Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttaaaaaatatagactatttaattacactcctggaatgtccatgtactaatgttattgcatattatgatgatcacttcctctgtgagaagcgttgtaaattcctatatttttgcagATGTGTACGGAATGGGAATTATGATGAAGCCCTAGATTTGGAAGCATTTGTTGGCAAACTTTCAACCATGCATCCAAA

Basic information

species Glycine max
transcript GLYMA02G04920.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G04920.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0008g01350.t01 (Vitis vinifera), 3'ss of exon 3
gtatgttaaaaaatatagactatttaattacactcctggaatgtccatgtactaatgttattgcatattatgatgatcacttcctctgtgagaagcgttgtaaattcctatatttt-tgcagATGTGTACGGAATGGGAATTATGATGAAGCCCTAGATTTGGAAGCATTTGTTGGCAAACTTTCAACCATGCATCCAAA
      |    | | | || | | ||     ||     |||||       |  |  |||  | | ||  |  |             |||   |  | |  | ||||||  | |||  ||||||||||||||||| || ||||||||||| || || ||||| || || |||||| ||||||||||||| ||||| |||||
------ttgtcactgttgattttatatgatgaccttaagaatgctt---catca--gttcctacctaagaaaaaa-----------tgtagaacacctctttaattcccctctttcatgcagATGTGTACGGAACGGCAATTATGATGAGGCTCTTGATTTAGAGGCTTTTGTTTGCAAACTTTCAACAATGCACCCAAA

upper sequence: GLYMA02G04920.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S120_27V6.2 (Physcomitrella patens), 3'ss of exon 3
gtatgttaaaaaatatagactatttaatta-cactcctggaatgtccatgtactaatgttattgcatattatgatgatcacttcctctgtgagaagcgttgtaaattcctatatttttgcagATGTGTACGGAATGGGAATTATGATGAAGCCCTAGATTTGGAAGCATTTGTTGGCAAACTTTCAACCATGCATCCAAA
            ||        |||  | | | |||   |  |||     |   | | ||      |  | |  || |   ||  ||  |||| |||         | || |||   ||||||||||| || |||||||||||||| ||||| || ||| ||||||| |||||    ||  |  |||| |||||| ||| 
------------atccgatgagttttgtcaactctcacaggttgtgaggatcagatttttgaaagctggtgttgtgttggatttttcactgagtagc---------ttct-tatcagtgcagATGTGTGCGAAATGGGAATTATGACGAAGCTCTTGATCTGGAAGCTTTTGTCACAAAGTTGGCAACAATGCATTCAAG
















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|254335101|gb|GR844886.1|GR844886
EST:     AATCACAGTACTTTGCTTGACTTGCTAGAAATTCCTCAACTCATGGACAC                         ATGTGTACGGAATGGGAATTATGATGAAGCCCTAGATTTGGAAGCATTTGT
genomic: AATCACAGTACTTTGCTTGACTTGCTAGAAATTCCTCAACTCATGGACACgtatgttaaa ... atttttgcagATGTGTACGGAATGGGAATTATGATGAAGCCCTAGATTTGGAAGCATTTGT
EST: gi|193466896|gb|FK430315.1|FK430315
EST:     AATCACAGTACTTTGCTTGACTTGCTAGAAATTCCTCAACTCATGGACAC                         ATGTGTACGGAATGGG
genomic: AATCACAGTACTTTGCTTGACTTGCTAGAAATTCCTCAACTCATGGACACgtatgttaaa ... atttttgcagATGTGTACGGAATGGG
EST: gi|208184356|gb|GD984552.1|GD984552
EST:     AATCACAGTACTTTGCTTGACTTGCTAGAAATTCCTCAACTCATGGACAC                         ATGTGTACGGAAT
genomic: AATCACAGTACTTTGCTTGACTTGCTAGAAATTCCTCAACTCATGGACACgtatgttaaa ... atttttgcagATGTGTACGGAAT
EST: gi|193671294|gb|FK613290.1|FK613290
EST:     AATCACAGTACTTTGCTTGACTTGCTAGAAATTCCTCAACTCATGGACAC                         ATGTGTACGGAATGGGAATTATGATGAAGCCCTAGATTTGGAAGCATTTGT
genomic: AATCACAGTACTTTGCTTGACTTGCTAGAAATTCCTCAACTCATGGACACgtatgttaaa ... atttttgcagATGTGTACGGAATGGGAATTATGATGAAGCCCTAGATTTGGAAGCATTTGT
EST: gi|209722418|gb|BW682794.1|BW682794
EST:     ATCACAGTAACTT-GCTTGACTTGCTAGAAATTCCTCAACTCATGGACAC                         ATGTGTACGGAATGGGAATTATGATGAA
genomic: ATCACAGTA-CTTTGCTTGACTTGCTAGAAATTCCTCAACTCATGGACACgtatgttaaa ... atttttgcagATGTGTACGGAATGGGAATTATGATGAA
EST: gi|254327754|gb|GR834719.1|GR834719
EST:     AATCACAGTACTTTGCTTGACTTGCTAGAAATTCCTCAACTCATGGACAC                         ATGTGTACGGAATGGGAATTATGATGAAGCCCTAGATTTGGAAGCATTTGT
genomic: AATCACAGTACTTTGCTTGACTTGCTAGAAATTCCTCAACTCATGGACACgtatgttaaa ... atttttgcagATGTGTACGGAATGGGAATTATGATGAAGCCCTAGATTTGGAAGCATTTGT
EST: gi|193626763|gb|FK574443.1|FK574443
EST:     AATCACAGTACTTTGCTTGACTTGCTAGAAATTCCTCAACTCATGGACAC                         ATGTGTACGGAATGGGAATTA
genomic: AATCACAGTACTTTGCTTGACTTGCTAGAAATTCCTCAACTCATGGACACgtatgttaaa ... atttttgcagATGTGTACGGAATGGGAATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatgatgatcacttcctctgtgagaagcgttgtaaattcctatatttttgcagATGTGTACGGAATGGGAATTATGATGAAGCCCTAGATTTGGAAGCATTTGTTGGCAAACTTTCAACCATGCATCCAAA
                                            tattttt  CT-rich tract
                                  taaattcctatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttaaaaaatatagactatttaattacactcctggaatgtccatgtactaatgttattgcatattatgatgatcacttcctctgtgagaagcgttgtaaattcctatatttttgcagATGTGTACGGAATGGGAATTATGATGAAGCCCTAGATTTGGAAGCATTTGTTGGCAAACTTTCAACCATGCATCCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG