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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcagagtaatcaacactataatatcatggaatgcaaatgtgtttgtcccttcaagattttaattgcttgaactcaatggaatttgatgttctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCCACCCCGCCTATGTCACCGCAGAAAGAATTAAGAAAGCCAAAAATTTGGA

Basic information

species Glycine max
transcript GLYMA19G01210.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G01210.4 (Glycine max), 3'ss of exon 2
lower sequence: Vv14s0066g01320.t01 (Vitis vinifera), 3'ss of exon 2
-----atcagagtaatcaacactataatatcatggaatgcaaatgtgtttgtcccttcaagattttaattgcttgaactcaatggaatttgatgttctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCCACCCCGCCTATGTCACCGCAGAAAGAATTAAGAAAGCCAAAAATTTGGA
           ||  |  |  ||  ||  | ||  ||   |||  || |  |   || |    |||  || |||    |  || |  ||| ||       |||||||||||| || |||||||| ||    |||||  |||||||||| || |||||||| |||||||| || ||||| || || ||||| ||||||||| |  |
atttacatgttgtttttgattcttgaaatttattcaaactaaagctggtc-tttatttattcgtttttttccttctttttgattgtgtttcata----attgcagAACTTGAAAAGCACATTCCCGACCTCCATGTTCTCATATCTACCCCCTTCCACCCTGCCTATGTAACGGCAGAGAGGATCAAGAAGGCCAAAAATCTACA
















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|151405370|gb|EV275184.1|EV275184
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTG                         AACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTGgttagtactt ... tctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
EST: gi|7233915|gb|AW569257.1|AW569257
EST:     GGACCTGATTCTG                         AACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
genomic: GGACCTGATTCTGgttagtactt ... tctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
EST: gi|209713324|gb|BW684411.1|BW684411
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTG                         AACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTGgttagtactt ... tctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
EST: gi|38192042|gb|CF921248.1|CF921248
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTG                         AACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTGgttagtactt ... tctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
EST: gi|19936599|gb|BQ080936.1|BQ080936
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTG                         AACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTGgttagtactt ... tctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
EST: gi|7589023|gb|AW704806.1|AW704806
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTG                         AACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTGgttagtactt ... tctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
EST: gi|151400680|gb|EV270494.1|EV270494
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTG                         AACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTGgttagtactt ... tctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
EST: gi|9986232|gb|BE660340.1|BE660340
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTG                         AACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTGgttagtactt ... tctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
EST: gi|254344632|gb|GR855503.1|GR855503
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTG                         AACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTGgttagtactt ... tctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
EST: gi|7233329|gb|AW568676.1|AW568676
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTG                         AACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTGgttagtactt ... tctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
EST: gi|46492766|gb|CN472322.1|CN472322
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTG                         AACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTGgttagtactt ... tctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
EST: gi|7233461|gb|AW568807.1|AW568807
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTG                         AACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTGgttagtactt ... tctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
EST: gi|21993661|gb|BQ785189.1|BQ785189
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTG                         AACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTGgttagtactt ... tctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
EST: gi|254340369|gb|GR858494.1|GR858494
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTG                         AACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTGgttagtactt ... tctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
EST: gi|24205436|gb|BU964689.1|BU964689
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTG                         AACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTGgttagtactt ... tctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
EST: gi|13481183|gb|BG510526.1|BG510526
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTG                         AACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTGgttagtactt ... tctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
EST: gi|105632826|gb|DW246547.1|DW246547
EST:     ACATTGTCACTGATGACAAAGAAGGACCTGATTCTG                         AACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
genomic: ACATTGTCACTGATGACAAAGAAGGACCTGATTCTGgttagtactt ... tctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
EST: gi|42722674|gb|CK768573.1|CK768573
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTG                         AACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTGgttagtactt ... tctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
EST: gi|298193513|gb|HO034119.1|HO034119
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTG                         AACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTGgttagtactt ... tctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
EST: gi|33389351|gb|CA852558.1|CA852558
EST:     ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTG                         AACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC
genomic: ACAGGGTCATCAGTACATTGTCACTGATGACAAAGAAGGACCTGATTCTGgttagtactt ... tctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcccttcaagattttaattgcttgaactcaatggaatttgatgttctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCCACCCCGCCTATGTCACCGCAGAAAGAATTAAGAAAGCCAAAAATTTGGA
                                            ttctgct  CT-rich tract
     ttcaagattttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcagagtaatcaacactataatatcatggaatgcaaatgtgtttgtcccttcaagattttaattgcttgaactcaatggaatttgatgttctgctgcagAACTTGAGAAACACATTCCAGATGCACATGTCATCATATCTACTCCATTCCACCCCGCCTATGTCACCGCAGAAAGAATTAAGAAAGCCAAAAATTTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA