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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacactctccctctgtattttaattttggacgatcttgaattcaattactgaattgctcgttgtgtttctcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAGTTCATGCAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTC

Basic information

species Glycine max
transcript GLYMA01G39720.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G39720.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g35580.1 (Oryza sativa), 3'ss of exon 2
----------------------gtaacactctccctctgtattttaattttgg--acgatcttg-aattcaattact-gaattgctcgttgtgtttctcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAGTTCATGCAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTC
                       ||  | ||       ||| |   | |  |     | ||||  ||||   ||  | |  |||||| || | | || ||||||||||| || | ||||||    || |||||||| || || || || || ||||||||||||||||| |||||||| ||||| ||||||   ||| |  
aaaaaacctgggattgttgcttatattaatcattgctagtactggtactgcgactgtgttcttacaattttcttgtttgctttgctccttat-tatcgcagCACATCGAAGTGAACAAGCTTACCAAGGGAAGGCCCCTTGACAATCTGGAATTCATGCAATGGATGAAGCGATACTGTGATTCGGTCAATGGAGGCTTCA

upper sequence: GLYMA01G39720.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G163409_T01 (Zea mays), 3'ss of exon 2
------------------------------------------------------------------------------gtaacactctccctctgtattttaattttgg-acgatcttgaattcaattactgaattgctcgttgtgttt-ctcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAGTTCATGCAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTC
                                                                               |   |||  |||   || ||||  |  |   | ||||||  |||   ||  ||  ||    |||   ||  | ||||| || ||||| | ||||||  | ||||||||||| || || || || ||||||||||| |||||||||||||| || ||||||||||||   ||| |  
gtgaatcacggctttggtttctcgcccttctcttgtgccgcccgcatgggattttttttattttattttctgaaatcgattgaactgccccatcgtgttttgttgctaatatgatctt--attt--ttgttgttttctctgttaatttggcgcagCATATAGAGGTGAACAAGCTTATCAAAGGAAGGCCCCTTGACAATCTGGAGTTCATGCAGTGGATGAAACGATATTGTGATTCTGTCAATGGTGGCTTCA

upper sequence: GLYMA01G39720.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0129g01080.t01 (Vitis vinifera), 3'ss of exon 2
--------------gtaacactctccctctgtattttaattttggacgatcttgaattcaa----ttactgaattgctcgttgtgttt-------ctcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAGTTCATGCAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTC
               |   |   | | |     |||||  ||     | | ||   ||  |    ||| ||| ||| |  |  || ||        |||||| || ||||| |||||||| ||||||||||| || || ||||| || ||||||||||||||||||||  ||||||| || || || |||   |||||| 
ggttattgatctctctgttagggttctttcaatttttagcttcttttgtttttttttttgaaaggttattgacttgtttatcttggttgaggggtttcagCATATTGAGGTAAGCAAGCTTGTGAAAGGAAGACCTCTTGATAATCTGGAGTTCATGCAATGGATGAAGAGATACTGTGACTCGGTTAATGGAGGCCTTT

upper sequence: GLYMA01G39720.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ12535 (Selaginella moellendorffii), 3'ss of exon 3
gtaacactctccctctgtattttaattttggacgatcttgaattcaattactgaattgctcgttgtgtttctcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAGTTCATGCAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTC
                     ||  || |  | | ||  | ||||      | | |     | | |  |   ||||| ||||||||    ||| || |||| ||| | || ||||| ||  | ||||| ||||||||| ||||||| ||||||||||||||| ||          
--------------------gttggttctc-atgctcgagtattcgggagttcactctggagcttttatctacagCATATCGAGGTGGCAAAGTTGATGAAGGGACGACCGCTGGACAATTTGGAGTTTATGCAATGGCTGAAACGTTACTGCGATTCTGTCCATGGA-------

upper sequence: GLYMA01G39720.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ10236 (Selaginella moellendorffii), 3'ss of exon 3
gtaacactctccctctgtattttaattttggacgatcttgaattcaattactgaattgctcgttgtgtttctcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAGTTCATGCAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTC
               ||  | | |   | |     |   | | |  | |   ||| |  |   |        ||||| ||||||||    ||| || |||| ||| | || ||||| ||  | ||||| ||||||||| ||||||| ||||||||||||||| ||    | |   
-------------gttggttctcatgctcgagtatttcgggaattcactctggaacttttatcta-------cagCATATCGAGGTGGCAAAGTTGATGAAGGGACGACCGCTGGACAATTTGGAGTTTATGCAATGGCTGAAACGTTACTGCGATTCTGTCCATGGAAGACCAA

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|151393328|gb|EV263203.1|EV263203
EST:     AGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAG                         CACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG
genomic: AGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAGgtaacactct ... tgtttctcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG
EST: gi|208269719|gb|GE072155.1|GE072155
EST:     AGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAG                         CACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG
genomic: AGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAGgtaacactct ... tgtttctcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG
EST: gi|192301066|gb|FG987991.1|FG987991
EST:     AGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAG                         CACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG
genomic: AGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAGgtaacactct ... tgtttctcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG
EST: gi|208289796|gb|GE088888.1|GE088888
EST:     AGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAG                         CACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG
genomic: AGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAGgtaacactct ... tgtttctcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG
EST: gi|192296790|gb|FG993088.1|FG993088
EST:     AGAACTACAAGGTCCTTCAGGATGTCTTCAATAAACTCAAAATCACCAAG                         CACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG
genomic: AGAACTACAAGGTCCTTCAAGATGTCTTCAATAAACTCAAAATCACCAAGgtaacactct ... tgtttctcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaattttggacgatcttgaattcaattactgaattgctcgttgtgtttctcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAGTTCATGCAATGGATGAAACGATACTGCGATTCTGTCAATTCCGGCCTTC
 ttttaat  putative branch site (score: 3)
                                             tgtttctc  putative PPT
                    aattcaatta  TA-rich tract