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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGTGTGTCCTTGGAAACCTTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAGgtaaaaatgatttgcttccccctctctttgtattaggtatgcttggtttttttttgggggatgattttcattctctctttgatgcttgttaaaatgaact...

Basic information

species Glycine max
transcript GLYMA03G22220.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G22220.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv12s0028g01400.t01 (Vitis vinifera), 5'ss of exon 4
-------------------------------TTGTGTGTCCTTGGAAACCTTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAGgtaaaaatgatttgcttccccctctctttgtattaggtatgcttggtttttttttgggggatgattttcattctctctttgatgcttgttaaaatgaact--
                                | || ||||| || ||||| ||||| ||||||||||| ||||||||||||||||||||||| |||||||||||     || |  ||  | | |   | |   || | ||  |  ||  | ||||  || | |     || ||   |  ||   |  || ||     |   
TCTGAGCCGATACCAGTTGGCTGAATTTGAGCTTTGCGTCCTCGGCAACCTCTGCCCCGAAACTGTGGAAGAAGCTATTGCCATGGTTCCATCCATCAAGgtaaattcatttggactcaacatgtggct-ttccagctgtgtgtatttgatatttgctggtttaaaaatatgctagata-gacattcattgaatcttccatc
















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|254340129|gb|GR858254.1|GR858254
EST:     TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAGgtaaaaatga ... ttacctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
EST: gi|6964421|gb|AW433114.1|AW433114
EST:     TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCACGATGATGAAGCCATCGAGATAATGTTGAATGAC
genomic: TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAGgtaaaaatga ... ttacctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
EST: gi|192308232|gb|FK001302.1|FK001302
EST:     TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAGgtaaaaatga ... ttacctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
EST: gi|6718725|gb|AW306372.1|AW306372
EST:     TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAGgtaaaaatga ... ttacctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
EST: gi|208162826|gb|GD958938.1|GD958938
EST:     TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAGgtaaaaatga ... ttacctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
EST: gi|208332106|gb|GE127713.1|GE127713
EST:     GGAAGCTATTTGTCCATTGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
genomic: GGAAGCTA-TTG-CCA-TGGTTCCATCTATCAAGgtaaaaatga ... ttacctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
EST: gi|207706084|gb|GD687874.1|GD687874
EST:     TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAGgtaaaaatga ... ttacctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
EST: gi|193512606|gb|FK471806.1|FK471806
EST:     TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAG                         TCAAGAGGACGGACTCAGGA
genomic: TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAGgtaaaaatga ... ttacctgcagTCAAGAGGACGGGCTCAGGA
EST: gi|192308233|gb|FK001303.1|FK001303
EST:     TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAGgtaaaaatga ... ttacctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
EST: gi|298185814|gb|HO030975.1|HO030975
EST:     TCTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAGgtaaaaatga ... ttacctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
EST: gi|4289246|gb|AI441448.1|AI441448
EST:     TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAGgtaaaaatga ... ttacctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
EST: gi|208244462|gb|GE036165.1|GE036165
EST:     TTGCCATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
genomic: TTGCCATGGTTCCATCTATCAAGgtaaaaatga ... ttacctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
EST: gi|6964283|gb|AW432976.1|AW432976
EST:     TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGGTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAGgtaaaaatga ... ttacctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
EST: gi|208194495|gb|GD988030.1|GD988030
EST:     TTGCCATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
genomic: TTGCCATGGTTCCATCTATCAAGgtaaaaatga ... ttacctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
EST: gi|208068170|gb|GD863682.1|GD863682
EST:     TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAGgtaaaaatga ... ttacctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
EST: gi|5057820|gb|AI736296.1|AI736296
EST:     TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAGgtaaaaatga ... ttacctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
EST: gi|298168983|gb|HO020287.1|HO020287
EST:     TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAGgtaaaaatga ... ttacctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
EST: gi|298164053|gb|HO013698.1|HO013698
EST:     TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCCATCG
genomic: TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAGgtaaaaatga ... ttacctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCCATCG
EST: gi|151409001|gb|EV278809.1|EV278809
EST:     TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCGTGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAGgtaaaaatga ... ttacctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
EST: gi|41145861|gb|CK606072.1|CK606072
EST:     TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAG                         TCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC
genomic: TTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAGgtaaaaatga ... ttacctgcagTCAAGAGGACGGGCTCAGGATGATGAAGCCATCGAGAAAATGTTAAATGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGTGTGTCCTTGGAAACCTTTGCCCGGAAACTGTGGAGGAAGCTATTGCCATGGTTCCATCTATCAAGgtaaaaatgatttgcttccccctctctttgtattaggtatgcttggtttttttttgggggatgattttcattctctctttgatgcttgttaaaatgaact

- - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggggatg