |  |     |  | |   ||  |||||||||| || || ||||| ||||| || |||||||| || ||||| |||||||| ||||  || || || || || ||||||||||| |||||||| |||
gtaagtagtttcatttgccaactcttgaaaatcgggaaatttaattttcttcgtttactgaatcacatgtttcaattttgtttgacgtctaattgaagctcgtttaatggttctttcgcacaatagatcttttttcttttttaaatttatgtgtcattttcaatttctgtttgccccttcgcagTGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGACTTTTCAGATGCTGCAGAACGAATGCCAGGTTTCTCTGAACACTGTTGAC

upper sequence: PP1S31_68V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 1
---------------------------------------------------------------cgtagtacgatgaaacagagcatttttgaatttgagctagaattcggtggat--ttctcctccactgtgtgtggtctaaagaccttt---------gtggggactgtgcagTGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGACTTTCCAGACACTACAAAATGAGTGTCAGGTTTCTCTCAACACTGTGGAC
                                                                 |   | | |  ||    | |||||| |  |  |  | ||| ||| |  ||  ||||    ||| ||   |  | |     | |||         ||  |  ||  |||||||||| ||||| ||||| ||||| || ||||| || || ||||| |||||||| ||||  || || || || || ||||||||||| ||||| || |||
gtaagtagtttcatttggcaactcttgaaaatcgggaaaatttaattttcttcgtttactaaatctcacatgtttcaattttgtatttttcatgtctaattggaactcgtttaatggttctttcgcacagtagatcttttcccctctttttgaattaaagtttgcccttcgcagTGTCATCAAGATTGTGCTTCAGTTTTGCAAAGAAAATTCGTTGCATCAGACTTTTCAGATGCTGCAGAACGAATGCCAGGTTTCTCTGAACACCGTTGAC

upper sequence: PP1S31_68V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT1G73720.1 (Arabidopsis thaliana), 3'ss of exon 1
-----cgtagtacgatgaaacagagcat-ttttgaatttgagctagaattcggtggatttctcctccactgtgtgtggtctaaagacctttgtggggactgtg-cagTGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGACTTTCCAGACACTACAAAATGAGTGTCAGGTTTCTCTCAACACTGTGGAC
       |||||  ||   |  ||| |  ||||||   |       |  |  ||| |  ||| |  | ||    |   ||||       |||||  || |||  |||||| || |||||  |||| |||||||| ||||| || || ||| | ||||| ||||||||| ||||||  ||||||||||||||  | || || || |||
attttgttagtaatattggatggagaacgttttgatgctatatgtcagctttgtgtagatcttcatccctaatagctctcta-------ttgtgttgaatgtctcagTGTAATAAAGATTATGCTTCAGTTCTGCAAAGAAAATTCCTTGAATCAGACATTCCAGACATTACAAAGCGAGTGTCAGGTTTCCTTGAATACAGTAGAC

upper sequence: PP1S31_68V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 1
cgtagtacgatgaaacagagcatttttgaat-ttgag----ctagaattcggtggatttctcctccactgtg--tgtggtctaaagacctttgtggggactgtgcagTGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGACTTTCCAGACACTACAAAATGAGTGTCAGGTTTCTCTCAACACTGTGGAC
    |   | | | |   |   ||  |  || || ||    |||  | |   | |  || |  |     ||   | |  | | | |   ||  |    |   | ||||||||||||||| ||||| ||||| |||||||| || || ||||| || || || |||||| |||||| |||||||||||| ||| | || || || |||
----ggttgtttatatgtattcttcctatatcttcagctgtctaatactttatagtgttttgatgtgaagtaaatctaattttatgtatttcttc---atctttcagTGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAACGTTTCAGACATTACAAAGTGAGTGTCAGGTATCTTTGAATACGGTCGAC

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|208378663|gb|DC903694.1|DC903694
EST:     GTTTATTTGTGGTACTTGGTCATGTCCACTCTCGAAATCGAAGCGCGTGA                         TGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGAC
genomic: GTTTATTTGTGGTACTTGGTCATGTCCACTCTCGAAATCGAAGCGCGTGAgtaagtatct ... gactgtgcagTGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGAC
EST: gi|18362895|gb|BJ194967.1|BJ194967
EST:     GTTTATTTGTGGTACTTGGTCATGTCCACTCTCGAAATCGAAGCGCGTGA                         TGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGAC
genomic: GTTTATTTGTGGTACTTGGTCATGTCCACTCTCGAAATCGAAGCGCGTGAgtaagtatct ... gactgtgcagTGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGAC
EST: gi|67717592|gb|BJ967851.1|BJ967851
EST:     GTTTATTTGTGGTACTTGGTCATGTCCACTCTCGAAATCGAAGCGCGTGA                         TGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGAC
genomic: GTTTATTTGTGGTACTTGGTCATGTCCACTCTCGAAATCGAAGCGCGTGAgtaagtatct ... gactgtgcagTGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGAC
EST: gi|208379508|gb|DC911119.1|DC911119
EST:     GTTTATTTGTGGTACTTGGTCATGTCCACTCTCGAAATCNAANCGCGTGA                         TGTCATTAANATAGTGCTGCANTTCTGTAAAGAGAACTCATTGCAGCAGAC
genomic: GTTTATTTGTGGTACTTGGTCATGTCCACTCTCGAAATCGAAGCGCGTGAgtaagtatct ... gactgtgcagTGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGAC
EST: gi|18352925|gb|BJ184980.1|BJ184980
EST:     GTTTATTTGTGGTACTTGGTCATGTCCACTCTCGAAATCGAAGCGCGTGA                         TGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGAC
genomic: GTTTATTTGTGGTACTTGGTCATGTCCACTCTCGAAATCGAAGCGCGTGAgtaagtatct ... gactgtgcagTGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGAC
EST: gi|67573598|gb|BJ946422.1|BJ946422
EST:     GTTTATTTGTGGTACTTGGTCATGTCCACTCTCGAAATCGAAGCGCGTGA                         TGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGAC
genomic: GTTTATTTGTGGTACTTGGTCATGTCCACTCTCGAAATCGAAGCGCGTGAgtaagtatct ... gactgtgcagTGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGAC
EST: gi|18356245|gb|BJ188304.1|BJ188304
EST:     GTTTATTTGTGGTACTTGGTCATGTCCACTCTCGAAATCGAAGCGCGTGA                         TGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGAC
genomic: GTTTATTTGTGGTACTTGGTCATGTCCACTCTCGAAATCGAAGCGCGTGAgtaagtatct ... gactgtgcagTGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGAC
EST: gi|100450837|gb|CJ974464.1|CJ974464
EST:     GTTTATTTGTGGTACTTGGTCATGTCCACTCTCGAAATCGAAGCGCGTGA                         TGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGAC
genomic: GTTTATTTGTGGTACTTGGTCATGTCCACTCTCGAAATCGAAGCGCGTGAgtaagtatct ... gactgtgcagTGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGAC
EST: gi|100431243|gb|BY960099.1|BY960099
EST:     GTTTATTTGTGGTACTTGGTCATGTCCACTCTCGAAATCGAAGCGCGTGA                         TGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGAC
genomic: GTTTATTTGTGGTACTTGGTCATGTCCACTCTCGAAATCGAAGCGCGTGAgtaagtatct ... gactgtgcagTGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGAC
EST: gi|18350111|gb|BJ182162.1|BJ182162
EST:     GTTTATTTGTGGTACTTGGTCATGTCCACTCTCGAAATCGAAGCGCGTGA                         TGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGAC
genomic: GTTTATTTGTGGTACTTGGTCATGTCCACTCTCGAAATCGAAGCGCGTGAgtaagtatct ... gactgtgcagTGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGAC
EST: gi|100407287|gb|BY974097.1|BY974097
EST:     GTTTATTTGTGGTACTTGGTCATGTCCACTCTCGAAATCGAAGCGC-TG-                         T--CATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGAC
genomic: GTTTATTTGTGGTACTTGGTCATGTCCACTCTCGAAATCGAAGCGCGTGAgtaagtatct ... gactgtgcagTGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtggatttctcctccactgtgtgtggtctaaagacctttgtggggactgtgcagTGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGACTTTCCAGACACTACAAAATGAGTGTCAGGTTTCTCTCAACACTGTGGAC
                          gtctaaa  putative branch site (score: 3)