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'   
11  
 5'  3'   
12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacctttttcttccgttttctcactcctcgttcttcgtttagggcttcattatttttttgattccctttctctctgtctccgtttcagAAAATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGA

Basic information

species Glycine max
transcript GLYMA18G47910.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47910.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G03340.1 (Arabidopsis thaliana), 3'ss of exon 1
--gtaacctttttcttccgttttctcactcctcgttcttcgtttagggcttcattatttt-tttgattcc-----ctttctctctgtctccgtt----tcagAAAATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGA
| || |||||| | ||| || | | || || | |||| | || ||| | || | || | | | || ||| |||||||||||||||||| || ||||| ||||| ||||| |||||||| ||||||||
gcttcactgttttctatgagtatctgtctagtaat--ttagtgcatggctactttggtttgcctaataactgatgctccttttacatttctgttgttatcagAAAATGGATATGGGACCATGCCCAAAGGTGCACTCTTTGCAGCTTCGGAAAGA

upper sequence: GLYMA18G47910.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G17440.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaacctttttcttccgttttctcactcctcgtt--cttcgtt-----tagggcttcattatttttttgattccctttctc---tctgtctccgtt-tcagAAAATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGA
||| | | | ||| | ||| || | | | |||| || ||| | | |||| | | ||| || |||||||||||||||||| || ||||| ||||| ||||| |||||||| |||||||
-taaaaatcctagcttgatttgggggaggttgttgatttaggtaacaatgtggctaatttggtttatgagtagtctttgacatgtttgttattattatcagAAAATGGATATGGGTCCTTGCCCAAAGGTGCACTCTTTGCAGCTGAGGAAAGA

upper sequence: GLYMA18G47910.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0023g00800.t01 (Vitis vinifera), 3'ss of exon 1
------gtaacctttttcttccgttttctcactcc--tcgttcttcgt--ttagggcttcattatttttttgattccctttctctctgtctccgtttcagAAAATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGA
| | || ||| || | | ||| | | ||||| | ||| || ||| | | | | || | | ||||||||||||||||||||| || || || ||||| |||||||||||||| |||||||
ctttgagggatattggaattcatgttagttattccatttggtcttcataattaaaattttattctgatctctttctaagacttcatcatttttgtttcagAAAATGGATATGGGGCCATGTCCGAAGGTGCACTCCTTGCAGCTAAGGAAAGA

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|192296271|gb|FG989063.1|FG989063
EST:     GTCGCCTCTACCTCGTCGGTCTCTGCCCTCACGAACTCTTCCAGTTAACG                         AAAATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAA
genomic: GTCGCCTCTACCTCGTCGGTCTCTGCCCTCACGAACTCTTCCAGTTAACGgtaacctttt ... tccgtttcagAAAATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAA
EST: gi|193555503|gb|FK515948.1|FK515948
EST:     GTCGCCTCTACCTCGTCGGTCTCTGCCCTCACGAACTCTTCCAGTTAACG                         GAAATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAA
genomic: GTCGCCTCTACCTCGTCGGTCTCTGCCCTCACGAACTCTTCCAGTTAACGgtaacctttt ... tccgtttcagAAAATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAA
EST: gi|209725035|gb|BW659770.1|BW659770
EST:     GTCGCCTCTACCTCGTCGGTCTCTGCCCTCACGAACTCTTCCAGTTAACG                         AAAATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAA
genomic: GTCGCCTCTACCTCGTCGGTCTCTGCCCTCACGAACTCTTCCAGTTAACGgtaacctttt ... tccgtttcagAAAATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAA
EST: gi|193492617|gb|FK455741.1|FK455741
EST:     GTCGCCTCTACCTCGTCGGTCTCTGCCCTCACGAACTCTTCCAGTTAACG                         AAAATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAA
genomic: GTCGCCTCTACCTCGTCGGTCTCTGCCCTCACGAACTCTTCCAGTTAACGgtaacctttt ... tccgtttcagAAAATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAA
EST: gi|193649862|gb|FK595459.1|FK595459
EST:     GTCGCCTCTACCTCGTCGGTCTCTGCCCTCACGAACTCTTCCAGTTAACG                         GAAATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAA
genomic: GTCGCCTCTACCTCGTCGGTCTCTGCCCTCACGAACTCTTCCAGTTAACGgtaacctttt ... tccgtttcagAAAATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAA
EST: gi|208276609|gb|GE074791.1|GE074791
EST:     GTCGCCTCTACCTCGTCGGTCTCTGCCCTCACGAACTCTTCCAGTTAACG                         AAAATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAA
genomic: GTCGCCTCTACCTCGTCGGTCTCTGCCCTCACGAACTCTTCCAGTTAACGgtaacctttt ... tccgtttcagAAAATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgtttagggcttcattatttttttgattccctttctctctgtctccgtttcagAAAATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGA
                      ttttgat  putative branch site (score: 4)
 cttcattatttttttg  CT-rich tract
 ttcattatttttttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacctttttcttccgttttctcactcctcgttcttcgtttagggcttcattatttttttgattccctttctctctgtctccgtttcagAAAATGGATATGGGCCCCTGCCCTAAGGTCCACTCCTTGCAGCTCCGGAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC