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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcactcaacttctctctcgtcttttaatttcatccctgttattctttaattttggacgatcttgatttcagttaccgaattgttcgttgtatattttcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAGTTCATGCAATGGATGAAACGATACTGCGATTCTGTCGATTCCGGCCTTC

Basic information

species Glycine max
transcript GLYMA11G05560.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G05560.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G163409_T01 (Zea mays), 3'ss of exon 2
-------------------------------------------gtatcactcaacttctctctcgtcttttaatttcatcc---ctgttattctttaattttggacgatcttgatttcagt--taccgaattgttcgttgtatattttcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAGTTCATGCAATGGATGAAACGATACTGCGATTCTGTCGATTCCGGCCTTC
                                           | ||        || | | |  | || | |  ||       |||        |  |||    | |   |||| | | |  |   |  || |  |||   |     ||||| || ||||| | ||||||  | ||||||||||| || || || || ||||||||||| |||||||||||||| || ||||||||| ||   ||| |  
gtgaatcacggctttggtttctcgcccttctcttgtgccgcccgcatgggattttttttattttattttctgaaatcgattgaactgccccatcgtgttttgttgctaatatgatcttatttttgttgttttctctgttaatttggcgcagCATATAGAGGTGAACAAGCTTATCAAAGGAAGGCCCCTTGACAATCTGGAGTTCATGCAGTGGATGAAACGATATTGTGATTCTGTCAATGGTGGCTTCA

upper sequence: GLYMA11G05560.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0129g01080.t01 (Vitis vinifera), 3'ss of exon 2
--gtatcactcaacttctctctcgtcttttaatttc--atccctgttattctttaattttggacgatcttgatttcagttaccgaattgttcgttgtatattttcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAGTTCATGCAATGGATGAAACGATACTGCGATTCTGTCGATTCCGGCCTTC
   |||   ||    | |      ||||| |||||       || || || |||  |||   | | | |||| ||   ||| |      || ||||     |||||||| || ||||| |||||||| ||||||||||| || || ||||| || ||||||||||||||||||||  ||||||| || || ||  ||   |||||| 
ggttattgatctctctgttagggttctttcaatttttagcttcttttgtttttttttttgaaaggttattgactt-gtttatc------ttggttgaggggtttcagCATATTGAGGTAAGCAAGCTTGTGAAAGGAAGACCTCTTGATAATCTGGAGTTCATGCAATGGATGAAGAGATACTGTGACTCGGTTAATGGAGGCCTTT

upper sequence: GLYMA11G05560.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ12535 (Selaginella moellendorffii), 3'ss of exon 3
gtatcactcaacttctctctcgtcttttaatttcatccctgttattctttaattttggacgatcttgatttcagttaccgaattgttcgttgtatattttcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAGTTCATGCAATGGATGAAACGATACTGCGATTCTGTCGATTCCGGCCTTC
                                        |||  |  | |   | |     ||  || |||| |  | | |   ||       ||| | ||||| ||||||||    ||| || |||| ||| | || ||||| ||  | ||||| ||||||||| ||||||| ||||||||||||||| ||          
----------------------------------------gttggttctcatgctcgagtattcgggagttcact--ctggagcttt-------tatctacagCATATCGAGGTGGCAAAGTTGATGAAGGGACGACCGCTGGACAATTTGGAGTTTATGCAATGGCTGAAACGTTACTGCGATTCTGTCCATGGA-------

upper sequence: GLYMA11G05560.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ10236 (Selaginella moellendorffii), 3'ss of exon 3
gtatcactcaacttctctctcgtcttttaatttcatccctgttattctttaattttggacgatcttgatttcagttaccgaattgttcgttgtatattttcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAGTTCATGCAATGGATGAAACGATACTGCGATTCTGTCGATTCCGGCCTTC
                                        |||  |  | |   | |     |   |   |    |   ||| | ||        || | ||||| ||||||||    ||| || |||| ||| | || ||||| ||  | ||||| ||||||||| ||||||| ||||||||||||||| ||    | |   
----------------------------------------gttggttctcatgctcgagtatttcgggaattcactctggaactttt--------atctacagCATATCGAGGTGGCAAAGTTGATGAAGGGACGACCGCTGGACAATTTGGAGTTTATGCAATGGCTGAAACGTTACTGCGATTCTGTCCATGGAAGACCAA

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|193682130|gb|FK621268.1|FK621268
EST:     AGAACTACAAGGTCCTTCAAGATGTCTTCAACAAACTCAAAATCACCAAG                         CACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG
genomic: AGAACTACAAGGTCCTTCAAGATGTCTTCAACAAACTCAAAATCACCAAGgtatcactca ... atattttcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG
EST: gi|193712643|gb|FK650968.1|FK650968
EST:     CCTTCAAGATGTCTTCAACAAACTCAAAATACACCAAG                         CACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGA
genomic: CCTTCAAGATGTCTTCAACAAACTCAAAAT-CACCAAGgtatcactca ... atattttcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGA
EST: gi|151397172|gb|EV267045.1|EV267045
EST:     AGAACTACAAGGTCCTTCAAGATGTCTTCAACAAACTCAAAATCACCAAG                         CACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG
genomic: AGAACTACAAGGTCCTTCAAGATGTCTTCAACAAACTCAAAATCACCAAGgtatcactca ... atattttcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaattttggacgatcttgatttcagttaccgaattgttcgttgtatattttcagCACATCGAGGTCAGCAAGCTGGTGAAAGGAAGGCCACTGGATAACCTCGAGTTCATGCAATGGATGAAACGATACTGCGATTCTGTCGATTCCGGCCTTC
              tcttgat  putative branch site (score: 4)
                                              tattttc  putative PPT
                                         ttgtatatttt  TA-rich tract