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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcgaagccaagggtagcttggtattatcgttgaagttagccttgtatatgccttggttttgcaaccttagtctacttgctgatgtggatttttttccagACTGCTGCACAAGATGGAGTTAAGCTGTGGGATCTGCGCAAGTTGAAGAACTTCCGTTCCTTTGCACCTTACGACAGTAACACACTAACAAATACAG

Basic information

species Physcomitrella patens
transcript PP1S14_250V6.2
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S14_250V6.2 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GLYMA10G26870.1 (Glycine max), 3'ss of exon 14
ttcgaagccaagggtagcttggtattatcgttgaagttagccttgtatatgcct-tggttttgcaaccttagtctacttgctgatgtggatttttttccagACTGCTGCACAAGATGGAGTTAAGCTGTGGGATCTGCGCAAGTTGAAGAACTTCCGTTCCTTTGCACCTTACGACAGTAACACACTAACAAATACAG
                     ||||    |   | || |    |   ||||    | |||||  |   |   | || |||      |  ||| |    ||||||||||| || ||||| |||||||| |||||||| || || |||||||||||| |    ||||| || || ||     | ||||  || |   | |
---------------------gtatgcaagaaaatgtaacgagtaagtatgatgattgttttatacagtatttttaattgtattcttaaattcta---cagACTGCTGCTCATGATGGTGTTAAGCTTTGGGATCTACGTAAATTGAAGAACTTCAGGAATTTTGCTCCATATGATTCAGAAACACCGACGAGCTCCG

upper sequence: PP1S14_250V6.2 (Physcomitrella patens), 3'ss of exon 14
lower sequence: GLYMA20G21330.1 (Glycine max), 3'ss of exon 14
ttcgaagccaagggtagcttggtattatcgttgaagttagccttgtatatgccttggttttgcaaccttagtctacttgctgatgtggatttttttccagACTGCTGCACAAGATGGAGTTAAGCTGTGGGATCTGCGCAAGTTGAAGAACTTCCGTTCCTTTGCACCTTACGACAGTAACACACTAACAAATACAG
                |  ||  |  |    || |  |||    ||||     ||| || | ||    || |||  |||      |  ||||     ||||||||||| || ||||| |||||||| |||||||| || ||  ||||||||||| |    ||||| || || ||     | |||| ||| |   | |
----------------gtatgtgagaa--aatgtaactagtaaagtatgatgattgtttatacag---tattcttattgtactcttaaatttga---cagACTGCTGCTCATGATGGTGTTAAGCTTTGGGATCTACGTAAACTGAAGAACTTCAGGAATTTTGCTCCATATGATTCGGAAACACCAACGAGCTCCG

upper sequence: PP1S14_250V6.2 (Physcomitrella patens), 3'ss of exon 14
lower sequence: AT1G04510.2 (Arabidopsis thaliana), 3'ss of exon 14
ttcgaagccaagggtagcttggtattatc---gttgaagttagccttgtatatgccttggttttgcaaccttagtctacttgctgatgtggatttttttccagACTGCTGCACAAGATGGAGTTAAGCTGTGGGATCTGCGCAAGTTGAAGAACTTCCGTTCCTTTGCACCTTACGACAGTAACACACTAACAAATACAG
   |    ||  |   | |||   | | |   || |||   ||  | | |   |  |   |||  |   |  |   || || ||  | |  |  || | | ||||||||||||  ||||| |||| | |||||||  |||||||||| |||||||||||  ||||||    |   ||    ||| |              
-gtgggtacattgactgattgacctaaactaagtagaaagaaggatagcaccaggttccttttgactgaccaa---tatttactattctttaaattgtac-agACTGCTGCACTGGATGGTGTTAGGTTGTGGGACTTGCGCAAGTTAAAGAACTTCCGAACCTTTGACTTTCCAGATGCAAACTCGG------------

upper sequence: PP1S14_250V6.2 (Physcomitrella patens), 3'ss of exon 14
lower sequence: AT2G33340.1 (Arabidopsis thaliana), 3'ss of exon 14
ttcgaagccaagggtagcttgg-tattatcgttgaagttagccttgtatatgccttggttttgcaaccttagtctacttgctgatgtggatttttttccagACTGCTGCACAAGATGGAGTTAAGCTGTGGGATCTGCGCAAGTTGAAGAACTTCCGTTCCTTTGCACCTTACGACAGTAACACACTAACAAATACAG
           | |||  |||   |  ||    ||||  ||  |      |   ||    || ||    |  | | |||  ||   |||| ||     ||||| |||||| | ||||| |||| | ||||||||||||||||||| | |||||||   || |||  | ||   ||    ||| |              
---------gtgagtactttgaacaaaatacgagaagagagaatacagcttaagttatgcttacatgaatgattttctttttgtcctggaattga---cagACAGCTGCAGAGGATGGTGTTAGGTTGTGGGATCTGCGCAAGTTAAGGAACTTCAAATCATTTTTATCTGCAGATGCGAACTCTG------------

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|67725231|gb|BJ975490.1|BJ975490
EST:     CAGGACCCGTGACGGATATATCTTTCTCTGAGAACGGTTACTTTTTGGCT                         ACTGCTGCACAAGATGGAGTTAAGCTGTGGGATCTGCGCAAGTTGAAGAAC
genomic: CAGGACCCGTGACGGATATATCTTTCTCTGAGAACGGTTACTTTTTGGCTgtaagtttgg ... ttttttccagACTGCTGCACAAGATGGAGTTAAGCTGTGGGATCTGCGCAAGTTGAAGAAC
EST: gi|162238755|gb|FC419053.1|FC419053
EST:     CAGGACCCGTGACGGATATATCTTTCTCTGAGAACGGTTACTTTTTGGCT                         ACTGCTGCACAAGATGGAGTTAAGCTGTGGGATCTGCGCAAGTTGAAGAAC
genomic: CAGGACCCGTGACGGATATATCTTTCTCTGAGAACGGTTACTTTTTGGCTgtaagtttgg ... ttttttccagACTGCTGCACAAGATGGAGTTAAGCTGTGGGATCTGCGCAAGTTGAAGAAC
EST: gi|37822061|gb|BJ580127.1|BJ580127
EST:     CTGAGAACGGTTACTTTTTGGCT                         ACTGCTGCACAAGATGGAGTTAAGCTGTGGGATCTGCGCAAGTTGAAGAAC
genomic: CTGAGAACGGTTACTTTTTGGCTgtaagtttgg ... ttttttccagACTGCTGCACAAGATGGAGTTAAGCTGTGGGATCTGCGCAAGTTGAAGAAC
EST: gi|6102231|gb|AW126701.1|AW126701
EST:     CAGGACCCGTGACGGATATATCTTTCTCTGAGAACGGTTACTTTTTGGCT                         ACTGCTGCACAAGATGGAGTTAAGCTGTGGGATCTGCGCAAGTTGAAGAAC
genomic: CAGGACCCGTGACGGATATATCTTTCTCTGAGAACGGTTACTTTTTGGCTgtaagtttgg ... ttttttccagACTGCTGCACAAGATGGAGTTAAGCTGTGGGATCTGCGCAAGTTGAAGAAC
EST: gi|19787424|gb|BQ040623.1|BQ040623
EST:     CAGGACCCGTGACGGATATATCTTTCTCTGAGAACGGTTACTTTTTGGCT                         ACTGCTGCACAAGATGGAGTTAAGCTGTGGGATCTGCGCAAGTTGAAGAAC
genomic: CAGGACCCGTGACGGATATATCTTTCTCTGAGAACGGTTACTTTTTGGCTgtaagtttgg ... ttttttccagACTGCTGCACAAGATGGAGTTAAGCTGTGGGATCTGCGCAAGTTGAAGAAC
EST: gi|67726008|gb|BJ976267.1|BJ976267
EST:     CAGGACCCGTGACGGATATATCTTTCTCTGAGAACGGTTACTTTTTGGCT                         ACTGCTGCACAAGATGGAGTTAAGCTGTGGGATCTGCGCAAGTTGAAGAAC
genomic: CAGGACCCGTGACGGATATATCTTTCTCTGAGAACGGTTACTTTTTGGCTgtaagtttgg ... ttttttccagACTGCTGCACAAGATGGAGTTAAGCTGTGGGATCTGCGCAAGTTGAAGAAC
EST: gi|162182529|gb|FC357504.1|FC357504
EST:     CAGGACCCGTGACGGATATATCTTTCTCTGAGAACGGTTACTTTTTGGCT                         ACTGCTGCACA
genomic: CAGGACCCGTGACGGATATATCTTTCTCTGAGAACGGTTACTTTTTGGCTgtaagtttgg ... ttttttccagACTGCTGCACA
EST: gi|162257669|gb|FC433596.1|FC433596
EST:     CAGGACCCGTGACGGATATATCTTTCTCTGAGAACGGTTACTTTTTGGCT                         ACTGCTGCACAAGATGGAGTTAAGCTGTGGGATCTGCGCAAGTTGAAGAAC
genomic: CAGGACCCGTGACGGATATATCTTTCTCTGAGAACGGTTACTTTTTGGCTgtaagtttgg ... ttttttccagACTGCTGCACAAGATGGAGTTAAGCTGTGGGATCTGCGCAAGTTGAAGAAC
EST: gi|162182528|gb|FC357503.1|FC357503
EST:     CAGGACCCGTGACGGATATATCTTTCTCTGAGAACGGTTACTTTTTGGCT                         ACTGCTGCACAAGATGGAGTTAAGCTGTGGGATCTGCGCAAGTTGAAGAAC
genomic: CAGGACCCGTGACGGATATATCTTTCTCTGAGAACGGTTACTTTTTGGCTgtaagtttgg ... ttttttccagACTGCTGCACAAGATGGAGTTAAGCTGTGGGATCTGCGCAAGTTGAAGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatgccttggttttgcaaccttagtctacttgctgatgtggatttttttccagACTGCTGCACAAGATGGAGTTAAGCTGTGGGATCTGCGCAAGTTGAAGAACTTCCGTTCCTTTGCACCTTACGACAGTAACACACTAACAAATACAG
                                tgctgat  putative branch site (score: 3)
                                            tttttttcc  putative PPT
                                           attttttt  TA-rich tract