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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttatctaatgataatatcatgtatatttttaagagcctaagtatgaatctttctttccactttgggtcttttctgaatatatttttactttcgccagATCAAATTGGGCTTTCTCCCGAAGAAGTCATTTCAAAGATTATGGCCAATCCTGAAGTTGCAATGGCATTTCAAAATCCTAGAGTTCAAGCAGCTATCAT

Basic information

species Glycine max
transcript GLYMA11G31810.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G31810.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G16620.1 (Arabidopsis thaliana), 3'ss of exon 11
attttatctaatgataatatcatgtatatttttaagagcctaagtatgaatctttctttccactttgggtcttttctgaatatatttttactttcgccagATCAAATTGGGCTTTCTCCCGAAGAAGTCATTTCAAAGATTATGGCCAATCCTGAAGTTGCAATGGCATTTCAAAATCCTAGAGTTCAAGCAGCTATCAT
                 ||  |   || |   |  |  || |  ||  | |   | |    |  |  | |  |   ||| |  || | || ||  | |||||||||| || ||  |||| ||||||||||| || ||||| ||||  || ||||| ||||| |||||||| || ||||||||||| ||||||||  | ||
----------------gtaagacaaatctcagtttgtaccaagttaatagtacgt-taaataggtctgatactcaatgattgaatctgtattt--gtcagATCAAATAGGACTAACTCCAGAAGAAGTCATATCTAAGATCATGGAGAACCCTGATGTTGCCATGGCATTCCAGAATCCTAGAGTCCAAGCAGCGTTAAT

upper sequence: GLYMA11G31810.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv18s0041g01360.t01 (Vitis vinifera), 3'ss of exon 11
attttatctaat--gataatatcatgtatatttttaagagcctaagtatgaatctttctttccactttgggtctt--ttctgaatatatttttactttcgccagATCAAATTGGGCTTTCTCCCGAAGAAGTCATTTCAAAGATTATGGCCAATCCTGAAGTTGCAATGGCATTTCAAAATCCTAGAGTTCAAGCAGCTATCAT
   |||| ||||  |||||    || |    |  |  |    ||| |  |  | ||| |||||  |||   | ||  |  |   |||||||    ||| || |||||||||||||||| | || |||||||| |||||||| ||||||||||||||||| |||||  |||||||||||||||| ||| |||||||||| |||||
---ttatgtaatcagataaatggatttgagctgctgtggatataactcagtttttttttttcctttttattttttaatcttttctatatttgatattttgc-agATCAAATTGGGCTTACACCTGAAGAAGTTATTTCAAAAATTATGGCCAATCCTGATGTTGCCCTGGCATTTCAAAATCCAAGAATTCAAGCAGCCATCAT
















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|27424818|gb|CA936338.1|CA936338
EST:     TACCTTGATTAATTTTGACCTTAATAGTCCTGAAGTGAAGCAGCAATTTG                         ATCAAATTGGGCTTTCTCCCGAAGAAGTCATTTCAAAGATTATGGCCAATC
genomic: TACCTTGAAGAATTTTGACCTTAATAGTCCTGAAGTGAAGCAGCAATTTGgtgagttatt ... ctttcgccagATCAAATTGGGCTTTCTCCCGAAGAAGTCATTTCAAAGATTATGGCCAATC
EST: gi|193619560|gb|FK572604.1|FK572604
EST:     TACCTTGAAGAATTTTGACCTTAATAGTCCTGAAGTGAAGCAGCAATTTG                         ATCAAATTGGGCTTTCTCCCGAAGAAGTCATTTCAAAGATTATGGCCAATC
genomic: TACCTTGAAGAATTTTGACCTTAATAGTCCTGAAGTGAAGCAGCAATTTGgtgagttatt ... ctttcgccagATCAAATTGGGCTTTCTCCCGAAGAAGTCATTTCAAAGATTATGGCCAATC
EST: gi|15813419|gb|BI785694.1|BI785694
EST:     TACCTTGAAGAATTTTGACCTTAATAGTCCTGAAGTGAAGCAGCAATTTG                         ATCAAATTGGGCTTTCTCCCGAAGAAGTCATTTCAAAGATTATGGCCAATC
genomic: TACCTTGAAGAATTTTGACCTTAATAGTCCTGAAGTGAAGCAGCAATTTGgtgagttatt ... ctttcgccagATCAAATTGGGCTTTCTCCCGAAGAAGTCATTTCAAAGATTATGGCCAATC
EST: gi|51342536|gb|CO983519.1|CO983519
EST:     TACCTTGAAGAATTTTGACCTTAATAGTCCTGAAGTGAAGCAGCAATTTG                         ATCAAATTGGGCTTTCTCCCGAAGAAGTCATTTCAAAGATTATGGCCAATC
genomic: TACCTTGAAGAATTTTGACCTTAATAGTCCTGAAGTGAAGCAGCAATTTGgtgagttatt ... ctttcgccagATCAAATTGGGCTTTCTCCCGAAGAAGTCATTTCAAAGATTATGGCCAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaatctttctttccactttgggtcttttctgaatatatttttactttcgccagATCAAATTGGGCTTTCTCCCGAAGAAGTCATTTCAAAGATTATGGCCAATCCTGAAGTTGCAATGGCATTTCAAAATCCTAGAGTTCAAGCAGCTATCAT
                                       tttttactttcgcc  CT-rich tract
                          ttttctgaatatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttatctaatgataatatcatgtatatttttaagagcctaagtatgaatctttctttccactttgggtcttttctgaatatatttttactttcgccagATCAAATTGGGCTTTCTCCCGAAGAAGTCATTTCAAAGATTATGGCCAATCCTGAAGTTGCAATGGCATTTCAAAATCCTAGAGTTCAAGCAGCTATCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - catgtat