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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctctctctctctctctctctctctctcttgtttctctatagacaatggcttgtcaattactgattgccaatgcttgtgttggatttgattgaaaaatagGTTGACTTGTGAGAATGTCCACTCCAGCAAGGAAGAGACTCATGAGAGATTTCAAAAGATTGCAACTAGATCCTCCTGCTGGCATCAGTGGGGCTCCCCA

Basic information

species Glycine max
transcript GLYMA01G05080.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G05080.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv01s0026g01770.t01 (Vitis vinifera), 3'ss of exon 2
tctctctctctctctctctctctctctcttgtttctctatagacaatggcttgtcaattactgattgccaatgcttgt-gttggatttgattgaaaaatagGTTGACTTGTGAGAATGTCCACTCCAGCAAGGAAGAGACTCATGAGAGATTTCAAAAGATTGCAACTAGATCCTCCTGCTGGCATCAGTGGGGCTCCCCA-----
      |   |      |   |  | |  | ||    |  |  || ||  ||||  |  | ||||| ||||    ||| |||    |||  |      | |  |     ||||| ||||| |||||||| |||||||| |||||||| |||||||| || |||||||  ||||| ||||| ||||||||||| ||||| ||     
-----ttgagtgataaacatgcattatactattgtaattgactcactgcattgtttaaga-tgattaccaagcaatgttgttttggttggcttctctttggaatagGCGGTGAGGATGTCGACTCCAGCCAGGAAGAGGCTCATGAGGGATTTCAAGAGGTTGCAACAGGATCCACCTGCAGGCATCAGTGGTGCTCCTCAAGACA
















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|22933973|gb|BU551112.1|BU551112
EST:     CAAGTCACAAGTATCTCTCTTAG                         GTTGACTTGTGAGAATGTCCACTCCAGCAAGGAAGAGACTCATGAGAGATT
genomic: CAAGTCACAAGTATCTCTCTTAGgttcttcttg ... tgaaaaatagGTTGACTTGTGAGAATGTCCACTCCAGCAAGGAAGAGACTCATGAGAGATT
EST: gi|14126011|gb|BG790449.1|BG790449
EST:     CAAGTCACAAGTATCTCTCTTAG                         GTTGACTTGTGAGAATGTCCACTCCAGCAAGGAAGAGACTCATGAGAGATT
genomic: CAAGTCACAAGTATCTCTCTTAGgttcttcttg ... tgaaaaatagGTTGACTTGTGAGAATGTCCACTCCAGCAAGGAAGAGACTCATGAGAGATT
EST: gi|19452681|gb|BM954091.1|BM954091
EST:     CCACAAGTCACAAGTATCTCTCTTAG                         GTTGACTTGTGAGAATGTCCACTCCAGCAAGGAAGAGACTCATGAGAGATT
genomic: CCACAAGTCACAAGTATCTCTCTTAGgttcttcttg ... tgaaaaatagGTTGACTTGTGAGAATGTCCACTCCAGCAAGGAAGAGACTCATGAGAGATT
EST: gi|19452497|gb|BM953907.1|BM953907
EST:     CCACAAGTCACAAGTATCTCTCTTAG                         GTTGACTTGTGAGAATGTCCACTCCAGCAAGGAAGAGACTCATGAGAGATT
genomic: CCACAAGTCACAAGTATCTCTCTTAGgttcttcttg ... tgaaaaatagGTTGACTTGTGAGAATGTCCACTCCAGCAAGGAAGAGACTCATGAGAGATT
EST: gi|151402063|gb|EV271876.1|EV271876
EST:     TTTCTCCTGGGACTGCACCCTTCACCACAAGTCACAAGTATCTCTCTTAG                         GTTGACTTGTGAGAATGTCCACTCCAGCAAGGAAGAGACTCATGAGAGATT
genomic: TTTCTCCTGGGACTGCACCCTTCACCACAAGTCACAAGTATCTCTCTTAGgttcttcttg ... tgaaaaatagGTTGACTTGTGAGAATGTCCACTCCAGCAAGGAAGAGACTCATGAGAGATT
EST: gi|11273919|gb|BF324308.1|BF324308
EST:     CACCACAAGTCACAAGTATCTCTCTTAG                         GTTGACTTGTGAGAATGTCCACTCCAGCAAGGAAGAGACTCATGAGAGATT
genomic: CACCACAAGTCACAAGTATCTCTCTTAGgttcttcttg ... tgaaaaatagGTTGACTTGTGAGAATGTCCACTCCAGCAAGGAAGAGACTCATGAGAGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggcttgtcaattactgattgccaatgcttgtgttggatttgattgaaaaatagGTTGACTTGTGAGAATGTCCACTCCAGCAAGGAAGAGACTCATGAGAGATTTCAAAAGATTGCAACTAGATCCTCCTGCTGGCATCAGTGGGGCTCCCCA
                                      atttgattgaaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctctctctctctctctctctctctctcttgtttctctatagacaatggcttgtcaattactgattgccaatgcttgtgttggatttgattgaaaaatagGTTGACTTGTGAGAATGTCCACTCCAGCAAGGAAGAGACTCATGAGAGATTTCAAAAGATTGCAACTAGATCCTCCTGCTGGCATCAGTGGGGCTCCCCA

-ctctctc
- - - - - - - - - - - - - - - - - - - - - - - - gcttgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccaatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgttgg