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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccatccagtacctgttgtattagaaccacataccataaaccaaaacctcatgtgtctttataaagctgaaatccgataactgttgtttgatttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACAAGAGATTTCCAAGGTGTGAACCCCAACAGCTTTGATGGGCATGGGAACT

Basic information

species Glycine max
transcript GLYMA18G47200.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47200.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g03360.1 (Oryza sativa), 3'ss of exon 2
--ccatccagtacctgttgtattagaaccacataccataaaccaaaacctcatgtgtctttataaagctgaaatccgataactgttgtttgatttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACAAGAGATTTCCAAGGTGTGAACCCCAACAGCTTTGATGGGCATGGGAACT
    |   |  |    |   ||  |||    || |  | |  |||    |   |   ||    ||          |||| |   |  ||||  ||    ||| | ||||     ||||| ||  |  | |||||||| || ||||||||||| |  || ||||  ||||| |||||||||||||||||||| ||||| ||||
tataagtgatcaaagttcaaatatgaatagtatccagtga--caagtatttgggaacctagggaatatgtttgatcgatgagcttattttggcttgctgcagGTAATGTTCAACTTCCTGGATAGGCTCATCAACCTTGGGCTTCCTAGGACCATGGACTTCCTTGGTGTCAACCCCAACAGCTTTGATGGCCATGGCAACT

upper sequence: GLYMA18G47200.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0046g01780.t01 (Vitis vinifera), 3'ss of exon 2
ccatccagtacctgttgtattagaaccacataccataaaccaaaacctcat-gtgtctttataaagctgaa-atccgataactgttgtt--tgatttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACAAGAGATTTCCAAGGTGTGAACCCCAACAGCTTTGATGGGCATGGGAACT
   |    |||   ||   | ||| ||| |        || | |  |  ||    |  ||| || ||  || |      | || |||||  ||  ||   |||||||||||| ||||| || || ||  | |||||| |||| ||||| || || || |||||||| |||||||| || |||||||||||||||||||||||||
-tgtatcatactgatt---taagagccaaaattatcttactacattcatattaaattcttagaatgccaaataaattccatcttttgttgatggattacaacagATGATGTACTCATTTCTGGATCGGCTCATCAACTTGGGGCTTCCCAGAACTAGGGATTTCCAGGGTGTGAATCCAAACAGCTTTGATGGGCATGGGAACT
















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|192324257|gb|FK018228.1|FK018228
EST:     AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAAT                         ATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
genomic: AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAATgtgagcattt ... tttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
EST: gi|151409347|gb|EV279155.1|EV279155
EST:     AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAAT                         ATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
genomic: AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAATgtgagcattt ... tttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
EST: gi|209710872|gb|BW653633.1|BW653633
EST:     AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAAT                         ATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
genomic: AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAATgtgagcattt ... tttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
EST: gi|213588516|gb|DB961633.1|DB961633
EST:     AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAAT                         ATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
genomic: AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAATgtgagcattt ... tttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
EST: gi|193303144|gb|FK267564.1|FK267564
EST:     AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAAT                         ATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
genomic: AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAATgtgagcattt ... tttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
EST: gi|213601180|gb|DB964673.1|DB964673
EST:     AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAAT                         ATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
genomic: AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAATgtgagcattt ... tttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
EST: gi|254328287|gb|GR835252.1|GR835252
EST:     AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAAT                         ATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
genomic: AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAATgtgagcattt ... tttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
EST: gi|151402487|gb|EV272300.1|EV272300
EST:     AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAAT                         ATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
genomic: AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAATgtgagcattt ... tttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
EST: gi|31562001|gb|CD487839.1|CD487839
EST:     AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAAT                         ATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
genomic: AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAATgtgagcattt ... tttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
EST: gi|151393151|gb|EV263026.1|EV263026
EST:     AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAAT                         ATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
genomic: AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAATgtgagcattt ... tttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
EST: gi|151404935|gb|EV274749.1|EV274749
EST:     AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAAT                         ATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
genomic: AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAATgtgagcattt ... tttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
EST: gi|193478234|gb|FK445371.1|FK445371
EST:     AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAAT                         ATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
genomic: AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAATgtgagcattt ... tttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
EST: gi|213610600|gb|DB960625.1|DB960625
EST:     AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAAT                         ATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
genomic: AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAATgtgagcattt ... tttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
EST: gi|208142787|gb|GD942337.1|GD942337
EST:     AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAAT                         ATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
genomic: AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAATgtgagcattt ... tttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
EST: gi|193393077|gb|FK357935.1|FK357935
EST:     AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAAT                         ATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
genomic: AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAATgtgagcattt ... tttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
EST: gi|193386093|gb|FK352407.1|FK352407
EST:     AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAAT                         ATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
genomic: AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAATgtgagcattt ... tttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
EST: gi|192321826|gb|FK013218.1|FK013218
EST:     AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAAT                         ATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
genomic: AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAATgtgagcattt ... tttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
EST: gi|151404038|gb|EV273848.1|EV273848
EST:     AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAAT                         ATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
genomic: AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAATgtgagcattt ... tttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
EST: gi|18735233|gb|BM528646.1|BM528646
EST:     AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAAT                         ATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
genomic: AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAATgtgagcattt ... tttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
EST: gi|193363478|gb|FK329200.1|FK329200
EST:     AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAAT                         ATGATGTATTCATCCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
genomic: AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAATgtgagcattt ... tttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
EST: gi|298166386|gb|HO010965.1|HO010965
EST:     AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAAT                         ATGATGTATTCATTCCTAGACCGAGTTATCAAC
genomic: AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAATgtgagcattt ... tttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAAC
EST: gi|208259806|gb|GE059276.1|GE059276
EST:     AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAAT                         ATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
genomic: AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAATgtgagcattt ... tttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
EST: gi|208211849|gb|GE013568.1|GE013568
EST:     AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAAT                         ATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA
genomic: AGATCAGGGAAGGTCAACCGCTTGGGATTGCTGTGACACTAAGAGGAAATgtgagcattt ... tttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctcatgtgtctttataaagctgaaatccgataactgttgtttgatttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACAAGAGATTTCCAAGGTGTGAACCCCAACAGCTTTGATGGGCATGGGAACT
                                             ttttt  CT-rich tract
         tctttataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccatccagtacctgttgtattagaaccacataccataaaccaaaacctcatgtgtctttataaagctgaaatccgataactgttgtttgatttttgacagATGATGTATTCATTCCTAGACCGAGTTATCAACCTGGGACTTCCTAGGACAAGAGATTTCCAAGGTGTGAACCCCAACAGCTTTGATGGGCATGGGAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
ccatcca
- - - - - cctgttg
- - - - - - - - - - - - - cacatac
- - - - - - - - - - - - - - - - - - - - caaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgttg