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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggatgaacaatcacctagatgacaaatattcctattaagctttctctgctgtcacatatctcattgttttccacccctggatggcattcctcttttacctaaaatatagGCAAAGTGCTTGGAGACTGGAGAAGCAGTGGCTATTAAAAAGGTCTTGCAAGACAGGCGGTACAAAAATCGTGAATTGCAGTTAATGCGCTTAATGGATC

Basic information

species Glycine max
transcript GLYMA12G15470.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 3'ss of exon 3
gtatggatgaacaatcacctagatgacaaatattcctattaagct--ttctctgctgtcacatatctcattgttttccacccctggatggcattcctcttttacctaaaatatagGCAAAGTGCTTGGAGACTGGAGAAGCAGTGGCTATTAAAAAGGTCTTGCAAGACAGGCGGTACAAAAATCGTGAATTGCAGTTAATGCGCTTAATGGATC
                      | ||    |  || |||  |  |   |   | | ||   ||    |||| |||   |    || ||   | |  | |  |   | | || ||||| |||||||||||||| || ||| | ||||| || || ||||| ||||| ||| |||| ||||| || |||||| ||||| | ||||||  |||||| |
--------------------gtacgatgcttggtcttatggaaatgcatgcttaccgt-gtattgtacattttttgatatgtttgaatcaaactgatttagt-tttcacatttagGCTAAGTGCTTGGAGACGGGGGAAACGGTGGCCATCAAGAAGGTGTTGCAGGACCGGCGTTACAAGAACCGTGAACTGCAGCTTATGCGCGCAATGGAAC

upper sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 3
lower sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 3
gtatggatgaacaatcacctagatgacaaatattcctattaagctttctctgctgtcacatatctcattgttttccacccctggatggcattcctcttttacctaaaatatagGCAAAGTGCTTGGAGACTGGAGAAGCAGTGGCTATTAAAAAGGTCTTGCAAGACAGGCGGTACAAAAATCGTGAATTGCAGTTAATGCGCTTAATGGATC
                       |      |  | ||  |   ||  |  | |    |||||  |  |  | || |   |   |||    |      |||||    | | ||||| || |||||||| ||||||||| |||| || ||||||||||||||||||||  | || || ||||| ||||| |||||  |||||||   ||||||||
----------------------gtattttgtgcttct-ctgtactagcggttccaggacataaattctcttctttctttct--gatcaagtctgaaatttac---gattttagGCGAAATGCTTGGAAACTGGAGAATCAGTAGCCATTAAAAAGGTCTTGCAAGATCGACGCTATAAAAACCGTGAGTTGCAACTAATGCGACCAATGGATC

upper sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 3
gtatggatgaacaatcacctagatgacaaatattcctattaagctttctctgctgtcacatatctcattgttttccacccctggatggcattcctcttttacctaaaatatagGCAAAGTGCTTGGAGACTGGAGAAGCAGTGGCTATTAAAAAGGTCTTGCAAGACAGGCGGTACAAAAATCGTGAATTGCAGTTAATGCGCTTAATGGATC
                  ||||   || | | || |||  ||   |||  |  | ||||   |||| || |        | | || |||    ||||| || ||    |  ||||||| |||||||| ||||||||| | || || || ||||||||||| |||||||||||||| |||||||||||  |||||||| ||||||| |||||||
---------------gtactagtataccagt-tttctagcaaa--ttcagtattctcacccgtctctttat--------cattgaaggc---tctcttgtaacttttttccagGCAAAATGCTTGGAAACTGGAGAAACTGTCGCAATAAAAAAGGTCTTACAAGACAGGCGGTATAAAAATCGTGAGCTGCAGTTATTGCGCTTGATGGATC

upper sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 3
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 4
gtatggatgaacaatcacctagatgacaaatattcctattaagctttctctgctgtcacatatctcattgttttccacccctggatggcattcctcttttacctaaaatatagGCAAAGTGCTTGGAGACTGGAGAAGCAGTGGCTATTAAAAAGGTCTTGCAAGACAGGCGGTACAAAAATCGTGAATTGCAGTTAATGCGCTTAATGGATC
                                            | |  ||  |  || | |   ||       | |  | |    |    | || | |       |||  |||| ||||||||||| || |||||| | |||||||| ||||||||| | ||||||| ||||||||| || || ||  | ||| |||||||| |  | || |
-------------------------------------------gtattgctagt-ccaaacagtgcaacaaaagc-aggctttatcgtttcttctttctctttgggaatgcagGCCAAGTGCTTGGAAACCGGAGAAACCGTGGCTATCAAAAAGGTCCTCCAAGACAAGCGGTACAAGAACCGAGAGCTCCAGATAATGCGCCTCCTCGACC

upper sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 3
lower sequence: EFJ07923 (Selaginella moellendorffii), 3'ss of exon 4
gtatggatgaacaatcacctagatgacaaatattcctattaagctttctctgctgtcacatatctcattgttttccacccctggatggcattcctcttttacctaaaatatagGCAAAGTGCTTGGAGACTGGAGAAGCAGTGGCTATTAAAAAGGTCTTGCAAGACAGGCGGTACAAAAATCGTGAATTGCAGTTAATGCGCTTAATGGATC
                                            | |  ||  |  || | |   ||       |   |  |    |    | || | |       |||  |||| ||||||||||| || |||||| | |||||||| ||||||||| | ||||||| ||| ||||| || || ||  | ||| |||||||| |  | || |
-------------------------------------------gtattgctagt-ccaaacagtgcaacaaaagcaggcttttatcgtttcttctttctctttgggaatgcagGCCAAGTGCTTGGAAACCGGAGAAACCGTGGCTATCAAAAAGGTCCTCCAAGACAAGCGCTACAAGAACCGAGAGCTCCAGATAATGCGCCTCCTCGACC

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|208271929|gb|GE068725.1|GE068725
EST:     ACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTTGTTTTTCAG                         GCAAAGTGCTTGGAGACTGGAGAAGCAGTGGCTATTAAAAAGGTCTTGCAA
genomic: ACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTTGTTTTTCAGgtatggatga ... taaaatatagGCAAAGTGCTTGGAGACTGGAGAAGCAGTGGCTATTAAAAAGGTCTTGCAA
EST: gi|37994214|gb|CF805960.1|CF805960
EST:     ACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTTGTTTTTCAG                         GCAAAGTGCTTGGAGACTGGAGAAGCAGTGGCTATTAAAAAGGTCTTGCAA
genomic: ACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTTGTTTTTCAGgtatggatga ... taaaatatagGCAAAGTGCTTGGAGACTGGAGAAGCAGTGGCTATTAAAAAGGTCTTGCAA
EST: gi|192301989|gb|FG995159.1|FG995159
EST:     ACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTTGTTTTTCAG                         GCAAAGTGCTTGGAGACTGGAGAAGCAGTGGCTATTAAAAAGGTCTTGCAA
genomic: ACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTTGTTTTTCAGgtatggatga ... taaaatatagGCAAAGTGCTTGGAGACTGGAGAAGCAGTGGCTATTAAAAAGGTCTTGCAA
EST: gi|254341725|gb|GR852862.1|GR852862
EST:     ACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTTGTTTTTCAG                         GCAAAGTGCTTGGAGACTGGAGAAGCAGTGGCTATTAAAAAGGTCTTGCAA
genomic: ACATGGCAGAACGTGTTGTTGGCACTGGATCATTTGGAGTTGTTTTTCAGgtatggatga ... taaaatatagGCAAAGTGCTTGGAGACTGGAGAAGCAGTGGCTATTAAAAAGGTCTTGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catatctcattgttttccacccctggatggcattcctcttttacctaaaatatagGCAAAGTGCTTGGAGACTGGAGAAGCAGTGGCTATTAAAAAGGTCTTGCAAGACAGGCGGTACAAAAATCGTGAATTGCAGTTAATGCGCTTAATGGATC
                                          acctaaa  putative branch site (score: 3)
                              cattcctcttttacct  CT-rich tract
                                      ttttacctaaaatata  TA-rich tract