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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATCATTCCTCACACTCACACCCTCCTCTTAATGAGAGGATTATTTCATCCATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaagcattcagaaataggtaaaaaacggtgacttgttagtgcttcaattggtttgccaaggtaaccaattctgttttaatgcag

Basic information

species Glycine max
transcript GLYMA03G33000.4
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33000.6 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os01g74350.1 (Oryza sativa), 5'ss of exon 3
TATCATTCCTCACACTCACAC-CCTCCTCTTAATGAGAGGATTATTTCATCCATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaag-cattcagaaataggtaaaaaacggtgacttgttag-tgct--tcaattggtttgccaaggtaaccaattctgttttaatgcag------------------------------------------------------------------------------------------
   ||  |   |     |  | ||  |||| |||||||||||  | ||||||||| |||  ||||||||||| |||||||| ||||| ||||||||||| |||||   | ||  || |   |     ||  |    |  ||  ||||  ||||     |  |   ||  |  | |||  |  || |   |                                                                                          
-TCCACCCGCGAGGGGAAGGCACCAGCTCTCAATGAGAGGATACTCTCATCCATGTCCAAGAGATCTGTTGCAGCACACCCATGGCATGACCTTGAGATTGgtaaaatactcgtaactctattctctactctactctactaactgctgctcaaccacctcactttgg--agtatttcgttactagtagtgatttccttgggtacacgttacccttcagatttctattatatttcttaggttcaaaaattcatcattttccctcctttgctttgcttgcag

upper sequence: GLYMA03G33000.6 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G137930_T02 (Zea mays), 5'ss of exon 3
TATCATTCCTCACACTCACACCCTCCTCTTAATGAGAGGATTATTTCATCCATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaa-gcattcagaaataggtaaaaaacggtgacttgttagtg-cttcaattggtttgccaaggt--aaccaattctgttttaatgcag
       |||  ||       ||| |  | || || |||||  | ||||||||| |||| || ||||||||||||||||| ||||| || || ||||||||||  | |  |         | | ||| ||| |   |||  |  || | ||| |    |  || |  |    ||  ||  || ||||||
ACAGGCACCTTCCAGAAGGTTCCTGCCTTGAACGAAAGGATACTGTCATCCATGTCCAGGAGGTCTGTTGCTGCACACCCTTGGCATGATCTGGAGATAGgtattgtacacgctctagcttgacaaatggtcagccgttgatctctgctatttgcaaccagagcttaagttcatcttggattcatgcag

upper sequence: GLYMA03G33000.6 (Glycine max), 5'ss of exon 4
lower sequence: AT3G53620.1 (Arabidopsis thaliana), 5'ss of exon 2
TATCATTCCTCACACT-CACACCCTCCTCTTAATGAGAGGATTATTTCATCCATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaagc-attcagaaataggtaaaaaacggtgacttgtt-----agtgcttcaattggtttgccaaggtaaccaattctgttttaatgcag-------------------
  |       ||   | |||  ||| ||||||||||||||||  |||| |||||||     ||||| || ||||||||||| ||||| || || ||||||||||||| || |  |||    |      |  |   |||         |  ||  |||| |||       ||||   |     |||  |||                     
-GTTGAGAAACATGTTTCACTTCCTACTCTTAATGAGAGGATACTTTCGTCCATGAGTCACAGATCAGTAGCTGCACACCCATGGCATGATCTCGAGATAGgtaagctatacgtaaaggtttctttttcttttttttggctctaagatcatttcattgttttttagtaataactcttataccttttttgcttcgcattcctttgtttacag

upper sequence: GLYMA03G33000.6 (Glycine max), 5'ss of exon 4
lower sequence: Vv08s0040g02470.t01 (Vitis vinifera), 5'ss of exon 2
TATCATTCCTCA-CACTCACACCCTCCTCTTAATGAGAGGATTATTTCATCCATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaagca-ttcagaaataggtaaaaaacggtgacttgttagtgcttcaatt--------ggtttgccaaggtaaccaattctgttttaatgcag
 | |  || ||| ||||||||||| ||||||||||| |||||| |||||||||||||| | ||  |||||||||||||||| ||||| || |||||||||||||   | ||  |   ||    |      || | || ||| ||  ||  ||        ||  |   |   | ||   || | ||| |||||||
-AACTCTCATCAACACTCACACCCACCTCTTAATGAAAGGATTCTTTCATCCATGACCCGGAGGGCTGTTGCTGCACACCCCTGGCATGATCTTGAGATAGgtacctacttttgttgtaacgcatgttgagttaattcttaatgtctcctttttactagtggccttttattatgacattttttatttcaatgcag

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|192298048|gb|FG991328.1|FG991328
EST:     CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAG                         GGCCTGGTGCTCCAACGATCTTCAATTGT
genomic: CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaagcattc ... tttaatgcagGGCCTGGTGCTCCAACGATCTTCAATTGT
EST: gi|207840938|gb|GD810193.1|GD810193
EST:     CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAG                         GGCCTGGTGCTCCAACGATCTTCAATTGT
genomic: CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaagcattc ... tttaatgcagGGCCTGGTGCTCCAACGATCTTCAATTGT
EST: gi|193320747|gb|FK283132.1|FK283132
EST:     CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAG                         GGCCTGGTGCTCCAACGATCTTCAATCGT
genomic: CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaagcattc ... tttaatgcagGGCCTGGTGCTCCAACGATCTTCAATTGT
EST: gi|27446381|gb|CA953504.1|CA953504
EST:     CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAG                         GGCCTGGTGCTCCAACGATCTTCAATTGT
genomic: CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaagcattc ... tttaatgcagGGCCTGGTGCTCCAACGATCTTCAATTGT
EST: gi|10236851|gb|BE805739.1|BE805739
EST:     GCACGACCTTGAGATAG                         GGCCTGGTGCTCCAACGATCTTCAATTGT
genomic: GCACGACCTTGAGATAGgtaagcattc ... tttaatgcagGGCCTGGTGCTCCAACGATCTTCAATTGT
EST: gi|208275603|gb|GE078223.1|GE078223
EST:     TGCTGCACACCCGTGGCACGACCTTGAGATAG                         GGCCTGGTGCTCCAACGATCTTCAATTGT
genomic: TGCTGCACACCCGTGGCACGACCTTGAGATAGgtaagcattc ... tttaatgcagGGCCTGGTGCTCCAACGATCTTCAATTGT
EST: gi|5510301|gb|AI856743.1|AI856743
EST:     CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAG                         GGCCTGGTGCTCCAACGATCTTCAATTGT
genomic: CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaagcattc ... tttaatgcagGGCCTGGTGCTCCAACGATCTTCAATTGT
EST: gi|7925031|gb|AW831057.1|AW831057
EST:     CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAG                         GGCCTGGTGCTCCAACGATCTTCAATTGT
genomic: CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaagcattc ... tttaatgcagGGCCTGGTGCTCCAACGATCTTCAATTGT
EST: gi|298199436|gb|HO042799.1|HO042799
EST:     CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAG                         GGCCTGGTGCTCCAACGATCTTCAATTGT
genomic: CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaagcattc ... tttaatgcagGGCCTGGTGCTCCAACGATCTTCAATTGT
EST: gi|192296495|gb|FG989111.1|FG989111
EST:     CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAG                         GGCCTGGTGCTCCAACGATCTTCAATTGT
genomic: CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaagcattc ... tttaatgcagGGCCTGGTGCTCCAACGATCTTCAATTGT
EST: gi|16105384|gb|BI893124.1|BI893124
EST:     CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAG                         GGCCTGGTGCTCCAACGATCTTCAATTGT
genomic: CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaagcattc ... tttaatgcagGGCCTGGTGCTCCAACGATCTTCAATTGT
EST: gi|8827754|gb|BE211484.1|BE211484
EST:     CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAG                         GGCCTGGTGCTCCAACGATCTTCAATTGT
genomic: CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaagcattc ... tttaatgcagGGCCTGGTGCTCCAACGATCTTCAATTGT
EST: gi|7588509|gb|AW704365.1|AW704365
EST:     CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAG                         GGCCTGGTGCTCCAACGATCTTCAATTGT
genomic: CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaagcattc ... tttaatgcagGGCCTGGTGCTCCAACGATCTTCAATTGT
EST: gi|9986811|gb|BE660919.1|BE660919
EST:     CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAG                         GGCCTGGTGCTCCAACGATCTTCAATTGT
genomic: CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaagcattc ... tttaatgcagGGCCTGGTGCTCCAACGATCTTCAATTGT
EST: gi|192324459|gb|FK015810.1|FK015810
EST:     CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAG                         GGCCTGGTGCTCCAACGATCTTCAATTGT
genomic: CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaagcattc ... tttaatgcagGGCCTGGTGCTCCAACGATCTTCAATTGT
EST: gi|7588510|gb|AW704234.1|AW704234
EST:     CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAG                         GGCCTGGTGCTCCAACGATCTTCAATTGT
genomic: CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaagcattc ... tttaatgcagGGCCTGGTGCTCCAACGATCTTCAATTGT
EST: gi|151404690|gb|EV274504.1|EV274504
EST:     CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAG                         GGCCTGGTGCTCCAACGATCTTCAATTGT
genomic: CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaagcattc ... tttaatgcagGGCCTGGTGCTCCAACGATCTTCAATTGT
EST: gi|207702226|gb|GD682981.1|GD682981
EST:     TTGCTGCACACCCGTGGCACGACCTTGAGATAG                         GGCCTGGTGCTCCAACGATCTTCAATTGT
genomic: TTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaagcattc ... tttaatgcagGGCCTGGTGCTCCAACGATCTTCAATTGT
EST: gi|17022987|gb|BM094021.1|BM094021
EST:     CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAG                         GGCCTGGTGCTCCAACGATCTTCAATTGT
genomic: CATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaagcattc ... tttaatgcagGGCCTGGTGCTCCAACGATCTTCAATTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATCATTCCTCACACTCACACCCTCCTCTTAATGAGAGGATTATTTCATCCATGACCAGAAGATCTGTTGCTGCACACCCGTGGCACGACCTTGAGATAGgtaagcattcagaaataggtaaaaaacggtgacttgttagtgcttcaattggtttgccaaggtaaccaattctgttttaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC