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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAGAAAGCTTATGAGCTTTCCGTTCTTTGTGATGCCGAGGTTGCTCTCATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAGgtattttttttttccaccgaaatgcaaaaacaaaaatggataataaacacatggaatggacacaacataaccaagaaaaaaaaatcctttctttctcttt...

Basic information

species Glycine max
transcript GLYMA11G36890.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G36890.1 (Glycine max), 5'ss of exon 1
lower sequence: AT1G24260.1 (Arabidopsis thaliana), 5'ss of exon 1
TGAAGAAAGCTTATGAGCTTTCCGTTCTTTGTGATGCCGAGGTTGCTCTCATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAGgtat---tttttttttccaccgaaatg--caaaaacaaaaatggataataaacacatggaatggacacaacataaccaagaaaaaaaaatcctttctttctcttt
|||||||||| || |||||||| ||||| |||||||| || |||||||||||||||||||| ||||||||||||| |||||||||||||||  |||| ||||||   | |  ||||  |   | ||     | |||| |||    | ||| ||| ||  | |  |||||| |    |  | |   |     || ||| |      
TGAAGAAAGCATACGAGCTTTCAGTTCTATGTGATGCAGAAGTTGCTCTCATCATCTTCTCAAATAGAGGAAAGCTGTACGAGTTTTGCAGTAGTTCGAGgtatatatctacttttgtatatatattacttataacataaacattttatatacatattaagta-acacaaaaatgtcttgtatgtatgggtctctctgtga----

upper sequence: GLYMA11G36890.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv01s0010g03900.t01 (Vitis vinifera), 5'ss of exon 1
TGAAGAAAGCTTATGAGCTTTCCGTTCTTTGTGATGCCGAGGTTGCTCTCATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAGgtattttttttttccaccgaaatgcaaaaa--caaaaatggataataaacacatggaatggacacaacataaccaagaaaaaaaaatcctttctttctcttt
| ||||| || || || ||||| || || || || |||||||||||||||||||||||||||||||||||||| |  |||||||| |||||  | || ||||| |          |   ||| | | |||  | ||| | ||||  ||     |       |||||| | |   |  || | ||||     |  ||||||  
TCAAGAAGGCGTACGAACTTTCGGTGCTCTGCGACGCCGAGGTTGCTCTCATCATCTTCTCCAATAGAGGAAAACTCTACGAGTTCTGCAGTAGCTCGAGgtaataacacaggaaaagaaaaagtagaaaacctaaatttgatacaaacttgcttttcataacacaaaacacaaagcaagagaaaaggaaattgttctct--
















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|193536759|gb|FK490055.1|FK490055
EST:     ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAG                         CATGCTCAAAACGTTGGAGAGGTACC
genomic: ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAGgtattttttt ... caacgtgcagCATGCTCAAAACGTTGGAGAGGTACC
EST: gi|208324622|gb|GE125755.1|GE125755
EST:     ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAG                         CATGCTCAAAACGTTGGAGAGGTACCAGAAATGCAACTATGGAGCGCCTGA
genomic: ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAGgtattttttt ... caacgtgcagCATGCTCAAAACGTTGGAGAGGTACCAGAAATGCAACTATGGAGCGCCTGA
EST: gi|208163590|gb|GD963552.1|GD963552
EST:     ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAG                         CATGCTCAAAACGTTGGAGAGGTACCAGAAATGCAACTATGGAGCGCCTGA
genomic: ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAGgtattttttt ... caacgtgcagCATGCTCAAAACGTTGGAGAGGTACCAGAAATGCAACTATGGAGCGCCTGA
EST: gi|208276695|gb|GE073366.1|GE073366
EST:     ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAG                         CATGCTCAAAACGTTGGAGAGGTACCAGAAATGCAACTATGGAGCGCCTGA
genomic: ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAGgtattttttt ... caacgtgcagCATGCTCAAAACGTTGGAGAGGTACCAGAAATGCAACTATGGAGCGCCTGA
EST: gi|208182440|gb|GD980775.1|GD980775
EST:     ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAG                         CATGCTCAAAACGCTGGAGAGGTACCAGAAATGCAACTATGGAGCGCCTGA
genomic: ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAGgtattttttt ... caacgtgcagCATGCTCAAAACGTTGGAGAGGTACCAGAAATGCAACTATGGAGCGCCTGA
EST: gi|208287087|gb|GE082217.1|GE082217
EST:     ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAG                         CATGCTCAAAACGTTGGAGAGGTACCAGAAATGCAACTATGGAGCGCCTGA
genomic: ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAGgtattttttt ... caacgtgcagCATGCTCAAAACGTTGGAGAGGTACCAGAAATGCAACTATGGAGCGCCTGA
EST: gi|193390580|gb|FK354484.1|FK354484
EST:     ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAG                         CATGCTCAAAACGTTGGAGAGGTACCAGA
genomic: ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAGgtattttttt ... caacgtgcagCATGCTCAAAACGTTGGAGAGGTACCAGA
EST: gi|193634385|gb|FK581178.1|FK581178
EST:     ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAG                         CATGCTCAAAACGTTGGAGAGGTACCAGAAATGCAACTATGGAGCGCCTGA
genomic: ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAGgtattttttt ... caacgtgcagCATGCTCAAAACGTTGGAGAGGTACCAGAAATGCAACTATGGAGCGCCTGA
EST: gi|18734332|gb|BM528121.1|BM528121
EST:     CTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAG                         CATGCTCAAAACGTTGGAGAGGTACCAGAAATGCAACTATGGAGCGCCTGA
genomic: CTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAGgtattttttt ... caacgtgcagCATGCTCAAAACGTTGGAGAGGTACCAGAAATGCAACTATGGAGCGCCTGA
EST: gi|193700286|gb|FK635881.1|FK635881
EST:     ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAG                         CATAGACTACAAAACGTTGGAGAGGTACC
genomic: ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAGgtattttttt ... caacgtgcagCAT-G-CT-CAAAACGTTGGAGAGGTACC
EST: gi|193718230|gb|FK653038.1|FK653038
EST:     ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAG                         CATGCTCAAAACGTTGGAGAGGTACC
genomic: ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAGgtattttttt ... caacgtgcagCATGCTCAAAACGTTGGAGAGGTACC
EST: gi|208045425|gb|GD841177.1|GD841177
EST:     ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAG                         CATGCTCAAAACGCTGGAGAGGTACCAGAAATGCAACTATGGAGCGCCTGA
genomic: ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAGgtattttttt ... caacgtgcagCATGCTCAAAACGTTGGAGAGGTACCAGAAATGCAACTATGGAGCGCCTGA
EST: gi|208146463|gb|GD946720.1|GD946720
EST:     ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAG                         CATGCTCAAAACGTTGGAGAGGTACCAGAAAT
genomic: ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAGgtattttttt ... caacgtgcagCATGCTCAAAACGTTGGAGAGGTACCAGAAAT
EST: gi|208263295|gb|GE064815.1|GE064815
EST:     ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAG                         CATGCTCAAAACGCTGGAGAGGTACCAGAAATGCAACTATGGAGCGCCTGA
genomic: ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAGgtattttttt ... caacgtgcagCATGCTCAAAACGTTGGAGAGGTACCAGAAATGCAACTATGGAGCGCCTGA
EST: gi|208086176|gb|GD881926.1|GD881926
EST:     ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAG                         CATGCTCAAAACGTTGGAGAGGTACCAGAAATGCAACTATGGAGCGCCTGA
genomic: ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAGgtattttttt ... caacgtgcagCATGCTCAAAACGTTGGAGAGGTACCAGAAATGCAACTATGGAGCGCCTGA
EST: gi|193401544|gb|FK368009.1|FK368009
EST:     ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAG                         CATGCTCAAAACGCTGGAGAGGTACCAGAAATGCAACTATGGAGCGCCTGA
genomic: ATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAGgtattttttt ... caacgtgcagCATGCTCAAAACGTTGGAGAGGTACCAGAAATGCAACTATGGAGCGCCTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAAGAAAGCTTATGAGCTTTCCGTTCTTTGTGATGCCGAGGTTGCTCTCATCATCTTCTCCAATAGAGGAAAGCAGTACGAGTTTTGCAGCGGTTCAAGgtattttttttttccaccgaaatgcaaaaacaaaaatggataataaacacatggaatggacacaacataaccaagaaaaaaaaatcctttctttctcttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaaaaa