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

TGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGAAGGAGCTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAGgtttgttgtgtttcttactgccttccttaattgctgggtttgaaccttcaatcaattagtgcaccccagtgtgtgtgtgtgtgtgtattgatattgtaattataatgacctataattattcttaatgcag

Basic information

species Glycine max
transcript GLYMA06G08480.2
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G08480.1 (Glycine max), 5'ss of exon 11
lower sequence: Vv04s0008g04220.t01 (Vitis vinifera), 5'ss of exon 11
TGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGAAGGAGCTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAGgtttgttgtgtttcttactgccttccttaattgc--tgggtttgaaccttcaatcaattagtgcaccccagtgtgtgtgtgtgtgtgtattgatattgtaattataatgacctataattattcttaatgcag
||  ||||| ||||||| | ||||||| ||  | |  |||||||||||||| ||||| ||||| || || || ||||||||||||||||  | ||| ||||||       |||  | || |   | || ||| |  |     ||||  | || |    | || ||       ||       ||| |||   |  | || |                                
TGTTGAAAAGTATTTCAGGGGAGGATCACGGTTGAATTGGCCTGAAGGAGCAGTTTCTAGGGAAAGTATCAGAGCAGTGAAGAAGCTTGACCGTCTGAAGgttccac-cattttctccttctgcctttgatttcaataaacctgaagttccacttttctggtacattttttagtaaac---tgtatgtccggtaaatgcag-------------------------------
















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|208061980|gb|GD856362.1|GD856362
EST:     CTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAG                         GATATTGTATCACGAAATGTGGACTCTTCAAGGTCCTCCT
genomic: CTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAGgtttgttgtg ... cttaatgcagGATATTGTATCACGAAATGTGGACTCTTCAAGGTCCTCCT
EST: gi|193724330|gb|FK657590.1|FK657590
EST:     CTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAG                         GATATTGTATCAACGAAATG
genomic: CTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAGgtttgttgtg ... cttaatgcagGATATTGTATCA-CGAAATG
EST: gi|193523484|gb|FK481775.1|FK481775
EST:     CTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAG                         GATATTGTATCACGAAATGTGGACTCTTCAAGGTCCTCCTTGACTGAATTG
genomic: CTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAGgtttgttgtg ... cttaatgcagGATATTGTATCACGAAATGTGGACTCTTCAAGGTCCTCCTTGACTGAATTG
EST: gi|9985118|gb|BE659226.1|BE659226
EST:     CTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAG                         GATATTGTATCACGAAATGTGGACTCTTCAAGGTCCTCCTTGACTGAATTG
genomic: CTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAGgtttgttgtg ... cttaatgcagGATATTGTATCACGAAATGTGGACTCTTCAAGGTCCTCCTTGACTGAATTG
EST: gi|193394767|gb|FK359948.1|FK359948
EST:     AGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAG                         GATATTGTATCACGAAATGTGGACTCTTCAAGGTCCTCCTTGACTGAATTG
genomic: AGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAGgtttgttgtg ... cttaatgcagGATATTGTATCACGAAATGTGGACTCTTCAAGGTCCTCCTTGACTGAATTG
EST: gi|193435485|gb|FK400713.1|FK400713
EST:     TGTTTCAAGGGAGAGCAATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAG                         GATATTGTATCACGAAATGTGGACTCTTCAAGGTCCTCCTTGACTGAATTG
genomic: TGTTTCAAGGGAGAGC-ATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAGgtttgttgtg ... cttaatgcagGATATTGTATCACGAAATGTGGACTCTTCAAGGTCCTCCTTGACTGAATTG
EST: gi|207699716|gb|GD678959.1|GD678959
EST:     CTGTTTCAAGGGGGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAG                         GATATTGTATCACGAAATGTGGACTCTTCAAGGTCCTCCTTGACTGAATTG
genomic: CTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAGgtttgttgtg ... cttaatgcagGATATTGTATCACGAAATGTGGACTCTTCAAGGTCCTCCTTGACTGAATTG
EST: gi|193438047|gb|FK399224.1|FK399224
EST:     CTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAG                         GATATTGTATCACGAAATGTGGACTCTTCAAGGTCCTCCTTGACTGAATTG
genomic: CTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAGgtttgttgtg ... cttaatgcagGATATTGTATCACGAAATGTGGACTCTTCAAGGTCCTCCTTGACTGAATTG
EST: gi|22933892|gb|BU551031.1|BU551031
EST:     CTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAG                         GATATTGTATCACGAAATGTGGACTCTTCAAGGTCCTCCTTGACTGAATTG
genomic: CTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAGgtttgttgtg ... cttaatgcagGATATTGTATCACGAAATGTGGACTCTTCAAGGTCCTCCTTGACTGAATTG
EST: gi|193521719|gb|FK479492.1|FK479492
EST:     CTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAG                         GATATTGTATCACGAAATGTGGACTCTTCAAGGTCCTCCTTGACTGAATTG
genomic: CTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAGgtttgttgtg ... cttaatgcagGATATTGTATCACGAAATGTGGACTCTTCAAGGTCCTCCTTGACTGAATTG
EST: gi|208250045|gb|GE049126.1|GE049126
EST:     CATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAG                         GATATTGTATACAACGAAATGTGGACTCTTCAAGGTCCTCCTTGACTGAAT
genomic: CATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAGgtttgttgtg ... cttaatgcagGATATTGTAT-C-ACGAAATGTGGACTCTTCAAGGTCCTCCTTGACTGAAT
EST: gi|120529842|gb|EH257976.1|EH257976
EST:     CTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAG                         GATATTGTATCACGAAATGTGGACTCTTCAAGGTCCTCCTTGACTGAATTG
genomic: CTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAGgtttgttgtg ... cttaatgcagGATATTGTATCACGAAATGTGGACTCTTCAAGGTCCTCCTTGACTGAATTG
EST: gi|208289609|gb|GE086756.1|GE086756
EST:     CTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAG                         GATATTGTATCACGAAATGTGGACTCTTCAAGGTCCT
genomic: CTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAGgtttgttgtg ... cttaatgcagGATATTGTATCACGAAATGTGGACTCTTCAAGGTCCT
EST: gi|208167418|gb|GD959554.1|GD959554
EST:     CTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAG                         GATATTGTATCACGAAATGTGGACTCTTCAAGGTCCTCCTTGACTGAATTG
genomic: CTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAGgtttgttgtg ... cttaatgcagGATATTGTATCACGAAATGTGGACTCTTCAAGGTCCTCCTTGACTGAATTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAGAAAAATATTTCAAGCGAGGATCGCGACTAAGATGGCCTGAAGGAGCTGTTTCAAGGGAGAGCATTAGTGCAGTGAAGAAGCTTGGTCATCTTAAGgtttgttgtgtttcttactgccttccttaattgctgggtttgaaccttcaatcaattagtgcaccccagtgtgtgtgtgtgtgtgtattgatattgtaattataatgacctataattattcttaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC