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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcaaatgttacatggttttgagtgtttttcttcaatttggaagttttactgctactaagctgggcttattgttcttgtccttttgtccacaatttctagGCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAAAGTTGAATTCGGCCTTCCTGACTTAGAGAGTAGGACTCAGATATTCAAG

Basic information

species Glycine max
transcript GLYMA16G01810.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 8
tgcaaatgttacatggttttgagtgtttttcttcaatttggaagttt-tactgcta-ctaagctgggctta-ttgttcttgtccttttgtccacaatttc-tagGCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAAAGTTGAATTCGGCCTTCCTGACTTAGAGAGTAGGACTCAGATATTCAAG
     ||  | |  | | |   || |  || |  | |||    || | | |  ||| || || ||    || ||    ||    ||| ||  |  ||||   ||||||||||| || ||||| |||||  |||| ||||| ||||| ||||| || ||||| || ||||||||||| || |||||||| || |||||||| |||
----cataattctagatataaggtttgattttcaagtttttgggtctcttccactagcttagatgtctctacttacaatttaaatttggtttatcattttacagGCCTGACACACTTGATCCAGCACTGTTACGCCCTGGACGGTTAGACCGCAAGGTTGAGTTTGGCCTTCCTGATTTGGAGAGTAGAACACAGATATTTAAG
















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|214005791|gb|DB988688.1|DB988688
EST:     ATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAG                         GCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
genomic: ATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
EST: gi|26269017|gb|CA820080.1|CA820080
EST:     GTTTTGATGGCAACTAACAG                         GCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
genomic: GTTTTGATGGCAACTAACAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
EST: gi|6847793|gb|AW350083.1|AW350083
EST:     GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAG                         GCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
EST: gi|4437003|gb|AI522868.1|AI522868
EST:     GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAG                         GCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
EST: gi|8827828|gb|BE211558.1|BE211558
EST:     GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAG                         GCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
EST: gi|18039872|gb|BM308166.1|BM308166
EST:     GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAG                         GCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
EST: gi|26269018|gb|CA820081.1|CA820081
EST:     GTTTTGATGGCAACTAACAG                         GCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
genomic: GTTTTGATGGCAACTAACAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
EST: gi|214007684|gb|DB986050.1|DB986050
EST:     ATGTG-CGGAATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAG                         GCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
genomic: ATGGGTTTG-ATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
EST: gi|19268833|gb|BM885089.1|BM885089
EST:     GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAATAG                         GCCTGACACTCTAGATCCAGCACTACTGCGGCCTGGGCGATTGGACCGTAA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
EST: gi|207700573|gb|GD683680.1|GD683680
EST:     GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAG                         GCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
EST: gi|17963522|gb|BM270270.1|BM270270
EST:     GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAG                         GCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
EST: gi|298174191|gb|HO017527.1|HO017527
EST:     GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAG                         GCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
EST: gi|298171740|gb|HO021332.1|HO021332
EST:     GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAG                         GCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
EST: gi|209717051|gb|BW668705.1|BW668705
EST:     GATGGGTTTTATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAG                         GCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAA
EST: gi|193590240|gb|FK545268.1|FK545268
EST:     GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAG                         GCCTGACACTCTAGATCCTGCACTA
genomic: GATGGGTTTGATGCTCGGGGAAACATCAAAGTTTTGATGGCAACTAACAGgttggttgat ... caatttctagGCCTGACACTCTAGATCCTGCACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttactgctactaagctgggcttattgttcttgtccttttgtccacaatttctagGCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAAAGTTGAATTCGGCCTTCCTGACTTAGAGAGTAGGACTCAGATATTCAAG
                                                tttct  CT-rich tract
                     ttattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcaaatgttacatggttttgagtgtttttcttcaatttggaagttttactgctactaagctgggcttattgttcttgtccttttgtccacaatttctagGCCTGACACTCTAGATCCTGCACTACTACGGCCTGGGCGGTTGGACCGTAAAGTTGAATTCGGCCTTCCTGACTTAGAGAGTAGGACTCAGATATTCAAG

- - - - - - - - - -tgagtgt
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