Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
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 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatacacttgactaattggtaagcattaagaatataatgtgttacttgtgctttgctttgaatattttctgctcacatgaaactgagtttcttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCTCGGATGTTTAGTGAAAACAAACGTGAATACAACAGAAGAGTACGAGATA

Basic information

species Glycine max
transcript GLYMA02G02400.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G02400.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0026g01770.t01 (Vitis vinifera), 3'ss of exon 6
aatacacttgactaattggtaagcattaagaatataatgtgttact-tgtgctttgctttgaatat---tttctgctcacatgaaactgagtttcttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCTCGGATGTTTAGTGAAAACAAACGTGAATACAACAGAAGAGTACGAGATA
   |   | || |||     ||    |||     |  | |  |      ||||||| |  |||| |   || ||  | |  |     |    || |  ||||||    |||||||||| ||||||||||||||||| || ||||||||||| || |||||||||||||| ||||| |||||||||||||||||||| || || |
---attttggattaaagaacaatttataatggctttttatagtgtagcttgctttg-tgagaatttggattgctaattatgttgccttcctcttatgattgcagTCGCTGCTTTGTGACCCAAACCCAAACTCTCCTGCAAATTCAGAAGCAGCACGGATGTTTAGTGAGAACAAGCGTGAATACAACAGAAGAGTGCGTGAGA

upper sequence: GLYMA02G02400.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ16328 (Selaginella moellendorffii), 3'ss of exon 4
aatacacttgactaattggtaagcattaagaatataatgtgttacttgtgctttgctttgaatattttctgctcacatgaaactgagtttcttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCTCGGATGTTTAGTGAAAACAAACGTGAATACAACAGAAGAGTACGAGATA
                                | |  | | ||   |  || ||  || |||||   | | || |||          || |   | ||||    ||||||||||||| ||||||||||| || ||||| || ||||| || ||||||| |||||| |||   || || |||||| | ||||| || || |
-------------------------------gtttggtttttttgct-cgcctttgttggaatagacttt-cttacac---------ttacccatcgcagTCACTGCTTTGTGATCCTAACCCAAACTCGCCGGCGAACTCCGAAGCAGCGCGGATGTATAGTGAGAACCGTCGAGAGTACAACCGGAGAGTCCGCGACA
















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|22541678|gb|BU091521.1|BU091521
EST:     ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAG                         AGCTTGCTTTGTGATCCAAACCCAGACTCTCCAGCGAATTCAGAAGCTTGC
genomic: ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAGgtcatagtga ... cttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCT-GC
EST: gi|15337304|gb|BI497960.1|BI497960
EST:     ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAG                         AGCTTGCTTTGTGATCCCAACCCAAACTCTCCAGCGAATTCAGAAGCTGCT
genomic: ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAGgtcatagtga ... cttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCT
EST: gi|192329123|gb|FK019738.1|FK019738
EST:     ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAG                         AGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCT
genomic: ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAGgtcatagtga ... cttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCT
EST: gi|192330836|gb|FK021609.1|FK021609
EST:     ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAG                         AGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCT
genomic: ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAGgtcatagtga ... cttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCT
EST: gi|298180824|gb|HO022263.1|HO022263
EST:     ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAG                         AGCTTGCTTTG
genomic: ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAGgtcatagtga ... cttgttgcagAGCTTGCTTTG
EST: gi|11413307|gb|BF425318.1|BF425318
EST:     ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAG                         AGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCT
genomic: ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAGgtcatagtga ... cttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCT
EST: gi|298178672|gb|HO024407.1|HO024407
EST:     ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAG                         AGCTTGCTTTGTGATC
genomic: ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAGgtcatagtga ... cttgttgcagAGCTTGCTTTGTGATC
EST: gi|151394718|gb|EV264589.1|EV264589
EST:     ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAG                         AGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCT
genomic: ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAGgtcatagtga ... cttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCT
EST: gi|298179938|gb|HO025153.1|HO025153
EST:     ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAG                         AGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCT
genomic: ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAGgtcatagtga ... cttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCT
EST: gi|192310693|gb|FK001117.1|FK001117
EST:     ATCAATGGAGCCCGATTTATGATGTTGCGGGGATAATTACCTCAATTCAG                         AGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGGGAATTCAGAAGCTGCT
genomic: ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAGgtcatagtga ... cttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCT
EST: gi|151405335|gb|EV275149.1|EV275149
EST:     ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAG                         AGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCT
genomic: ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAGgtcatagtga ... cttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCT
EST: gi|254334254|gb|GR849172.1|GR849172
EST:     ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAG                         AGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCT
genomic: ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAGgtcatagtga ... cttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCT
EST: gi|298175146|gb|HO014949.1|HO014949
EST:     ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAG                         AGCTTGCTTTGCGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCT
genomic: ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAGgtcatagtga ... cttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCT
EST: gi|5509647|gb|AI856205.1|AI856205
EST:     ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAG                         AGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCT
genomic: ATCAATGGAGCCCGATTTATGATGTTGCGGCGATACTTACCTCAATTCAGgtcatagtga ... cttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgctttgctttgaatattttctgctcacatgaaactgagtttcttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCTCGGATGTTTAGTGAAAACAAACGTGAATACAACAGAAGAGTACGAGATA
                        tgctcac  putative branch site (score: 2)
                                          tttcttgtt  putative PPT
           tttgaatattttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatacacttgactaattggtaagcattaagaatataatgtgttacttgtgctttgctttgaatattttctgctcacatgaaactgagtttcttgttgcagAGCTTGCTTTGTGATCCAAACCCAAACTCTCCAGCGAATTCAGAAGCTGCTCGGATGTTTAGTGAAAACAAACGTGAATACAACAGAAGAGTACGAGATA

- - cacttga
- - - - - - - - - - - - - - - - - - - - - - cttgtgc
- - - - - - - - - - - - - - - - - - - - - - - - tgctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgagtt