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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtactaaaagcaatgtcttcctgtaatcaattctagcatcaaaacaagaaaaaccaacaaaaaagaatctgcttagttaatttgctaatcattttgcagGATACGAGGATTATCTAGGGTTCTTGTGCACAACACCTGGCATTGATGTTCATGAGATAAAGAACTACACAAACTCCCCATGTAACAACACCATGGGCCA

Basic information

species Glycine max
transcript GLYMA15G17830.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G17830.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G30020.1 (Arabidopsis thaliana), 3'ss of exon 10
------------------------tgtactaaaagcaatgtcttcctgtaatcaat-tctag-catcaaaaca------agaaaaaccaacaaaaaagaatctgcttagttaatttgctaatcattttgcagGATACGAGGATTATCTAGGGTTCTTGTGCACAACACCTGGCATTGATGTTCATGAGATAAAGAACTACACAAACTCCCCATGTAACAACACCATGGGCCA
                        |  ||   |      |||   |  |  ||||| ||| | ||  |  | |       |    |       |     ||   ||| || | |     |||  | ||| ||| || ||||||||| |||||||||||||||| |||||||| || |||| ||| |||||||| |||| ||||||| | ||||| ||   ||  ||||  ||
gtaaatactcttactccattgacataaacctcagttttcgtcactccctcttcaatctctggtcactaggatactcattggttttattcttgtatggccatacactttgtgattgattgaattttcttgaagGTTATGAGGATTATATAGGGTTCTTGTGCACCACACCTGGTATCGATGCTCACGAGATAAAAAACTTCACAAACACTCCATGCAATTTCAAAATGGTTCA

upper sequence: GLYMA15G17830.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 10
--tgtactaaaagca-atgtcttcctgtaatcaattctagcatcaaaacaagaaaaaccaacaaaaaagaatctgcttagttaatttgctaatcattttgcagGATACGAGGATTATCTAGGGTTCTTGTGCACAACACCTGGCATTGATGTTCATGAGATAAAGAACTACACAAACTCCCCATGTAACAACACCATGGGCCA
  | || |  ||  | || | ||     | |      |   |    | ||  |   | || |||     ||||        | |||  ||  |  ||||| ||  || ||||| ||  |||||||||||||||||||||| || ||||||| ||||||||||||||||||||||| ||  ||||| ||  |||||||||||| 
gatatattggaaatatatattttaagacatttttggattatactggagcatcattgagca-caatctcaaatcattgacactcattccctctt--ttttgtagCTTATGAGGACTACATAGGGTTCTTGTGCACAACACCAGGAATTGATGCTCATGAGATAAAGAACTACACAAGCTTACCATGCAATTACACCATGGGCCG
















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|19054233|gb|BM732900.1|BM732900
EST:     ACACGTTAATCCCAGAGCTGCCTTGGACCCTGGCCTCATCTTTGATGCAG                         GATACGAGGATTATCTAGGGTTCTTGTGCACAACACCTGGCATTGATGTTC
genomic: ACACGTTAATCCCAGAGCTGCCTTGGACCCTGGCCTCATCTTTGATGCAGgtttgtttac ... cattttgcagGATACGAGGATTATCTAGGGTTCTTGTGCACAACACCTGGCATTGATGTTC
EST: gi|10237804|gb|BE806692.1|BE806692
EST:     ACACGTTAATCCCAGAGCTGCCTTGGACCCTGGCCTCATCTTTGATGCAG                         GATACGAGGATTATCTAGGGTTCTTGTGCACAACACCTGNCATTGATGTTC
genomic: ACACGTTAATCCCAGAGCTGCCTTGGACCCTGGCCTCATCTTTGATGCAGgtttgtttac ... cattttgcagGATACGAGGATTATCTAGGGTTCTTGTGCACAACACCTGGCATTGATGTTC
EST: gi|57574980|gb|CX547955.1|CX547955
EST:     ACACGTTAATCCCAGAGCTGCCTTGGACCCTGGCCTCATCTTTGATGCAG                         GATACGAGGATTATCTAGGGTTCTTGTGCACAACACCTGGCATTGATGTTC
genomic: ACACGTTAATCCCAGAGCTGCCTTGGACCCTGGCCTCATCTTTGATGCAGgtttgtttac ... cattttgcagGATACGAGGATTATCTAGGGTTCTTGTGCACAACACCTGGCATTGATGTTC
EST: gi|33390055|gb|CA853262.1|CA853262
EST:     ACACGTTAATCCCAGAGCTGCCTTGGACCCTGGCCTCATCTTTGATGCAG                         GATACGAGGATTATCTAGGGTTCTTGTGCACAACACCTGGCATTGATGTTC
genomic: ACACGTTAATCCCAGAGCTGCCTTGGACCCTGGCCTCATCTTTGATGCAGgtttgtttac ... cattttgcagGATACGAGGATTATCTAGGGTTCTTGTGCACAACACCTGGCATTGATGTTC
EST: gi|14990293|gb|BI315966.1|BI315966
EST:     ACACGTTAATCCCAGAGCTGCCTTGGACCCTGGCCTCATCTTTGATGCAG                         GATACGAGGATTATCTAGGGTTCTTGTGCACAACACCTGGCATTGATGTTC
genomic: ACACGTTAATCCCAGAGCTGCCTTGGACCCTGGCCTCATCTTTGATGCAGgtttgtttac ... cattttgcagGATACGAGGATTATCTAGGGTTCTTGTGCACAACACCTGGCATTGATGTTC
EST: gi|58016897|gb|CX703639.1|CX703639
EST:     ACACGTTAATCCCAGAGCTGCCTTGGACCCTGGCCTCATCTTTGATGCAG                         GATACGAGGATTATCTAGGGTTCTTGTGCACAACACCTGGCATTGATGTTC
genomic: ACACGTTAATCCCAGAGCTGCCTTGGACCCTGGCCTCATCTTTGATGCAGgtttgtttac ... cattttgcagGATACGAGGATTATCTAGGGTTCTTGTGCACAACACCTGGCATTGATGTTC
EST: gi|13789463|gb|BG652054.1|BG652054
EST:     ACACGTTAATCCCAGAGCTGCCTTGGACCCTGGCCTCATCTTTGATGCAG                         GATACGAGGATTATCTAGGGTTCTTGTGCACAACACCTGGCATTGATGTTC
genomic: ACACGTTAATCCCAGAGCTGCCTTGGACCCTGGCCTCATCTTTGATGCAGgtttgtttac ... cattttgcagGATACGAGGATTATCTAGGGTTCTTGTGCACAACACCTGGCATTGATGTTC
EST: gi|15663109|gb|BI700480.1|BI700480
EST:     ACACGTTAATCCCAGAGCTGCCTTGGACCCTGGCCTCATCTTTGATGCAG                         GATACGAGGATTATCTAGGGTTCTTGTGCACAACACCTGGCATTGATGTTC
genomic: ACACGTTAATCCCAGAGCTGCCTTGGACCCTGGCCTCATCTTTGATGCAGgtttgtttac ... cattttgcagGATACGAGGATTATCTAGGGTTCTTGTGCACAACACCTGGCATTGATGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagaaaaaccaacaaaaaagaatctgcttagttaatttgctaatcattttgcagGATACGAGGATTATCTAGGGTTCTTGTGCACAACACCTGGCATTGATGTTCATGAGATAAAGAACTACACAAACTCCCCATGTAACAACACCATGGGCCA
                                      tgctaat  putative branch site (score: 2)
                                            tcatttt  CT-rich tract
                            ttagttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtactaaaagcaatgtcttcctgtaatcaattctagcatcaaaacaagaaaaaccaacaaaaaagaatctgcttagttaatttgctaatcattttgcagGATACGAGGATTATCTAGGGTTCTTGTGCACAACACCTGGCATTGATGTTCATGAGATAAAGAACTACACAAACTCCCCATGTAACAACACCATGGGCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - -caatgtc
- - - - - - - - - -tcctgta
- - - - - - - - - - - - - - - - - - - -tcaaaac
- - - - - - - - - - - - - - - - - - - - - - - aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - ccaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaagaa