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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgatcatcgactttaatatataccttatctgtccttttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgcacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG

Basic information

species Glycine max
transcript GLYMA12G06980.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G382038_T01 (Zea mays), 3'ss of exon 8
--aatgatcatcgactttaatatataccttatctgtcct--tttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgca-cagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG
  ||   || ||  ||  ||  |  |  |||| ||   |  ||| |||| |  | |   |    | || |||     ||  |  |  |||   | | |  | |||| ||| ||||||||||||||||||| |||||||| ||||| |  ||||||||||| ||||| |||||||| || || |
gtaaatttcttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttac----agtttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGATGTTGATGTTTGACTATCACAGGCAGCATGGCATTG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G177373_T02 (Zea mays), 3'ss of exon 7
--aatgatcatcgactttaatatataccttatctgtcct--tttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgca-cagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG
  ||   |  ||  ||  ||  |  |  |||| ||   |  ||| |||| |  | |   |    | || |||     ||  |  |  |||   | | |  | |||| ||| ||||||||||||||||||| |||||||| ||||| |  ||||||||||| ||||| |||||||| || || |
gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttac----agtttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGATGTTGATGTTTGACTATCACAGGCAGCATGGCATTG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G165357_T02 (Zea mays), 3'ss of exon 6
--aatgatcatcgactttaatatataccttatctgtcct--tttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgca-cagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG
  ||   |  ||  ||  ||  |  |  |||| ||   |  ||| |||| |  | |   |    | || |||     |   |  |  |||   | | |  | |||| ||| ||||||||||||||||||| |||||||| ||||| ||  ||||||| || ||||| |||||||| || || |
gtaaatttgttcatctgaaaattgaaatttatttgctttggtttttcataaattatctttcaagttctcttac----aatttttatttaactttttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G300412_T01 (Zea mays), 3'ss of exon 13
--aatgatcatcgactttaatatataccttatctgtcct--tttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgcacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG
  ||   |  ||  ||  ||| |  |  |||| ||   |  ||| |||| |  | |   |    | || |||    |    | ||| |     | |     |||| ||| ||||||||||||||||||| |||||||| || || || ||||||||||| ||||| | |||||| || || |
gtaaatttgttcatctgaaatttgaaatttatttgctttggtttttcataaattatctttcaagttctcttacagttttatttaacttt----ttttctatcagGTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G044027_T02 (Zea mays), 3'ss of exon 7
-aatgatcatcgactttaatatataccttatctgtccttttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgcacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG
  |   |  |  | | | | |  | |  ||| | | |||| ||  | ||   ||   ||     || | | |   |  |  |  | |   | | |   |||||||  |||| |||||||||||||| |||||||| ||||| ||  ||||||| || ||||| |||||||| || || |
gtaaatttgttca-tctgacaattgcaatatatttgctttgattttcataaattatcattcaagttatctta-cggttttgatttgattttttctat-cagGAGTCAGGAGCTGTTATGATGAGGGTAAGCGTGTAGCAGAGACGCTGATGTTCGACTATCACAGGCAGCATGGCATTG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G157772_T01 (Zea mays), 3'ss of exon 4
-aatgatcatcgactttaatat-ataccttatctgtcct--tttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgcacagGAGTTC-GGAGTTGTTATGATGAGGGCAAGCGTGTTGCA-GAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG
  |   |  |  |  | || ||   |  |||| ||   |  ||| |||| |  | |   |    | || |||     ||  |  |  |||   | |      ||| |||  ||||||||||||||||||| |||||||| ||| || || |||||||| || ||||| |||||||| || || |
gtaaatttgttcatctgaacattgaaaattatttgctttggtttttcataaattatctttcaagttctcttac----agtttttatttaacttttttctattagGTGTTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAAGAGACGTTGATGTTCGACTATCACAGGCAGCATGGCATTG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 6
aatgatcatcgactttaatatataccttatctgtccttttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgcacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG
        | |   | || |  || |   | |    | | | | |     | ||  |  |  | ||  |  ||| | |       |  |||     | ||| ||| |||| ||||||||||| |||||||||||||| || || ||||||||||| || || ||||| || ||||| |
-------gtaggagtaaacacttatcagcttttaattctcaacttatctgcgtgtcaattcacattctt--ataacttggtttctattatg-----atagGTGTTAGGAGCTGTTATGATGAAGGCAAGCGTGTTGCTGAGACCTTGATGTTTGACTACCACAGGCAACATGGAATTG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 3'ss of exon 6
aatgatcatcgactttaatatataccttatctgtccttttatcatg-----atctcttgatatgttgcttttatcaatagcctaaacataa---aaatg----tgtgcacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG
                    || |||| |  ||| ||  | | ||      ||||  |   || |   ||||  ||      ||||| |||      ||    | |  | ||| ||||||||||| ||||| || |||||||| || || ||||| ||||||||||| || || || || || || || |
-------------------gtaaacctcaaatgttctcatcttatagaggaatcttcttgcatttcagtttttacagctttgtaaacttaacctggttgctattatcaaaagGGGTTCGGAGTTGCTATGACGAAGGCAAGCGGGTAGCCGAAACCTTGATGTTTGACTACCACAGACAACATGGCATTG

upper sequence: GLYMA12G06980.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 7
aatgatcatcgactttaatatataccttatctgtccttttatcatgatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtg---cacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG
|||  |  |   |||   | | |     |  ||      | || |||    |   ||||    |||          || || |||        ||    ||||| || ||||| || ||||||||||| |||||||| || || |||||||||||||||||||||||||| || || || |
aatactgttactcttctttctcttttaaaattgaagacatgtcttgagaaat---tatgagaatttagcaccctcactgaagatagtctcacttgacttacagGTGTGCGGAGCTGCTATGATGAGGGGAAGCGTGTGGCTGAGACTTTGATGTTTGATTATCATAGGCAACATGGGATAG

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|193540711|gb|FK494361.1|FK494361
EST:     TCTTGAGCATCCACAACCAGAAAGCTATTGGGGCAATGTTAATCCTATTG                         GAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGT
genomic: TCTTGAGCATCCACAACCAGAAAGCTATTGGGGCAATGTTAATCCTATTGgtacatacac ... gtgtgcacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGT
EST: gi|213606684|gb|DB959073.1|DB959073
EST:     TCTTGAGCATCCACAACCAGAAAGCTATTGGGGCAATGTTAATCCTATTG                         GAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGT
genomic: TCTTGAGCATCCACAACCAGAAAGCTATTGGGGCAATGTTAATCCTATTGgtacatacac ... gtgtgcacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGT
EST: gi|209703510|gb|BW656548.1|BW656548
EST:     TCTTGAGCATCCACAACCAGAAAGCTATTGGGGCAATGTTAATCCTATTG                         GAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGT
genomic: TCTTGAGCATCCACAACCAGAAAGCTATTGGGGCAATGTTAATCCTATTGgtacatacac ... gtgtgcacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatctcttgatatgttgcttttatcaatagcctaaacataaaaatgtgtgcacagGAGTTCGGAGTTGTTATGATGAGGGCAAGCGTGTTGCAGAAACTTTGATGTTTGATTATCATAGGCAGCACGGAATCG
                             gcctaaa  putative branch site (score: 3)
                                taaacataaaaatgt  TA-rich tract