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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatatagttgttcttatagcgtgtttacatattgatgtacacatacattggaattcaaattaagggattttactgaatagctacttttgttcctttgaagCAAATTTGGACCTGTACAAGATGTGAGAATTCCATATCAGCAAAAGCGAATGTTTGGGTTTGTTACCTTTGTCTACCCAGAGACAGTGAGACTCATATTA

Basic information

species Glycine max
transcript GLYMA01G43700.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G43700.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G21100.1 (Arabidopsis thaliana), 3'ss of exon 1
------------------------gatatagt-tgttcttatagcgtgtttacatattgatgtacacatac-attggaattcaaattaagggatttta--ctgaatagctacttttgttcctttgaagCAAATTTGGACCTGTACAAGATGTGAGAATTCCATATCAGCAAAAGCGAATGTTTGGGTTTGTTACCTTTGTCTACCCAGAGACAGTGAGACTCATATTA
                        | | |  | ||||  | |      || | |  ||| || |    ||| | ||     |    |  |  ||| ||  |||| ||  |  | |||||   ||| ||||| |||||||| || |||||||| || |||||||| ||||| || || |||||||||||||| || ||| || || | || || |||||| ||||||| 
gtaatcttttacaattgtatcaaagctgttatgtgtttgtttgcatcattaaaagtttggtggatgtctactaatgtttgcctggctctgttattgtagactgattatgt-ttgttgttttcttgtagCAATTTTGGACCAGTGCAAGATGTTAGGATTCCATACCAGCAGAAACGGATGTTTGGGTTTGTCACTTTTCTCCACTCTGAAACTGTGAGAATCATATTG

upper sequence: GLYMA01G43700.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ28712 (Selaginella moellendorffii), 3'ss of exon 2
gatatagttgttcttatagcgtgtttacatattgatgtacacatacattggaattcaaattaagggattttactgaatagctacttttgttc-ctttgaagCAAATTTGGACCTGTACAAGATGTGAGAATTCCATATCAGCAAAAGCGAATGTTTGGGTTTGTTACCTTTGTCTACCCAGAGACAGTGAGACTCATATTA
                                           ||| |||   || || |     | |   |  | |  | |||     ||  || || ||    |  || || ||  |||| ||||||||||||   ||||| |||||||||||||||||||| || ||    ||| | ||||| |||||  | ||  | 
------------------------------------------gtacgttgtg-tttaattccttcgctacaagaggagcgatacgaaactttactgtgcagAGCTTACGGTCCCGTGGAAGACGTGAGAATTCCAACCCAGCACAAGCGAATGTTTGGGTTTGTGACGTTCACGTACGCTGAGACGGTGAGGATGATTCTG

upper sequence: GLYMA01G43700.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ30675 (Selaginella moellendorffii), 3'ss of exon 2
gatatagttgttcttatagcgtgtttacatattgatgtacacatacattggaattcaaattaagggattttactgaatagctacttttgttc-ctttgaagCAAATTTGGACCTGTACAAGATGTGAGAATTCCATATCAGCAAAAGCGAATGTTTGGGTTTGTTACCTTTGTCTACCCAGAGACAGTGAGACTCATATTA
                                           ||| |||   || || |     | |   |  | |  | |||     ||  |  || ||    |  || || ||  |||| ||||||||||||   ||||| |||||||||||||||||||| || ||    ||| | ||||| |||||  | ||  | 
------------------------------------------gtacgttgtc-tttaattccttcgttacaagaggagcgatacgaaactttaccgtgcagAGCTTACGGTCCCGTGGAAGACGTGAGAATTCCAACCCAGCACAAGCGAATGTTTGGGTTTGTGACGTTCACGTACGCTGAGACGGTGAGGATGATTCTG

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|208303806|gb|GE105275.1|GE105275
EST:     ATGAAGATGTTTCCGAGTACTTCAG                         CAAATTTGGACCTGTACAAGATGTGAGAATTCCATATCAGCAAAAGCGAAT
genomic: ATGAAGATGTTTCCGAGTACTTCAGgtattatacg ... tcctttgaagCAAATTTGGACCTGTACAAGATGTGAGAATTCCATATCAGCAAAAGCGAAT
EST: gi|7042736|gb|AW472630.1|AW472630
EST:     TTTCCTGCCGAAAGTACATTCAAAGATGAAGATGTTTCCGAGTACTTCAG                         CAAATTTGGACCTGTACAAGATGTGAGAATTCCATATCAGCAAAAGCGAAT
genomic: TTTCCTGCCGAAAGTACATTCAAAGATGAAGATGTTTCCGAGTACTTCAGgtattatacg ... tcctttgaagCAAATTTGGACCTGTACAAGATGTGAGAATTCCATATCAGCAAAAGCGAAT
EST: gi|15202990|gb|BI425758.1|BI425758
EST:     TTTCCTGCCGAAAGTACATTCAAAGATGAAGATGTTTCCGAGTACTTCAG                         CAAATTTGGACCTGTACAAGATGTGAGAATTCCATATCAGCAAAAGCGAAT
genomic: TTTCCTGCCGAAAGTACATTCAAAGATGAAGATGTTTCCGAGTACTTCAGgtattatacg ... tcctttgaagCAAATTTGGACCTGTACAAGATGTGAGAATTCCATATCAGCAAAAGCGAAT
EST: gi|208056022|gb|GD855451.1|GD855451
EST:     TTTCCTGCCGAAAGTACATTCAAAGATGAAGATGTTTCCGAGTACTTCAG                         CAAATTTGGACCTGTACAAGATGTGAGAATTCCATATCAGCAAAAGCGAAT
genomic: TTTCCTGCCGAAAGTACATTCAAAGATGAAGATGTTTCCGAGTACTTCAGgtattatacg ... tcctttgaagCAAATTTGGACCTGTACAAGATGTGAGAATTCCATATCAGCAAAAGCGAAT
EST: gi|6915919|gb|AW397449.1|AW397449
EST:     TTTCCTGCCGAAAGTACATTCAAAGATGAAGATGTTTCCGAGTACTTCAG                         CAAATTTGGACCTGTACAAGATGTGAGAATTCCATATCAGCAAAAGCGAAT
genomic: TTTCCTGCCGAAAGTACATTCAAAGATGAAGATGTTTCCGAGTACTTCAGgtattatacg ... tcctttgaagCAAATTTGGACCTGTACAAGATGTGAGAATTCCATATCAGCAAAAGCGAAT
EST: gi|7146570|gb|AW508492.1|AW508492
EST:     TTTCCTGCCGAAAGTACATTCAAAGATGAAGATGTTTCCGAGTACTTCAG                         CAAATTTGGACCTGTACAAGATGTGAGAATTCCATATCAGCAAAAGCGAAT
genomic: TTTCCTGCCGAAAGTACATTCAAAGATGAAGATGTTTCCGAGTACTTCAGgtattatacg ... tcctttgaagCAAATTTGGACCTGTACAAGATGTGAGAATTCCATATCAGCAAAAGCGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattggaattcaaattaagggattttactgaatagctacttttgttcctttgaagCAAATTTGGACCTGTACAAGATGTGAGAATTCCATATCAGCAAAAGCGAATGTTTGGGTTTGTTACCTTTGTCTACCCAGAGACAGTGAGACTCATATTA
                                   ctacttttgttccttt  CT-rich tract
      aattcaaattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatatagttgttcttatagcgtgtttacatattgatgtacacatacattggaattcaaattaagggattttactgaatagctacttttgttcctttgaagCAAATTTGGACCTGTACAAGATGTGAGAATTCCATATCAGCAAAAGCGAATGTTTGGGTTTGTTACCTTTGTCTACCCAGAGACAGTGAGACTCATATTA

- - - - - - - - - gcgtgtt
- - - - - - - - - - - - - - - - tgatgta
- - - - - - - - - - - - - - - - - - - -cacatac