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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatagctcattttctttcattttattatcacttctcactgtgtgtgctaagtaaaatagtgtacttgctgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTGATACTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGA

Basic information

species Glycine max
transcript GLYMA17G12430.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G12430.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G063184_T01 (Zea mays), 3'ss of exon 2
-----------gtatatagctcattttctttcattttattatcacttctcactgtgtgtgcta--agtaaaatagtgtacttgc-tgtgt-tgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTGATACTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGA
            |  || |  ||  | |  |  |  ||| |||  ||    ||| |  |  ||  | | || | ||||  |||  | |    ||||| || | ||||||||| ||||| || || || |||||||||||||| || ||||| ||||| |||||||| || || || || ||  |  | ||||||||
gtaccgcaccaatccattgtgcacgtcccat-gtcctataatctgttagttctgaggcttatactattcaagttgtgtctttgtgtctacgcgcagCGACGATAACCCTGAATAGGGGGATATCAGAGTTTGTTGTGATGGCGGCGGATACAGAGCCTCTTGAGATCCTACTCCACCTCCCCTTGTTAGCTGAGGA

upper sequence: GLYMA17G12430.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G061143_T01 (Zea mays), 3'ss of exon 1
-------------gtatatagctcattttctttcattttat-tatcacttctcactgtgtgtgctaagtaaaatagtgtacttgctgtgt---tgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTGATACTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGA
               ||   || | |   || || | | || | | | |||| |  |  | | |||  | || | ||||  ||  ||| |    ||||| || || |||||||| ||||| || || || |||||||||||||| || ||||| ||||| |||||||| || || || || ||  |  | ||||||||
gtaccgcaccaatccattgtgcacgtcccctgtcctgtaatctgttagttctgag-gcttatactat-tcaagttgtgtcttttgtgtctacgcgcagCGACGAATACCCTGAATAGGGGGATATCAGAGTTTGTTGTGATGGCGGCGGATACAGAGCCTCTTGAGATCCTACTCCACCTCCCCTTGTTAGCTGAGGA

upper sequence: GLYMA17G12430.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G033388_T01 (Zea mays), 3'ss of exon 2
-------------gtatatagctcattttctttcattttat-tatcacttctcactgtgtgtgctaagtaaaatagtgtacttgctgtgt---tgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTGATACTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGA
               ||   || |||   || || | | || | | | |||| |  |  | | |||  | || | ||||  ||  ||| |    ||||| || || |||||||| ||||| || || || |||||||||||||| || ||||| ||||| |||||||| || || || || ||  |  | ||||||||
gtaccgcaccaatccattgtgcacatcccctgtcctgtaatctgttagttctgag-gcttatactat-tcaagttgtgtcttttgtgtctacgcgcagCGACGAATACCCTGAATAGGGGGATATCAGAGTTTGTTGTGATGGCGGCGGATACAGAGCCTCTTGAGATCCTACTCCACCTCCCCTTGTTAGCTGAGGA

upper sequence: GLYMA17G12430.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G018593_T01 (Zea mays), 3'ss of exon 2
-------------gtatatagctcattttctttcattttat-tatcacttctcactgtgtgtgctaagtaaaatagtgtacttgctgtgt---tgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTGATACTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGA
               ||   || | |   || || | | || | | | |||| |  |  | | |||  | || | ||||  ||  ||| |    ||||| || || |||||||| ||||| || || || |||||||||||||| || ||||| ||||| |||||||| || || || || ||  || | ||||||||
gtaccgcaccaatccattgtgcacgtaccctgtcctgtaatctgttagttctgag-gcttatactat-tcaagttgtgtcttttgtgtctacgcgcagCGACGAATACCCTGAATAGGGGGATATCAGAGTTTGTTGTGATGGCGGCGGATACAGAGCCTCTTGAGATCCTACTCCACCTCCCCTTATTAGCTGAGGA

upper sequence: GLYMA17G12430.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G20160.1 (Arabidopsis thaliana), 3'ss of exon 2
------gtatatagctcattttctttcattt-tattatcactt---ctcactgtgtgtgc-----taagtaaaatagtgtacttgctgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTGATACTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGA
      |  | |  ||||| |   ||  | | | ||||   ||    | | ||| ||||      |   | |  || |  | ||  |   || |||| || || || || ||  | || ||||| || |||||||| |||||||| ||| ||||||| || ||||||||||| |||||||| ||||||||||||||
gtatccgcttgttactcatgtgtgtttgtctctcttatttattgagtttaatgtttgtgaagttgttcctgatttatttaaatttgttcatttcagCTACGAAGACTCTTAATCGTGGAATCTCCGAGTTTGTTGTCATGGCTGCAGATGCTGAGCCTCTAGAGATTCTTCTTCATCTTCCCCTACTTGCTGAGGA

upper sequence: GLYMA17G12430.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0016g05140.t01 (Vitis vinifera), 3'ss of exon 2
gtatatagctcattttctttcattttattatcacttctcactgtgtgtgctaagtaaaatagtgtacttgctgtg---ttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTGATACTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGA
||   |  ||    |   |  ||||   || | |   |   | | | |  |   ||| ||  | ||| |||| ||   || |||| || |||||||| || |||||||||||||| || || || ||||||||||| || ||||||||||| || || || ||||||||| | |||||||||||
gtccctttctgcaataactctatttatatagctcgatttgttttttctatttcataatatt-tatacgtgctttgaaatttcagCAACCAAAACCCTCAATAGGGGTATCTCTGAGTTCGTAGTTATGGCTGCTGACACGGAGCCCCTTGAAATCCTACTCCATCTTCCTTTGCTTGCTGAGGA

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|298182539|gb|HO031274.1|HO031274
EST:     TGTTCAACAAGCAGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
EST: gi|298180380|gb|HO025581.1|HO025581
EST:     TGTTCAACAAGCAGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
EST: gi|6725768|gb|AW310167.1|AW310167
EST:     TGTTCAACAAGCTGCCAACTACAAGCAGCTCAANAAAGGTGCTAATGAAG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
EST: gi|208173600|gb|GD970263.1|GD970263
EST:     TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTG
EST: gi|298185053|gb|HO030266.1|HO030266
EST:     TGTTCAACAAGCAGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
EST: gi|298171220|gb|HO016252.1|HO016252
EST:     TGTTCAACAAGCAGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
EST: gi|298195944|gb|HO044335.1|HO044335
EST:     TGTTCAACAAGCAGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAGG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
EST: gi|6566245|gb|AW233926.1|AW233926
EST:     TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
EST: gi|26059372|gb|CA802286.1|CA802286
EST:     TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
EST: gi|298189335|gb|HO037738.1|HO037738
EST:     TGTTCAACAAGCAGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
EST: gi|18039291|gb|BM307585.1|BM307585
EST:     TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
EST: gi|298164419|gb|HO014064.1|HO014064
EST:     TGTTCAACAAGCAGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAG                         CCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG
genomic: TGTTCAACAAGCTGCCAACTACAAGCAGCTCAAAAAAGGTGCTAATGAAGgtatatagct ... tgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatcacttctcactgtgtgtgctaagtaaaatagtgtacttgctgtgttgcagCCACTAAAACCCTGAACAGGGGTATCTCTGAATTTGTTGTGATGGCTGCTGATACTGAGCCCCTTGAGATTCTTCTACATCTTCCTCTACTTGCTGAGGA
        ttctcac  putative branch site (score: 2)
                        taagtaaaata  TA-rich tract