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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGAAAGAAGGACTACAAGGATGGCAAGTATTCTCAGGTGGTGTCAAATGCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaattaagattttgattgtggatttatacgggaaaatgtttagatataactgatcctcactgttttgtgcaaatcaacctgtttattcttgcaatggtt...

Basic information

species Glycine max
transcript GLYMA20G30730.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G30730.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os07g07770.1 (Oryza sativa), 5'ss of exon 2
ACAGAAAGAAGGACTACAAGGATGGCAAGTATTCTCAGGTGGTGTCAAATGCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaattaagattttgattgtggatttatacgggaaaatgtttagatataactgatcctcactgttttgtgcaaatcaacctgtttattcttgcaatggtt--
     |||||||||||||||||||| | ||  |||||||| || || || || ||||| |||||| | ||||||||| | ||||| || ||||| ||||||| |||     ||   |||||   | |      | | | ||||| |  |    | | |   ||| | | | | ||  | || || || |||    ||     
----GAAGAAGGACTACAAGGATGGGAGGTTCTCTCAGGTTGTTTCTAACGCTCTGGACATGAAGCTCAGGGATGACCTTGAGAGGCTGAAGAAGATCAGgtgatttctgattaatttgtg--ctcacgtaccacattttttaggttcatggtaacttgcatgtgtagggtagatttatcttttcatgcttttgttgcactg

upper sequence: GLYMA20G30730.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os07g07719.1 (Oryza sativa), 5'ss of exon 2
ACAGAAAGAAGGACTACAAGGATGGCAAGTATTCTCAGGTGGTGTCAAATGCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaattaagattttgattgtggatttatacgggaaaatgtttagatataactgatcctcactgttttgtgcaaatcaacctgtttattcttgcaatggtt-----
|||| |||||||||||||||||||| | ||  || ||||| || || || || ||||| |||||| | ||||||||| | ||||| || ||||| |||||||  ||  | || || | |   |   | |       |  |||  |  |  |   |      || | |    | | |   |    | || ||| | || |      
ACAGGAAGAAGGACTACAAGGATGGGAGGTTCTCCCAGGTTGTTTCTAACGCCCTGGACATGAAGCTCAGGGATGACCTTGAGAGGCTGAAGAAGATCAGgt--tt--ggttctgctcgcttacc-acatttttgtagctttgtaacttgcatgtgtgaggtgctgtacatatacctttcatgcttttgttggattgatagaaat

upper sequence: GLYMA20G30730.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os07g07709.1 (Oryza sativa), 5'ss of exon 3
ACAGAAAGAAGGACTACAAGGATGGCAAGTATTCTCAGGTGGTGTCAAATGCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaattaagattttgattgtggatttatacgggaaaatgtttagatataac-tgatcctca-ctgttttgtgcaaatcaacctgtttattcttgcaatggtt
|||| |||||||||||||||||||| | ||  || ||||| || || || || ||||| |||||| | ||||||||| | ||||| || ||||| |||||||          || ||| ||   |        | | | |||||   |    | |    || ||||   ||||    ||     |   | | | |||     
ACAGGAAGAAGGACTACAAGGATGGGAGGTTCTCCCAGGTTGTTTCTAACGCCCTGGACATGAAGCTCAGGGATGACCTTGAGAGGCTGAAGAAGATCAGgtttggttctgcttaatt-tgtgctcgcttaccacattttttaggcttgttgtaacttgcatctgtaaggtgctgtacatatactccctccgtccaaaaaa-

upper sequence: GLYMA20G30730.1 (Glycine max), 5'ss of exon 3
lower sequence: AT4G09800.1 (Arabidopsis thaliana), 5'ss of exon 3
ACAGAAAGAAGGACTACAAGGATGGCAAGTATTCTCAGGTGGTGTCAAATGCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaatta-agattttgattgtggatt--tatacgggaaaatgtttagatataactgatcctcactgttttgtgcaaatcaacctgtttattcttgcaatggtt
||||  ||||||| ||||| ||||||||||||||||| || || || ||||| || || |||||| |||| |||||  | ||  | || ||||| ||||||||| || | |     |  |   |||  |||    |   |   ||  ||| |||        | |||||  | ||  |    |   |   |            
ACAGGCAGAAGGATTACAAAGATGGCAAGTATTCTCAAGTTGTCTCCAATGCTCTTGACATGAAGCTGAGAGATGATCTTGAACGTCTCAAGAAGATCAGgtaaatacaaaaaccaacagataattcttatctttgttcacaattgcataaaacatggtgataatgtttctttcatgtttgacaaatggatag----------

upper sequence: GLYMA20G30730.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv18s0072g00060.t01 (Vitis vinifera), 5'ss of exon 4
ACAGAAAGAAGGACTACAAGGATGGCAAGTATTCTCAGGTGGTGTCAAATGCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaattaagattttgattgtggatttatacgggaaaatgtttagatataactgatcctcactgttttgtgcaaatcaacctgtttattcttgcaatggtt---
| || || ||||| |||||||||||||  |||||||||||||| ||||||||| |||||||||||||||| |||||||||||| || | ||||||||||||| ||||   ||   ||  |    |||      |   | |||  | | |  |     || || | ||||  | || || |  ||  ||  ||  |   |    
ATAGGAAAAAGGATTACAAGGATGGCAGATATTCTCAGGTGGTTTCAAATGCATTGGATATGAAGTTGAGAGATGACTTGGAGCGATTGAAGAAAATCAGgttatta--tttcccatgttatccttaatgattattctatttgaacacagatccaggtctctttcttgt-tacatgaatccattggtttctgtcaacctgcag

upper sequence: GLYMA20G30730.1 (Glycine max), 5'ss of exon 3
lower sequence: EFJ22352 (Selaginella moellendorffii), 5'ss of exon 3
ACAGAAAGAAGGACTACAAGGATGGCAAGTATTCTCAGGTGGTGTCAAATGCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaattaagattttgattgtggatttatacgggaaaatgtttagatataactgatcctcactgttttgtgcaaatcaacctgtttattcttgcaatggtt
|||| ||||||||||||||||| || | ||| || ||||| ||| |||| || ||||| |||||| | ||||| ||| | ||||| || ||||| |||||| ||    | ||||   | |  || | |  ||||   ||  | ||| | |||  || | | |||||                                  
ACAGGAAGAAGGACTACAAGGACGGGAGGTACTCGCAGGTTGTGGCAAACGCGCTGGACATGAAGCTCAGGGACGACCTCGAGAGGCTCAAGAAGATCAGgcaagcc-gtttttccctttcaatctcttgggga---tggatggat-tgact--tctttattgtttgacag-----------------------------

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|213595082|gb|DB971871.1|DB971871
EST:     GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAG                         GAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA
genomic: GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaattaaga ... ttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA
EST: gi|298196088|gb|HO044479.1|HO044479
EST:     GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAG                         GAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA
genomic: GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaattaaga ... ttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA
EST: gi|298197095|gb|HO041838.1|HO041838
EST:     GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAG                         GAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA
genomic: GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaattaaga ... ttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA
EST: gi|192324370|gb|FK015721.1|FK015721
EST:     GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAG                         GAACCATCGAGGTTTGGGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA
genomic: GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaattaaga ... ttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA
EST: gi|6668027|gb|AW279478.1|AW279478
EST:     GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAG                         GAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA
genomic: GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaattaaga ... ttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA
EST: gi|208085605|gb|GD884561.1|GD884561
EST:     GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAG                         GAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGAC
genomic: GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaattaaga ... ttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAG-C
EST: gi|192300277|gb|FG988784.1|FG988784
EST:     GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAG                         GAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA
genomic: GCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaattaaga ... ttgcatgcagGAACCATCGAGGTTTGAGACACTACTGGGGTCTTCGTGTACGTGGCCAGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAGAAAGAAGGACTACAAGGATGGCAAGTATTCTCAGGTGGTGTCAAATGCACTGGATATGAAGTTGAGGGATGACTTGGAGAGACTTAAGAAAATCAGgtaattaagattttgattgtggatttatacgggaaaatgtttagatataactgatcctcactgttttgtgcaaatcaacctgtttattcttgcaatggtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA