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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcaattcaatgccaaagctttggaccgtgttaaaatttgtaacatgaatctgtctgcttatgtgaaaaattattaagaatgatttttgtccaattgcagGTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAGAAAGCAAGCTTGAATTATTATGCATAGGCACTCAACGCAAGGAAAAACG

Basic information

species Glycine max
transcript GLYMA03G39500.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G09100.1 (Arabidopsis thaliana), 3'ss of exon 9
tgcaattcaatgccaaagctttggaccgtgttaaaatttgtaacatgaatctgtctgcttatgtgaaaaattattaagaatgatttttgtccaattgcagGTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAGAAAGCAAGCTTGAATTATTATGCATAGGCACTCAACGCAAGGAAAAACG-
         ||||  |    ||    ||| |||    ||||||| | |   |||  | | || || |  |        |||| |   |||     ||||||||||||||||||| || |||||||| || || ||||| ||||| ||||||||||||||||||||||| || || || |  |||     | | | |  |  
-------gtatgcatatatctt---tcgtcttagtggttgtaactttaggatgtg-gatgatatggagga--------aatggtaaatgtgtg--tgcagGTGAACCATGAGGATTTCAATGAAGGTATAATTCAAGTACAAGCCAAGAAGAAAGCAAGCTTGAATTACTACGCCTAAGTCCTCTTT-TATGTACACTCTT

upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 9
tgcaattcaatgccaaagctttggaccgtgttaaaatttgtaac---atgaatctgtctgcttat--gtgaaaaattattaagaatgatttttgtccaattgcagGTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAGAAAGCAAGCTTGAATTATTATGCATAGGCACTCAACGCAAGGAAAAACG
 | ||   || | || | || |  |   | || |  ||| | |     |   |  ||||| || |    |     || |      |  | |||||     | |||||||||||||| ||||| |||||||| |||||||||||||| || |||||||||||||||||||| || || || |   | |||      |  |   |  
-gtaaa--aaagacagaactcttaatgat-ttgagctttatgattgtgtagtttggtctgttttttaaggtggggttctctgttgttgtgtttgtgtg--ttcagGTGAACCATGAAGACTTCAATGAAGGTATCATCCAAGTCCAGGCCAAGAAGAAAGCAAGCTTGAACTACTACGCCTGATCTCTCTCTCTCATCATTTATT

upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 9
tgcaattcaatgccaaagctttggaccgtgttaaaatttgtaacatgaatctgtctgcttatgtgaaaaattattaa--gaatgatt---tttgtccaattgcagGTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAGAAAGCAAGCTTGAATTATTATGCATAGGCACTCAACGCAAGGAAAAACG-
   | |||  ||  |    |||      | | |    ||| ||| |   |  |       ||| ||  || || |||  | |   |    || ||   ||| |||||||||||||||||||| || ||||| || || ||||| || || ||||||||| ||||||| |||||||||||||||||  ||  | | |   |   |  
-agagttctgtg--atgtttttatgtactatcacgtattgaaactt--ttgagctctaccatgggagcaagtactaatcggactgtcaaattggtttgattccagGTGAACCATGAGGACTTCAACGAAGGTATAATTCAAGTACAGGCCAAGAAGAAATCAAGCTTAAATTATTATGCATAGGC-TTCTCCTCCAAACATGTCAT

upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ15061 (Selaginella moellendorffii), 3'ss of exon 9
tgcaattcaatgccaaagctttggaccgtgttaaaatttgtaacatgaatctgtctgcttatgtgaaaaattattaagaatgatttttgtccaattgcagGTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAGAAAGCAAGCTTGAATTATTATGCATAGGCACTCAACGCAAGGAAAAACG
                                             | |    |  || |    |  | |  | ||  || |     | |  |  |  ||||| |  || |||||||| || || |||||||||||||| ||||| |||||||| || |||||||| || || ||||  |||    |   |||| | |   
--------------------------------------------gtaacgacgcgtgatcgaatacacagctttttcga-tctcactcgctctttcacagGTTACGCACGAGGACTTCAACGATGGCATCATCCAAGTGCAAGCCAAGAAGAAGGCCAGCTTGAACTACTACGCATGAGCAAATCATAGAAGGGATAGAA

upper sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 9
tgcaattcaatgccaaagctttggaccgtgttaaaatttgtaacatgaatctgtctgcttatgtgaaaaattattaagaatgatttttgtccaattgcagGTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAGAAAGCAAGCTTGAATTATTATGCATAGGCACTCAACGCAAGGAAAAACG
                                             | |    |  || |    |  | |  | ||  || |     | |  |  |  ||||| |  || |||||||| || || |||||||||||||| ||||| |||||||| || |||||||| || || ||||                        
--------------------------------------------gtaacgacgcgtgatcgaatacacagctttttcga-tctcactcgctctttcacagGTTACGCACGAGGACTTCAACGATGGCATCATCCAAGTGCAAGCCAAGAAGAAGGCCAGCTTGAACTACTACGCATGA----------------------

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|208244769|gb|GE037494.1|GE037494
EST:     ATGTTGGCCCTTCGCCGTGATGCAACTGAG                         GTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAG
genomic: ATGTTGGCCCTTCGCCGTGATGCAACTGAGgtttgctttc ... ccaattgcagGTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAG
EST: gi|9984894|gb|BE659002.1|BE659002
EST:     CTGTCTGTGTTGAGGCTGGCATGTTGGCCCTTCGCCGTGATGCAACTGAG                         GTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAG
genomic: CTGTCTGTGTTGAGGCTGGCATGTTGGCCCTTCGCCGTGATGCAACTGAGgtttgctttc ... ccaattgcagGTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAG
EST: gi|7030457|gb|AW460240.1|AW460240
EST:     CTGTCTGTGTTGAGGCTGGCATGTTGGCCCTTCGCCGTGATGCAACTGAG                         GTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAG
genomic: CTGTCTGTGTTGAGGCTGGCATGTTGGCCCTTCGCCGTGATGCAACTGAGgtttgctttc ... ccaattgcagGTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAG
EST: gi|193410672|gb|FK376323.1|FK376323
EST:     TTGGCCCTTCGCCGTGATGCAACTGAG                         GTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAG
genomic: TTGGCCCTTCGCCGTGATGCAACTGAGgtttgctttc ... ccaattgcagGTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAG
EST: gi|209727654|gb|BW663794.1|BW663794
EST:     CTGTCTGTGTTGAGGCTGGCATGTTGGCCCTTCGCCGTGATGCAACTGAG                         GTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAG
genomic: CTGTCTGTGTTGAGGCTGGCATGTTGGCCCTTCGCCGTGATGCAACTGAGgtttgctttc ... ccaattgcagGTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAG
EST: gi|209718166|gb|BW657812.1|BW657812
EST:     CTGTCTGTGTTGAGGCTGGCATGTTGGCCCTTCGCCGTGATGCAACTGAG                         GTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAG
genomic: CTGTCTGTGTTGAGGCTGGCATGTTGGCCCTTCGCCGTGATGCAACTGAGgtttgctttc ... ccaattgcagGTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAG
EST: gi|208096116|gb|GD895058.1|GD895058
EST:     GTTGGCCCTTCGCCGTGATGCAACTGAG                         GTGAACCATGAGGACCTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAG
genomic: GTTGGCCCTTCGCCGTGATGCAACTGAGgtttgctttc ... ccaattgcagGTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaatctgtctgcttatgtgaaaaattattaagaatgatttttgtccaattgcagGTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAGAAAGCAAGCTTGAATTATTATGCATAGGCACTCAACGCAAGGAAAAACG
                                      tttttgtcc  CT-rich tract
             ttatgtgaaaaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcaattcaatgccaaagctttggaccgtgttaaaatttgtaacatgaatctgtctgcttatgtgaaaaattattaagaatgatttttgtccaattgcagGTGAACCATGAGGACTTTAATGAAGGCATCATCCAAGTCCAAGCAAAGAAGAAAGCAAGCTTGAATTATTATGCATAGGCACTCAACGCAAGGAAAAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - -caatgcc
- - - - - - - - -gctttgg
- - - - - - - - - - - - -ccgtgtt
- - - - - - - - - - - - - - - - - - - - - acatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaaat