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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ttcaatcgaaacgacaccaattcctctatcgttttcacctttcttcttcttcttcttcttcttcttcttttcgtaattttttctgttgtttgaattggtagtTCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGACAGGGATTCTCCCTTCAGCTTCACGCTCGGACAAGG

Basic information

species Glycine max
transcript GLYMA18G32830.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G32830.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv00s0769g00010.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------ttcaatcgaaacgacaccaattcctctatcgttttcacctttcttcttcttcttcttcttcttcttc--ttttcgtaattttttctgttgtttg--aattggtagtTCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGACAGGGATTCTCCCTTCAGCTTCACGCTCGGACAAGG
                          ||||  | | | |  |   || || | |  ||||  | ||||||||| |  || ||  | | || |  || | | | |  |||    | ||||   |||   |||||||||||| ||||||||||| || || ||| |||||||||| ||||| || ||||   |||| ||||  ||||| || || |||| 
gtactcatcccccgatcacccatttctcaactgtatcaattctttttgcttt-tttttttttcttttcttcttttcttttttactatgctgcaattattggattgattttgagtttttgttgattttcagTTCATTACACTGGGACTTTGCTTGATGGAACTCAGTTCGATTCCAGCCGTGATAGGGGGACTCCGTTCAAGTTCACCCTTGGCCAAG-

upper sequence: GLYMA18G32830.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv00s0260g00070.t01 (Vitis vinifera), 3'ss of exon 1
-------------------------ttcaatcgaaacgacaccaattcctctatcgttttcacctttcttcttcttcttcttcttcttcttcttttcgtaattttttctgttgtttg--aattggtagtTCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGACAGGGATTCTCCCTTCAGCTTCACGCTCGGACAAGG
                          ||||  | | | |  |   || || | |  |||||   | |  | ||||| ||     |  |    || | | | |  |||    | ||||   |||   |||||||||||| ||||||||||| || || ||| |||||||||| ||||| || ||||   |||| ||||  ||||| || || |||| 
gtactcatcccccgatcacccatttctcaactgtatcaattcttttttctttttttttttcttttcttcttttcttttttactatgctgcaattattggattgattttgagtttttgttgattttcagTTCATTACACTGGGACTTTGCTTGATGGAACTCAGTTCGATTCCAGCCGTGATAGGGGGACTCCGTTCAAGTTCACCCTTGGCCAAG-
















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|192334304|gb|FK024403.1|FK024403
EST:     AAGGAAGGTCAAGGCTGGGAAACCCCCGAAGTCGGTGACGAAGTCCAAGT                         TCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGA
genomic: AAGGAAGGTCAAGGCTGGGAAACCCCCGAAGTCGGTGACGAAGTCCAAGGttcaatcgaa ... aattggtagtTCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGA
EST: gi|209697647|gb|BW663902.1|BW663902
EST:     AAGGAAGGTCAAGGCTGGGAAACCCCCGAAGTCGGTGACGAAGTCCAAGT                         TCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGA
genomic: AAGGAAGGTCAAGGCTGGGAAACCCCCGAAGTCGGTGACGAAGTCCAAGGttcaatcgaa ... aattggtagtTCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGA
EST: gi|209712203|gb|BW681409.1|BW681409
EST:     AAGGAAGGTCAAGGCTGGGAAACCCCCGAAGTCGGTGACGAAGTCCAAGT                         TCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGA
genomic: AAGGAAGGTCAAGGCTGGGAAACCCCCGAAGTCGGTGACGAAGTCCAAGGttcaatcgaa ... aattggtagtTCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGA
EST: gi|209701554|gb|BW655856.1|BW655856
EST:     AAGGAAGGTCAAGGCTGGGAAACCCCCGAAGTCGGTGACGAAGTCCAAGT                         TCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGA
genomic: AAGGAAGGTCAAGGCTGGGAAACCCCCGAAGTCGGTGACGAAGTCCAAGGttcaatcgaa ... aattggtagtTCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGA
EST: gi|298197720|gb|HO045199.1|HO045199
EST:     AAGGAAGGTCAATGCTGGGAAACCCCCGAAGTCGGTGACGAAGTCCAAGT                         TCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGA
genomic: AAGGAAGGTCAAGGCTGGGAAACCCCCGAAGTCGGTGACGAAGTCCAAGGttcaatcgaa ... aattggtagtTCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGA
EST: gi|9986256|gb|BE660364.1|BE660364
EST:     AAGGAAGGTCAAGGCTGGGAAACCCCCGAAGTCGGTGACGAAGTCCAAGT                         TCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGA
genomic: AAGGAAGGTCAAGGCTGGGAAACCCCCGAAGTCGGTGACGAAGTCCAAGGttcaatcgaa ... aattggtagtTCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGA
EST: gi|213588372|gb|DB967858.1|DB967858
EST:     AAGGAAGGTCAAGGCTGGGAAACCCCCGAAGTCGGTGACGAAGTCCAAGT                         TCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGA
genomic: AAGGAAGGTCAAGGCTGGGAAACCCCCGAAGTCGGTGACGAAGTCCAAGGttcaatcgaa ... aattggtagtTCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGA
EST: gi|213587157|gb|DB965903.1|DB965903
EST:     AAGGAAGGTCAAGGCTGGGAAACCCCCGAAGTCGGTGACGAAGTCCAAGT                         TCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGA
genomic: AAGGAAGGTCAAGGCTGGGAAACCCCCGAAGTCGGTGACGAAGTCCAAGGttcaatcgaa ... aattggtagtTCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGA
EST: gi|15662426|gb|BI699797.1|BI699797
EST:     AAGGAAGGTCAAGGCTGGGAAACCCCCGAAGTCGGTGACGAAGTCCAAGT                         TCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGA
genomic: AAGGAAGGTCAAGGCTGGGAAACCCCCGAAGTCGGTGACGAAGTCCAAGGttcaatcgaa ... aattggtagtTCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGA
EST: gi|192300545|gb|FG988872.1|FG988872
EST:     AAGGAAGGTCAAGGCTGGGAAACCCCCGAAGTCGGTGACGAAGTCCA-GG                         TTCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCG
genomic: AAGGAAGGTCAAGGCTGGGAAACCCCCGAAGTCGGTGACGAAGTCCAAGGttcaatcgaa ... aattggtagtT-CATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCG
EST: gi|208299049|gb|GE100060.1|GE100060
EST:     AAGGAAGGTCAAGGCTGGGAAACCCCCGAAGTCGGTGACGAAGTCCAAGT                         TCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGA
genomic: AAGGAAGGTCAAGGCTGGGAAACCCCCGAAGTCGGTGACGAAGTCCAAGGttcaatcgaa ... aattggtagtTCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcttcttcttcttcttcttttcgtaattttttctgttgtttgaattggtagtTCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGACAGGGATTCTCCCTTCAGCTTCACGCTCGGACAAGG
                    ttttcgtaatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcaatcgaaacgacaccaattcctctatcgttttcacctttcttcttcttcttcttcttcttcttcttttcgtaattttttctgttgtttgaattggtagtTCATTACACGGGGACTTTGCTCGACGGGACTAAGTTCGATTCGAGCCGCGACAGGGATTCTCCCTTCAGCTTCACGCTCGGACAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT