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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGCGGGATCCACTTATTGAGTATAAGCTTGAAGGCTATAACCTTTTCTTGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTATATCAGgtttgcttttaatctagatttttaggctactgagctttccgccttatcagttttataactgcgtaaccctttcttttgaacttttggcag

Basic information

species Glycine max
transcript GLYMA02G01060.3
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G01060.1 (Glycine max), 5'ss of exon 20
lower sequence: LOC_Os01g21820.1 (Oryza sativa), 5'ss of exon 18
GCAGCGGGATCCACTTATTGAGTATAAGCTTGAAGGCTATAACCTTTTCTTGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTATATCAGgtttgcttttaatctagatttttaggctactgagctttccgccttatcagttttataactgcgtaaccctttcttttgaacttttggcag------------
 || || ||||| |||||||| ||||| || || || ||||| |||||||||||||||||||| |||||  || | ||||| || || ||||| ||||||||| |  | |  ||| || |   |     | |  | || |    | ||   |  | ||    | |  |   |       | |      ||            
CCAACGAGATCCTCTTATTGAATATAAACTGGAGGGATATAATCTTTTCTTGGATATGATGGCTCAAATTCGACGGAATGTAATTTACTCTGTTTATCAGgttagtctgtcctct-gactcaaacttgcccggtcctttcagtgtttct-ctagagaataaagcatgcacattacagagaatcagaagagtgctgtggttac

upper sequence: GLYMA02G01060.1 (Glycine max), 5'ss of exon 20
lower sequence: GRMZM5G895400_T01 (Zea mays), 5'ss of exon 1
GCAGCGGGATCCACTTATTGAGTATAAGCTTGAAGGCTATAACCTTTTCTTGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTATATCAGgtttgcttttaatctagatttttaggctactgagctttccgccttatcagtttta-taactgcgtaaccctttcttttgaacttttggcag----------
 || || ||||| |||||||||||||| ||||| || ||||| |||||||| || |||||||| ||||| || || ||||| || |||||||||||||||||  | |  |   |  |   |  |   | ||   | | |  | || |   ||| | |||      ||||  |   |||| | |  ||  |           
CCAACGAGATCCCCTTATTGAGTATAAACTTGAGGGATATAATCTTTTCTTAGACATGATGGCTCAAATCAGGAGGAATGTTATTTATTCTGTATATCAGgtaagttcatccacatgtcctaaaaatttcttt-catgctacgtttttgttttaaataatatttgaaccactaagtttggagtaatgtaattactacttca

upper sequence: GLYMA02G01060.1 (Glycine max), 5'ss of exon 20
lower sequence: AT4G01800.1 (Arabidopsis thaliana), 5'ss of exon 19
GCAGCGGGATCCACTTATTGAGTATAAGCTTGAAGGCTATAACCTTTTCTTGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTATATCAGgtt-tgcttttaatctagatttttaggctactgagctttccgccttatcagttttataactgcgtaaccctttcttttgaacttttggcag
||| || |||||||| || ||||||||||| ||||| || || || ||  |||| |||||||| |||||| |||||||||| ||||| ||  ||||||||||| | | || |||| | |  | |     |||   |        |||    ||  |    ||    |  |||| ||||    || ||||||
GCAACGCGATCCACTCATCGAGTATAAGCTCGAAGGATACAATCTATTTCTGGAAATGATGGCTCAAATACGAAGAAATGTGATATACTCCATATATCAGgttcttcattaaatcaaaacctctgcttcacttcacacaataatttactcattcaagttttg----attctttttttt----ttgtggcag

upper sequence: GLYMA02G01060.1 (Glycine max), 5'ss of exon 20
lower sequence: Vv07s0005g02610.t01 (Vitis vinifera), 5'ss of exon 20
GCAGCGGGATCCACTTATTGAGTATAAGCTTGAAGGCTATAACCTTTTCTTGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTATATCAGgtttgcttttaatc-----tagatttttaggctactgagctttccgccttatcagttttataactgcgtaaccctttcttttgaactt-ttggcag-------------------
 ||||||||||| ||||||||||| |||||||||||||| || || |||||||| ||||||||||| |||||||||||||| || |||||  |||| ||||| |   || || |     ||||| ||    || | |    | |   | | |||        |||    ||  || | |||| | ||     |||                    
ACAGCGGGATCCGCTTATTGAGTACAAGCTTGAAGGCTACAATCTATTCTTGGAGATGATGGCACAGATAAGAAGAAATGTTATTTATTCAATATACCAGgtatatattaaaccagagctagatattgtatcttcagtttgtgcacacatgtcacacagtacactcaccaattctctatttttatctcacctgcaatgcccttttcctatggcag

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|31308594|gb|CD393797.1|CD393797
EST:     TGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTATATCAG                         TTCCAACCTGTGCTGGTAAAGCAAGATCAGGACNAAACAGAGAATCGGAAA
genomic: TGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTATATCAGgtttgctttt ... cttttggcagTTCCAACCTGTGCTGGTAAAGCAAGATCAGGACAAAACAGAGAATCGGAAA
EST: gi|31468527|gb|CD410555.1|CD410555
EST:     TGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTATATCAG                         TTCCAACCTGTGCTGGTAAAGCAAGATCAGGACCAAACAGAGAATCGGAAA
genomic: TGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTATATCAGgtttgctttt ... cttttggcagTTCCAACCTGTGCTGGTAAAGCAAGATCAGGACAAAACAGAGAATCGGAAA
EST: gi|4294358|gb|AI442179.1|AI442179
EST:     TGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTATAT-AG                         TTCCAACCTGTGCTGGTAAAGCAA-ATCAGGACAAAACAGAGAATCGGAAA
genomic: TGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTATATCAGgtttgctttt ... cttttggcagTTCCAACCTGTGCTGGTAAAGCAAGATCAGGACAAAACAGAGAATCGGAAA
EST: gi|6847020|gb|AW349310.1|AW349310
EST:     TGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTATATCAG                         TTCCAACCTGTGCTGGTAAAGCAAGATCAGGACAAAACAGAGAATCGGAAA
genomic: TGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTATATCAGgtttgctttt ... cttttggcagTTCCAACCTGTGCTGGTAAAGCAAGATCAGGACAAAACAGAGAATCGGAAA
EST: gi|193322946|gb|FK292024.1|FK292024
EST:     TGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTATATCAG                         TTCCAACCTGTGCTGGTAAAGCAAGATCAGGACAAAACAGAGAATCGGAAA
genomic: TGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTATATCAGgtttgctttt ... cttttggcagTTCCAACCTGTGCTGGTAAAGCAAGATCAGGACAAAACAGAGAATCGGAAA
EST: gi|208140910|gb|GD935252.1|GD935252
EST:     TGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTATATCAG                         TTCCAACCTGTGCTGGTAAAGCAAGATCAGGACAAAACAGAGAATCGGAAA
genomic: TGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTATATCAGgtttgctttt ... cttttggcagTTCCAACCTGTGCTGGTAAAGCAAGATCAGGACAAAACAGAGAATCGGAAA
EST: gi|22930133|gb|BU547272.1|BU547272
EST:     TGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTATATCAG                         TTCCAACCTGTGCTGGTAAAGCAAGATCAGGACAAAACAGAGAATCGGAAA
genomic: TGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTATATCAGgtttgctttt ... cttttggcagTTCCAACCTGTGCTGGTAAAGCAAGATCAGGACAAAACAGAGAATCGGAAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGCGGGATCCACTTATTGAGTATAAGCTTGAAGGCTATAACCTTTTCTTGGATATGATGGCACAAATAAGAAGAAATGTCATATATTCTGTATATCAGgtttgcttttaatctagatttttaggctactgagctttccgccttatcagttttataactgcgtaaccctttcttttgaacttttggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA