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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaatttttctgtttgggggcagcagagatgaactttacctactggtttgtctcctctggcagaccaattgacgttgcttcccctgctgaactgttgtagGGATACTGCAGGGCAAGAAAGGTTTCGAAGTCTAATTCCTAGCTATATCCGTGATTCATCAGTCGCAGTGGTCGTTTATGACGTGTCAA

Basic information

species Physcomitrella patens
transcript PP1S353_41V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S353_41V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA11G38110.1 (Glycine max), 3'ss of exon 2
---------------------------------------------acaatttttctgtttgggggcagcagagatgaactttacctactggtttgt----ctcctctggcagaccaattgacgtt----gcttcccctgctgaactgttgtagGGATACTGCAGGGCAAGAAAGGTTTCGAAGTCTAATTCCTAGCTATATCCGTGATTCATCAGTCGCAGTGGTCGTTTATGACGTGTCAA
                                                 ||||| ||| |      ||      |  | || || |  |  | |       |  | |  | |  |  |  | |||    |  |  | |  |  |   |   ||||||||||||||||||||||||||| ||||||| ||||| ||||| ||  | ||||| || || |||||  | || ||||| ||  | |
gtaggccatattcctcttcaactcataccacaagatctatttatatttgtttttttgtattttaaaagttatattagatttcacattgttatgtaggcaattttttttaccgttctttgtatgttaaaagtgtgtcgtattttaacttcacagGGATACTGCAGGGCAAGAAAGGTTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATTGTATATGATGTAGCCA

upper sequence: PP1S353_41V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA08G14390.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------acaatttttctgtttgggggcagcagagatgaactttac-ctactggtttgtctcctctggcagaccaattgacgttgcttcc---cctgctgaac-----tgttgtagGGATACTGCAGGGCAAGAAAGGTTTCGAAGTCTAATTCCTAGCTATATCCGTGATTCATCAGTCGCAGTGGTCGTTTATGACGTGTCAA
                                                      ||| | | |||     ||       |  | |  ||  | ||||| || ||  |  |        |||        |||    | |  |  |        |   ||||||||||||||||||||||| ||| ||||||| ||||| ||||| ||  | ||||| || || |||||  | || ||||| ||  | |
gtaggatgaattcctcttcaaatcatatatacaagctcagtctttttatatttgtttgtttatttttcaacaattatattagagtgcacattgctggtatgcctagtaggcattgtttatttttacaatttctgagcttagtatatgttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTATAGTATATGATGTTGCTA

upper sequence: PP1S353_41V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA18G02040.1 (Glycine max), 3'ss of exon 2
--------------------------------------acaatttttctgtttgggggcagcagagatgaactttac-ctactggtttgtctcctctggcagacca----------attgacgttgcttcccctgctgaactgttgtagGGATACTGCAGGGCAAGAAAGGTTTCGAAGTCTAATTCCTAGCTATATCCGTGATTCATCAGTCGCAGTGGTCGTTTATGACGTGTCAA
                                      |    | || | |||      ||      |  | || ||  |  ||  | | | | | |   |  |||           || |  ||| |||   |  | |||| |   ||||||||||||||||||||||| ||| ||||||| ||||| ||||| ||  | ||||| || || ||||| || || || || ||  | |
gtaggccatattcctctttaactcatgccacaagacctatttatatttttttttctaaaagttatattagatttcacattgttgtgtaggcactttttttaacccattctttgtatgttaaaattgtttcatatttt-aact-tcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTGATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTGTTGTATACGATGTAGCCA

upper sequence: PP1S353_41V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA05G31200.1 (Glycine max), 3'ss of exon 2
----------------------------------------------acaatttttctgtttgggggcagcagagatgaactttac-ctactggtttgtctcctctggcagaccaattgacgttgcttcc---cctgctgaac-----tgttgtagGGATACTGCAGGGCAAGAAAGGTTTCGAAGTCTAATTCCTAGCTATATCCGTGATTCATCAGTCGCAGTGGTCGTTTATGACGTGTCAA
                                              | | || || | |||     ||       |  | |  ||  | |||||  | ||  |  |        |||        |||    | |  |  |        |   ||||||||||||||||||||||| ||| ||||||| ||||| ||||| ||  | ||||| || || || ||  | || ||||| ||  | |
gtaggatgactcctcttcaaatcataaatacaagctcagtctatttatatttgttttatttttcaacaattatattagagtacacattgctggtacgccttataggcactctttattcttacaatttctgagcttagtatatgttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTCATTCCAAGCTACATAAGAGATTCTTCTGTTGCGGTTATAGTATATGATGTTGCTA

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|100372220|gb|BY985492.1|BY985492
EST:     CTTTCAAAGACGATGTACCTAGAGGATCGCACTGTACGCCTACAGCTCTG                         GGATACTGCAGGGCAAGAAAGGTTTCGAAGTCTAATTCCTAGCTATATCCG
genomic: CTTTCAAAGACGATGTACCTAGAGGATCGCACTGTACGCCTACAGCTCTGgtagcttgcg ... actgttgtagGGATACTGCAGGGCAAGAAAGGTTTCGAAGTCTAATTCCTAGCTATATCCG
EST: gi|162272435|gb|FC449061.1|FC449061
EST:     CTTTC-AAGACGATGTACCTAGAGGATCGCACTGTACGCCTACAGCTCTG                         GGATACTGCAGGGCAAGAAAGGTTTCGAAGTCTAATTCCTAGCTATATCCG
genomic: CTTTCAAAGACGATGTACCTAGAGGATCGCACTGTACGCCTACAGCTCTGgtagcttgcg ... actgttgtagGGATACTGCAGGGCAAGAAAGGTTTCGAAGTCTAATTCCTAGCTATATCCG
EST: gi|18329546|gb|BJ161552.1|BJ161552
EST:     CTTTCAAAGACGATGTACCTAGAGGATCGCACTGTACGCCTACAGCTCTG                         GGATACTGCAGGGCAAGAAAGGTTTCGAAGTCTAATTCCTAGCTATATCCG
genomic: CTTTCAAAGACGATGTACCTAGAGGATCGCACTGTACGCCTACAGCTCTGgtagcttgcg ... actgttgtagGGATACTGCAGGGCAAGAAAGGTTTCGAAGTCTAATTCCTAGCTATATCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgtctcctctggcagaccaattgacgttgcttcccctgctgaactgttgtagGGATACTGCAGGGCAAGAAAGGTTTCGAAGTCTAATTCCTAGCTATATCCGTGATTCATCAGTCGCAGTGGTCGTTTATGACGTGTCAA
                     aattgac  putative branch site (score: 3)