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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTGAATGATGCTTTCGGCACTGCCCACAGAGCTCATGCTTCTACAGAAGGAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAGgtttgtaggaactaggaagtaattgttagcttcattatatgaatgttgggtaatttatgtaatttatgcagtttattcatctgttatttgtttaattgtttcag

Basic information

species Glycine max
transcript GLYMA08G17600.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G17600.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os02g07260.1 (Oryza sativa), 5'ss of exon 4
CGTGAATGATGCTTTCGGCACTGCCCACAGAGCTCATGCTTCTACAGAAGGAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAGgt-ttgtaggaactagga---------agtaattgttagcttcattatatgaatgttgggtaatttatgtaatttatgcagtttattcatctgttatttgtttaattgtttcag
 || ||||||||||| |||||||| ||||||||||||||||| || || |||||| ||||||  ||||||||  ||||||| || ||||| ||||||||||| |||    ||  | |           || | |||| |||| | |||||  ||     |||||  |  ||  |   |  ||  | | |    | ||| |   |||||      
TGTAAATGATGCTTTTGGCACTGCACACAGAGCTCATGCTTCAACTGAGGGAGTGACCAAATTTTTGAAGCCTGCTGTTGCTGGCTTCCTGATGCAGAAGgtattgccaaaatgaagtctccatcctggtcaatgtttgcttaaatatat--attcctagtaat--acataggtcccgtggt--aataactcataattagg--aattg------

upper sequence: GLYMA08G17600.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os06g45710.1 (Oryza sativa), 5'ss of exon 4
CGTGAATGATGCTTTCGGCACTGCCCACAGAGCTCATGCTTCTACAGAAGGAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAGgt-ttgtaggaactaggaagtaattgttagcttcattatatgaatgttgggtaatttatgtaatttatgcagtttattcatctgttatttgtttaattgtttcag
 || |||||||| || ||||| || ||||||||||||||||| ||||| |||||  | || || ||||  || |||||||| || ||||| ||||||||||| ||| |  |  |         ||||    | |   | ||          | |  | | |        | ||||  | | |  | ||||  ||   |||||   
TGTAAATGATGCCTTTGGCACAGCACACAGAGCTCATGCTTCAACAGAGGGAGTTACGAAGTATTTGAGACCTTCTGTTGCTGGTTTCCTCATGCAGAAGgtattgcacaagtttccttact-ttgtgcattgctcaagattttcaccatctgaactgttttgacataactgtttggtgaac-ataatttcgtttggtgttt---

upper sequence: GLYMA08G17600.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G382914_T03 (Zea mays), 5'ss of exon 4
CGTGAATGATGCTTTCGGCACTGCCCACAGAGCTCATGCTTCTACAGAAGGAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAGgtttgtaggaactaggaagtaattgttagcttc--attatatgaa-----tgtt-----gggtaatttatgtaatttatgcagtttattc---atctgttatttgtttaattgtttcag----------------------------------------------------
 || ||||||||||| ||||| || ||||||||||||||||| || ||||||||  |||| || ||||||||  ||||||| || ||||| |||||||||||   ||  |  |      |  |  | | |||   | |||||  |     ||||     || |    ||  || ||| | |  || |      | |  | | |  ||| |   ||||||                                                    
TGTCAATGATGCTTTTGGCACGGCACACAGAGCTCATGCTTCAACCGAAGGAGTTACCAAGTATTTGAAGCCTGCTGTTGCTGGCTTCCTCATGCAGAAGgta-ataaaatgtcacccatgctcatgatcttttaagtatatttaggtactgttcagtaggatggggtaaatattttctacctttcaaaagagaccaataaatctttttaacatttcagttttttcataaataaaaaaggaaagatttgacaaatgactttattatctcag

upper sequence: GLYMA08G17600.1 (Glycine max), 5'ss of exon 4
lower sequence: AT1G79550.1 (Arabidopsis thaliana), 5'ss of exon 3
CGTGAATGATGCTTTCGGCACTGCCCACAGAGCTCATGCTTCTACAGAAGGAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAGgtttgtaggaactaggaagtaattgttagcttcattatatgaatgttgggtaatttatgtaatttatgcagtttattcatctgttatttgtttaattgtttcag
||| |||||||| ||||| ||||| ||||||||||||||||| || || ||||| ||||||| ||||||||| || ||||| || ||||| ||||||||||| | ||  |  |      |||    || |||| ||| |||| | |                |||||     | ||    || ||| |||||| ||||| ||||
CGTTAATGATGCCTTCGGAACTGCTCACAGAGCTCATGCTTCCACTGAGGGAGTTGCCAAATTCTTGAAGCCTTCAGTTGCTGGTTTCCTCATGCAGAAGgtatttaaaatttgcagcataaagagtatcttc-ttagatgagtctc---------------tttattttactgatcagactattacttgttttattgtgtcag

upper sequence: GLYMA08G17600.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv19s0085g00370.t01 (Vitis vinifera), 5'ss of exon 3
CGTGAATGATGCTTTCGGCACTGCCCACAGAGCTCATGCTTCTACAGAAGGAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAGgtttgtaggaactaggaagtaattgttagcttcattatatgaatgttgggtaattta--tgtaattt-atgcagtttattcatctgttatttgtttaattgtttcag
 ||||||||||| || || || || |||||||| ||||| |||||||| ||||| || ||||||||||| || || ||||| || ||||| ||||||||||| ||  ||   |      | | |      | | ||  |||          || | |  | |||| |  |  | |  || ||| | | |||    |  | |      
TGTGAATGATGCATTTGGAACCGCTCACAGAGCCCATGCATCTACAGAGGGAGTTGCTAAATACTTGAAACCTTCGGTTGCTGGCTTCCTCATGCAGAAGgtatggtggtgatcactttttaatacatcttcctttccatgccctccaataaaataagttctaatctcgtagaatccatacatgtat-attaagctcttgg------

upper sequence: GLYMA08G17600.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ26420 (Selaginella moellendorffii), 5'ss of exon 3
CGTGAATGATGCTTTCGGCACTGCCCACAGAGCTCATGCTTCTACAGAAGGAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAGgtttgtaggaactaggaagtaattgttagcttcattatatgaatgttgggtaatttatgtaatttatgcagtttattcatctgttatttgtttaattgtttcag
|||||| |||||||| || || || |||||||||||||||||||| || || ||| |||| | | | |||||||| || || ||||||||  |||| |||||   |      |      |      | |||||  |   |  | |  |  |     |                                               
CGTGAACGATGCTTTTGGTACCGCTCACAGAGCTCATGCTTCTACCGAGGGCGTGACCAAGTTCCTCAAGCCCTCCGTGGCTGGATTCCTCTTGCAAAAGgtagattttcttttcctttttcccaat-gcttccctgagttgacgacgaatttgccag----------------------------------------------

upper sequence: GLYMA08G17600.1 (Glycine max), 5'ss of exon 4
lower sequence: EFJ26731 (Selaginella moellendorffii), 5'ss of exon 5
CGTGAATGATGCTTTCGGCACTGCCCACAGAGCTCATGCTTCTACAGAAGGAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAGgtttgtaggaactaggaagtaattgttagcttcattatatgaatgttgggtaatttatgtaatttatgcagtttattcatctgttatttgtttaattgtttcag
|||||| |||||||| || || || |||||||||||||||||||| || || ||| |||| | | | |||||||| || || ||||||||  |||| |||||   |      |      |        |||||  |   |  | |  |  |     |                                               
CGTGAACGATGCTTTTGGTACCGCTCACAGAGCTCATGCTTCTACCGAGGGCGTGACCAAGTTCCTCAAGCCCTCCGTGGCTGGATTCCTCTTGCAAAAGgtagattttcttttttctttttcccaatgcttccctgagttgacgacgaatttgccag----------------------------------------------

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|13481436|gb|BG510779.1|BG510779
EST:     CTTATGCAGAAG                         GAACTTGACTATCTAGTTGGAGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: CTTATGCAGAAGgtttgtagga ... attgtttcagGAACTTGACTATCTAGTTGGAGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|193639315|gb|FK586102.1|FK586102
EST:     GAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAG                         GAACTTGACTATCTAGTTGGAGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAGgtttgtagga ... attgtttcagGAACTTGACTATCTAGTTGGAGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|209714549|gb|BW662212.1|BW662212
EST:     GAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAG                         GAACTTGACTATCTAGTT
genomic: GAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAGgtttgtagga ... attgtttcagGAACTTGACTATCTAGTT
EST: gi|193423576|gb|FK387241.1|FK387241
EST:     AATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAG                         GAACTTGACTATCTAGTTGGAGCTGTGTCCAAACCCCAAGAGACCATTTGC
genomic: AATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAGgtttgtagga ... attgtttcagGAACTTGACTATCTAGTTGGAGCTGTGT-CAAACCCCAAGAGACCATTTGC
EST: gi|7028539|gb|AW458322.1|AW458322
EST:     GAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAG                         GAACTTGACTATCTAGTTGGAGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAGgtttgtagga ... attgtttcagGAACTTGACTATCTAGTTGGAGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|192314966|gb|FK010784.1|FK010784
EST:     GAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAG                         GAACTTGACTATCTAGTTGGAGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAGgtttgtagga ... attgtttcagGAACTTGACTATCTAGTTGGAGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|5606888|gb|AI900986.1|AI900986
EST:     GAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAG                         GAACTTGACTATCTAGTTGGAGCTGTGTCANACCCCAAGAGACCATCTGCT
genomic: GAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAGgtttgtagga ... attgtttcagGAACTTGACTATCTAGTTGGAGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|151412432|gb|EV282244.1|EV282244
EST:     GAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAG                         GAACTTGACTATCTAGTTGGAGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAGgtttgtagga ... attgtttcagGAACTTGACTATCTAGTTGGAGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|192295471|gb|FG987085.1|FG987085
EST:     GAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAG                         GAACTTGACTATCTAGTTGGGAGCTGTGTCAAACCCCAAGAGACCATTTGC
genomic: GAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAGgtttgtagga ... attgtttcagGAACTTGACTATCTAGTTGG-AGCTGTGTCAAACCCCAAGAGACCATTTGC
EST: gi|207798345|gb|GD769525.1|GD769525
EST:     AATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAG                         GAACTTGACTATCTAGTTGGAGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: AATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAGgtttgtagga ... attgtttcagGAACTTGACTATCTAGTTGGAGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|192306299|gb|FG995093.1|FG995093
EST:     GAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAG                         GAACTTGACTATCTAGTTGGAGCTGTGTCGAACCCCAAGAGACCATTTGCT
genomic: GAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAGgtttgtagga ... attgtttcagGAACTTGACTATCTAGTTGGAGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|18732324|gb|BM526992.1|BM526992
EST:     GAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAG                         GAACTTGACTATCTAGTTGGAGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAGgtttgtagga ... attgtttcagGAACTTGACTATCTAGTTGGAGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|208107698|gb|GD906550.1|GD906550
EST:     GAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAG                         GAACTTGACTATCTAGTTGGAGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAGgtttgtagga ... attgtttcagGAACTTGACTATCTAGTTGGAGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|254341877|gb|GR853014.1|GR853014
EST:     GAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAG                         GAACTTGACTATCTAGTTGGAGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAGgtttgtagga ... attgtttcagGAACTTGACTATCTAGTTGGAGCTGTGTCAAACCCCAAGAGACCATTTGCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTGAATGATGCTTTCGGCACTGCCCACAGAGCTCATGCTTCTACAGAAGGAGTGGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTTATGCAGAAGgtttgtaggaactaggaagtaattgttagcttcattatatgaatgttgggtaatttatgtaatttatgcagtttattcatctgttatttgtttaattgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC