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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatcctcattccactttttttcctttctccaaatcacttatcttctctgatctttcatctccaatttaatgcattattatttagTCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAGGAGCTCGAGAGAGTTTCCGGCATCGACACCGGCGCCCTCACCGTCGACG

Basic information

species Glycine max
transcript GLYMA16G05470.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G05470.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0068g01280.t01 (Vitis vinifera), 3'ss of exon 2
gtgaatcctcattccactttttttcctttctccaaatcact-tatcttctctgatctttcatctcca---atttaatgcattattattta--gTCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAGGAGCTCGAGAGAGTTTCCGGCATCGACACCGGCGCCCTCACCGTCGACG
|| ||   ||  |||| ||    |||    | || ||  || | | || | |    ||  | ||  |   ||||       |   |||||  ||| ||||  ||||| |||||||| ||||||||||||||||||||||| |||||  | ||||  |  || ||| | || ||  | || || || || || |
gtaaaatttc--tccaattgaactccaaatttcatatttctatcttttttattgaattgaaactttagagattttgattggtgaaatttacagTCAAACAGCTTCGTCGAAGGAGTGACGCACAAGATCAGGCGCCAGATCGAGGATTTAGAGAAGGCATCGGGCGTGGAGACAAGTGCACTTACGGTGGATG
















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|209716470|gb|BW653884.1|BW653884
EST:     GCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAG                         TCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAG
genomic: GCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAGgtgaatcctc ... tattatttagTCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAG
EST: gi|209711508|gb|BW681444.1|BW681444
EST:     GCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAG                         TCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAG
genomic: GCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAGgtgaatcctc ... tattatttagTCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAG
EST: gi|213602669|gb|DB956605.1|DB956605
EST:     GCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAG                         TCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAG
genomic: GCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAGgtgaatcctc ... tattatttagTCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAG
EST: gi|298191152|gb|HO038631.1|HO038631
EST:     GCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAG                         TCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAG
genomic: GCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAGgtgaatcctc ... tattatttagTCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAG
EST: gi|16105980|gb|BI893720.1|BI893720
EST:     GCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAG                         TCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAG
genomic: GCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAGgtgaatcctc ... tattatttagTCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAG
EST: gi|207747400|gb|GD718425.1|GD718425
EST:     CCCTCAGCGATGACCTCGCCAAG                         TCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAG
genomic: CCCTCAGCGATGACCTCGCCAAGgtgaatcctc ... tattatttagTCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAG
EST: gi|213620335|gb|DB961480.1|DB961480
EST:     GCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAG                         TCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAG
genomic: GCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAGgtgaatcctc ... tattatttagTCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAG
EST: gi|213587989|gb|DB957448.1|DB957448
EST:     GCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAG                         TCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAG
genomic: GCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAGgtgaatcctc ... tattatttagTCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAG
EST: gi|19452653|gb|BM954063.1|BM954063
EST:     GCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAG                         TCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAG
genomic: GCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAGgtgaatcctc ... tattatttagTCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAG
EST: gi|193413979|gb|FK376573.1|FK376573
EST:     GCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAG                         TCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAG
genomic: GCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAGgtgaatcctc ... tattatttagTCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAG
EST: gi|213602677|gb|DB956613.1|DB956613
EST:     GCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAG                         TCCAACAATTTCGTGGAAGGAGATACGCACAAGATCAGGCGCCAGATTGAG
genomic: GCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAGgtgaatcctc ... tattatttagTCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAG
EST: gi|298194575|gb|HO043047.1|HO043047
EST:     GCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAG                         TCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAG
genomic: GCATCGGAACCCTAGACTCTCTCCTCTCCCTCAGCGATGACCTCGCCAAGgtgaatcctc ... tattatttagTCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaatcacttatcttctctgatctttcatctccaatttaatgcattattatttagTCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAGGAGCTCGAGAGAGTTTCCGGCATCGACACCGGCGCCCTCACCGTCGACG
                                  atttaat  putative branch site (score: 4)
                                 aatttaatgcattatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaatcctcattccactttttttcctttctccaaatcacttatcttctctgatctttcatctccaatttaatgcattattatttagTCCAACAATTTCGTGGAAGGAGTTACGCACAAGATCAGGCGCCAGATTGAGGAGCTCGAGAGAGTTTCCGGCATCGACACCGGCGCCCTCACCGTCGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT