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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATTCTCGAGGGAAGGAAATAAATGATGCTGATATTTTAGAGTGGGCCAACAGCAAGGTTAGCAGCTCTGGAAGCCAAAGCCGCATGGACAGTTTTAAGgtattgaaattgtacagtccattcactcaagcatctgtttattaatttagatttttggccacattttctttgttaataatgtctattttaattggcattt...

Basic information

species Glycine max
transcript GLYMA03G22450.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G22450.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv00s1365g00010.t01 (Vitis vinifera), 5'ss of exon 9
TCATTCTCGAGGGAAGGAAATAAATGATGCTGATATTTTAGAGTGGGCCAACAGCAAGGTTAGCAGCTCTGGAAGCCAAAGCCGCATGGACAGTTTTAAGgtattgaaatt-gtacagtccattcactcaagcatctgtttattaatttagatttttggccacattttctttgttaataatgtct--attttaattggcattt
|||||| |  ||||||||||| | ||||||||||||| | || ||||| |||||||| || || || |  ||| | ||||| | |||||| ||||||||||||||     | | || |    || |   |   |||| | |||  || ||    | |  ||| || |  | | | | | |    |  | |  | |      | 
TCATTCCCATGGGAAGGAAATCATTGATGCTGATATTCTTGAATGGGCTAACAGCAAAGTGAGAAGTTTGGGAGGTCAAAGTCACATGGATAGTTTTAAGgtattattcctagaactgcttttttatcta--tatctatctatctatctatccatctatccatatatg-tatatcattcacccttgaagtccagtcttggctc
















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|193731030|gb|FK663204.1|FK663204
EST:     GGTTAGCAGCTCTGGAAGCCAAAGCCGCATGGACAGTTTTAAG                         GATAAAAGTTTATCCGATGGAATATTTTTCCTTGAGCTTCTTAGTTCAGTG
genomic: GGTTAGCAGCTCTGGAAGCCAAAGCCGCATGGACAGTTTTAAGgtattgaaat ... caaatttcagGATAAAAGTTTATCCGATGGAATATTTTTCCTTGAGCTTCTTAGTTCAGTG
EST: gi|193728064|gb|FK667620.1|FK667620
EST:     TTAGCAGCTCTGGAAGCCAAAGCCGCATGGACAGTTTTAAG                         GATAAAAGTTTATCCGATGGAATATTTTTCCTTGAGCTTCTTAGTTCAGTG
genomic: TTAGCAGCTCTGGAAGCCAAAGCCGCATGGACAGTTTTAAGgtattgaaat ... caaatttcagGATAAAAGTTTATCCGATGGAATATTTTTCCTTGAGCTTCTTAGTTCAGTG
EST: gi|208068976|gb|GD864180.1|GD864180
EST:     ACAGCAAGGTTAGCAGCTCTGGAAGCCAAAGCCGCATGGACAGTTTTAAG                         GATAAAAGTTTAATACCGATGGAATATTTTTC
genomic: ACAGCAAGGTTAGCAGCTCTGGAAGCCAAAGCCGCATGGACAGTTTTAAGgtattgaaat ... caaatttcagGATAAAAGTTTA-T-CCGATGGAATATTTTTC
EST: gi|16348640|gb|BI974235.1|BI974235
EST:     GCAAGGTTAGCAGCTCTGGAAGCCAAAGCCGCATGGACAGTTTTAAG                         GATAAAAGTTTATCCGATGGAATATTTTTCCTTGAGCTTCTTAGTTCAGTG
genomic: GCAAGGTTAGCAGCTCTGGAAGCCAAAGCCGCATGGACAGTTTTAAGgtattgaaat ... caaatttcagGATAAAAGTTTATCCGATGGAATATTTTTCCTTGAGCTTCTTAGTTCAGTG
EST: gi|9258812|gb|BE346959.1|BE346959
EST:     ACAGCAAGGTTAGCAGCTCTGGAAGCCAAAGCCGCATGGACAGTTTTAAG                         GATAAAAGTTTATCCGATGGAATATTTTTCCTTGAGCTTCTTAGTTCAGTG
genomic: ACAGCAAGGTTAGCAGCTCTGGAAGCCAAAGCCGCATGGACAGTTTTAAGgtattgaaat ... caaatttcagGATAAAAGTTTATCCGATGGAATATTTTTCCTTGAGCTTCTTAGTTCAGTG
EST: gi|193611213|gb|FK561723.1|FK561723
EST:     ACAGCAAGATTAGCAGCTCTGGAAGCCAAAGCCGCGTGGACAGTTTTAAG                         GATAAAAGTTTATCCGATGGAATATTTTTCCTTGAGCTTCTTAGTTCAGTG
genomic: ACAGCAAGGTTAGCAGCTCTGGAAGCCAAAGCCGCATGGACAGTTTTAAGgtattgaaat ... caaatttcagGATAAAAGTTTATCCGATGGAATATTTTTCCTTGAGCTTCTTAGTTCAGTG
EST: gi|208059512|gb|GD858326.1|GD858326
EST:     ACAGCAAGGTTAGCAGCTCTGGAAGCCAAAGCCGCATGGACAGTTTTAAG                         GATAAAAGTTTATCCGAT
genomic: ACAGCAAGGTTAGCAGCTCTGGAAGCCAAAGCCGCATGGACAGTTTTAAGgtattgaaat ... caaatttcagGATAAAAGTTTATCCGAT
EST: gi|208269610|gb|GE069470.1|GE069470
EST:     ACAGCAAGGTTAGCAGCTCTGGAAGCCAAAGCCGCATGGACAGTTTTAAG                         GATAAAAGTTTATCCGATGGAATATTTTTCCTTGAGCTTCTTAGTTCAGTG
genomic: ACAGCAAGGTTAGCAGCTCTGGAAGCCAAAGCCGCATGGACAGTTTTAAGgtattgaaat ... caaatttcagGATAAAAGTTTATCCGATGGAATATTTTTCCTTGAGCTTCTTAGTTCAGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATTCTCGAGGGAAGGAAATAAATGATGCTGATATTTTAGAGTGGGCCAACAGCAAGGTTAGCAGCTCTGGAAGCCAAAGCCGCATGGACAGTTTTAAGgtattgaaattgtacagtccattcactcaagcatctgtttattaatttagatttttggccacattttctttgttaataatgtctattttaattggcattt

- - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA