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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactgcgttccttgtcactccttttggcttttgttttataacaacgcttctactgatgcatctggtgcaacgatccatggttcagGTTTTTCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCCCCAAAACTTCGTTACAGTGCA

Basic information

species Glycine max
transcript GLYMA12G33950.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os05g11730.1 (Oryza sativa), 3'ss of exon 9
---------------------------------------------------------------------------gtaactgcgttccttgtcact----ccttttggctt-----ttgttttataa--caacgcttctact----gatgcat-------ctggtgcaacgatccatggttcagGTTTTTCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCCCCAAAACTTCGTTACAGTGCA
                                                                           ||| ||| | || ||  || |      || |||        | | |||| ||  ||| |  |  |      | |||||       ||| |    | | |    |   ||||||| |||||| | ||||||||||||||||| ||||| || ||| | ||||| |||||||| || |  || || | || ||| 
gtaagcatacaatcttatccatgttgagtcatatatcacgtcatcttttatagtttcctggacaactatgaaaatgtagctgggctcatttccaataatagattctggacaccagatagctttacaatgcaatgtataaataaggaggtgcatacaggtactgatttttctaacttctgcgtagGTTTTCCACAAGAGGATGCCTCCTGAAGCAATAGACCTCGCTTCACGCCTTCTTCAATATTCACCGAGTCTCCGCTGCACTGCT

upper sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 3'ss of exon 9
------------------------------------------------------------------------------gtaactgcgttccttgtcactccttttggcttttgttttataacaacgcttctactgatgcatctggtgcaacgatccatggt-tcagGTTTTTCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCCCCAAAACTTCGTTACAGTGCA
                                                                              ||  |||| |    | | | |     |        | |     || |   |  |||||| |||||| ||        | |     ||| |||| |||||| |||||||||| ||||| || |||||||| ||  | |||||||||||||| ||||  || || | || ||| 
gtagccatgttttcttatattggatcaccttcctcataccattttacttgcagggcattgtaggccacttcaaaaccagtttctgcatcatgtttaatttgaaataaaaaaaatgtatctgcagctgcttaactgatccatctgttgttctttcgcttaccaccagATTTTCCACAAGAGAATGCCTCCAGAAGCCATAGACCTTGCTTCCCGTCTTCTCCAATATTCACCAAGTCTACGCTGCACTGCT

upper sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 9
---------------------------gtaactgcgttccttgtcactccttt--tggcttttgttttataacaacgcttctactgatgcatct-----ggtgcaa---cgatccatgg--ttcagGTTTTTCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCCCCAAAACTTCGTTACAGTGCA
                             |||| | || ||  |||  |  ||  |  ||| | |     ||||||  |  |    | | | ||     ||||||     | || |||   | |||||||| |||||||| |||||||| ||||| ||||||||||||||  ||||||| ||||| || ||||  || |||| || ||| 
gtaatatatatatatgcatgtcactttcgaacttc-tttctaatcatacaattgcttacttctctacctaaacaacattcatggaaaagaagctaacacggtgcacaactgctctatgacctccagGTTTTCCACAAGCGGATGCCTCCGGAAGCCATTGACCTTGCATCTCGGCTTCTTCAATACTCACCAAGTCTACGTTGCACTGCG

upper sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 9
--------------------------gtaactgcgttccttg--tcactccttttggcttttgttttataacaacgcttctactgatgcatctggtgcaacg-atccatgg--ttcagGTTTTTCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCCCCAAAACTTCGTTACAGTGCA
                          || |     || ||    ||| | | |      | |   ||  | | |  | | ||  |   || |   |  |  | | || ||   | ||||||||||| || || |||||||| |||||||| |||||||||||  ||||||| |||||||| ||||  || || | || ||| 
gtagttcatctcaccttttgttcctggttaagcaattactgaactcattacctacacagtatacattgaagcgattcatttatagcatcaacca-tatactgtacccttgacctccagGTTTTTCATAAACGGATGCCTCCAGAAGCAATAGACCTTGCATCTCGGCTTCTTCAATATTCACCAAGTCTACGCTGCACTGCG

upper sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ07216 (Selaginella moellendorffii), 3'ss of exon 10
gtaactgcgttccttgtcactccttttggcttttgttttataacaacgcttctactgatgcatctggtgcaacgatccatggttcagGTTTTTCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCCCCAAAACTTCGTTACAGTGCA
                       |    ||  |  |    ||  | | ||    |||   |   || ||   |  ||  ||   |||||||| |||||||| ||||||||||||||| | ||| | |  || ||||| || || |||||||| |  || || | || ||| 
----------------------gtaagagcaatcatccggta-tatctctctctctgtctctcttgatgtggc--tcgttga--cagGTTTTCCACAAGCGGATGCCTCCTGAAGCAGTGGACTTGGTGTCGAGGCTGCTTCAGTATTCCCCCAGCCTCCGATGCAATGCC

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|31456092|gb|CD398120.1|CD398120
EST:     ATTATACAGATTTCAGATTCCCCCATATCAAAGCTCATCCTTGGCATAAG                         GTTTTTCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
genomic: ATTATACAGATTTCAGATTCCCCCATATCAAAGCTCATCCTTGGCATAAGgtaactgcgt ... catggttcagGTTTTTCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
EST: gi|31309866|gb|CD395069.1|CD395069
EST:     TATCAAAGCTCATCCTTGGCATAAG                         GTTTTTCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
genomic: TATCAAAGCTCATCCTTGGCATAAGgtaactgcgt ... catggttcagGTTTTTCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
EST: gi|11687934|gb|BF595610.1|BF595610
EST:     ATTATACAGATTTCAGATTCCCCCATATCAAAGCTCATCCTTGGCATAAG                         GTTTTTCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
genomic: ATTATACAGATTTCAGATTCCCCCATATCAAAGCTCATCCTTGGCATAAGgtaactgcgt ... catggttcagGTTTTTCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
EST: gi|31470238|gb|CD412206.1|CD412206
EST:     ATTATACAGATTTCAGATTCCCCCATATCAAAGCTCATCCTTGGCATAAG                         GTTTTTCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT
genomic: ATTATACAGATTTCAGATTCCCCCATATCAAAGCTCATCCTTGGCATAAGgtaactgcgt ... catggttcagGTTTTTCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttttataacaacgcttctactgatgcatctggtgcaacgatccatggttcagGTTTTTCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCCCCAAAACTTCGTTACAGTGCA
                    tactgat  putative branch site (score: 2)
     ttataacaa  TA-rich tract