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'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagtttcatttgccaactcttgaaaatcgggaaatttaattttcttcgtttactgaatcacatgtttcaattttgtttgacgtctaattgaagctcgtttaatggttctttcgcacaatagatcttttttcttttttaaatttatgtgtcattttcaatttctgtttgccccttcgcagTGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGACTTTTCAGATGCTGCAGAACGAATGCCAGGTTTCTCTGAACACTGTTGAC

Basic information

species Glycine max
transcript GLYMA05G30430.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g21940.1 (Oryza sativa), 3'ss of exon 1
gtaagtagtttcatttgccaactcttgaaaatcgggaaatttaattttcttcgtttactgaatcacatgtttcaattttgtttgacgtctaattgaagctcgtttaatggttctttcgcacaatagatcttttttct---tttttaaatttatgtgtcattttcaatttctgtttgccccttcgcagTGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGACTTTTCAGATGCTGCAGAACGAATGCCAGGTTTCTCTGAACACTGTTGAC
                                                                                        |         | | ||   | || || | ||  |  | ||  ||   |    ||  ||  |||    ||  || |    |  |||       |  |||| ||  | || || ||||| ||||| ||||| ||||| ||| |||| ||||| || |||| |||||||||||| |||||||| || || ||||| || |||
-------------------------------------------------------------------------------------gaaccccccccctcccattgggtagtgctatagcttaggaaattattacgcaaggttgctaggtttgatagtgtttcttgcgtgatgtccatggat--gcagCGTGGTGAAGATAGTGCTGCAGTTCTGCAAGGAGAACTCGCTGCAGCAGACGTTCCAGACGCTGCAGAACGAGTGCCAGGTCTCGCTCAACACCGTCGAC

upper sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G037683_T01 (Zea mays), 3'ss of exon 1
gtaagtagtttcatttgccaactcttgaaaatcgggaaatttaattttcttcgtttactgaatcacatgtttcaattttgtttgacgtctaattgaagctcgtttaatggttctttcgcacaatagatcttttttcttttttaaatttatgtgtcattttcaatttctgtttgccccttcgcagTGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGACTTTTCAGATGCTGCAGAACGAATGCCAGGTTTCTCTGAACACTGTTGAC
                                                                          || || ||  |  ||||   ||    ||  | |   | |  | |||  |  |   |    ||        ||||  | |  || ||   ||| |||         ||||| ||  | || || ||||| ||||| ||||| ||||||||| |||| ||||| || |||| |||||| ||||| |||||||| || || ||||||||||||
-------------------------------------------------------------------------catcttattgaa--tctatccgagaaccgcctgact-tgcagtagcattagtgtcttaaggtcgacaaaggatttgagcgcgatgttttttttttgtg--------cgcagCGTGGTTAAGATAGTGCTGCAGTTCTGCAAGGAGAATTCGCTGCAGCAGACGTTCCAGACGCTGCAAAACGAGTGCCAGGTCTCCCTCAACACTGTTGAC

upper sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 1
gtaagtagtttcatttgccaactcttgaaaatcgggaaatttaattttcttcgtttactgaatcacatgtttcaattttgtttgacgtctaattgaagctcgtttaatggttctttcgcacaatagatcttttttctttttta-aatttatgtgtcattttcaatttctgtttgccccttcgcagTGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGACTTTTCAGATGCTGCAGAACGAATGCCAGGTTTCTCTGAACACTGTTGAC
                                                                                   |  || ||  || |       ||    |||    |   ||||  |  |  |  |||  |   |  ||  | | |||||   | | | ||   |  |   ||||||||| || || |||||||||||||| ||||| ||||| ||||| || || |||||||   | || |  || || ||||| ||| |||| || || |||
----------------------------------------------------------------------------------ggttgtttatatgtattcttcctatatcttcagctgtctaatactttatagtgttttgatgtgaagtaaatctaattttatgtatttcttcatcttt---cagTGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAACGTTTCAGACATTACAAAGTGAGTGTCAGGTATCTTTGAATACGGTCGAC

upper sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S136_176V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaagtagtttcatttgccaactcttgaaaatcgggaaatttaattttcttcgtttactgaatcacatgtttcaattttgtttgacgtctaattgaagctcgtttaatggttctttcgcacaatagatcttttttcttttttaaatttatgtgtcattttcaatttctgtttgccccttcgcagTGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGACTTTTCAGATGCTGCAGAACGAATGCCAGGTTTCTCTGAACACTGTTGAC
                                                              |||  | ||| | |||||   |   ||  |||||        | |  | | ||      || |||| |  |||         |  |  ||||       |   | |  |||    |  |||||||||| ||||| ||||| ||||| || || ||||| || ||||| |||||||||||||  ||||| || || || |||||||| || |||||||| |||
--------------------------------------------------------------tcaggtcttttagttttggaagtgctcagattga--------tgagagctttt------aacagatttcattt--------gacctcagtgttcaccgaaggcttttgttggagttgtgcagTGTCATTAAAATAGTGCTGCAGTTCTGTAAGGAGAACTCCTTGCAGCAGACTTTTCAGACACTGCAAAATGAGTGTCAGGTTTCCCTCAACACTGTGGAC

upper sequence: GLYMA05G30430.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S31_68V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaagtagtttcatttgccaactcttgaaaatcgggaaatttaattttcttcgtttactgaatcacatgtttcaattttgtttgacgtctaattgaagctcgtttaatggttctttcgcacaatagatcttttttcttttttaaatttatgtgtcattttcaatttctgtttgccccttcgcagTGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGACTTTTCAGATGCTGCAGAACGAATGCCAGGTTTCTCTGAACACTGTTGAC
                                                                               ||   |||   ||    |||   ||| |       || |  | | |  ||  |    || |       | |||||  | |  |     |  | |   ||  |||||||||| || || ||||| ||||| || |||||||| || ||||| |||||||| ||||  || || || || || ||||||||||| |||||||| |||
------------------------------------------------------------------------------cgtagtacgatgaaacagagcatttttgaa------tttgagctagaattcggtggatttctcctccactgtgtgtggtctaaagacctttgtggggactgtgcagTGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGACTTTCCAGACACTACAAAATGAGTGTCAGGTTTCTCTCAACACTGTGGAC

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|209727601|gb|BW669925.1|BW669925
EST:     AGTCCAATCGATATAGCAACAATGTCTACTCTTGAAATTGAAGCTCGAGA                         TGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGAC
genomic: AGTCCAATCGATATAGCAGCAATGTCTACGCTTGAAATTGAAGCTCGAGAgtaagtagtt ... cccttcgcagTGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGAC
EST: gi|193414190|gb|FK377876.1|FK377876
EST:     AGTCCAATCGATATAGCAGCAATGTCTACGCTTGAAATTGAAGCTCGAGA                         TGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGAC
genomic: AGTCCAATCGATATAGCAGCAATGTCTACGCTTGAAATTGAAGCTCGAGAgtaagtagtt ... cccttcgcagTGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGAC
EST: gi|208216077|gb|GE008985.1|GE008985
EST:     AGTCCAATCGATATAGCAGCAATGTCTACGCTTGAAATTGAAGCTCGAGA                         TGTCATCAAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGA
genomic: AGTCCAATCGATATAGCAGCAATGTCTACGCTTGAAATTGAAGCTCGAGAgtaagtagtt ... cccttcgcagTGTCATCAAAA-TTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGA
EST: gi|193695429|gb|FK631283.1|FK631283
EST:     AGTCCAATCGATATAGCAGCAATGTCTACGCTTGAAATTGAAGCTCGAGA                         TGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGAC
genomic: AGTCCAATCGATATAGCAGCAATGTCTACGCTTGAAATTGAAGCTCGAGAgtaagtagtt ... cccttcgcagTGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGAC
EST: gi|192300630|gb|FG989632.1|FG989632
EST:     AGTCCAATCGATATAGCAGCAATGTCTACGCTTGAAATTGAAGCTCGAGA                         TGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGAC
genomic: AGTCCAATCGATATAGCAGCAATGTCTACGCTTGAAATTGAAGCTCGAGAgtaagtagtt ... cccttcgcagTGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGAC
EST: gi|208180491|gb|GD973748.1|GD973748
EST:     AGTCCAATCGATATAGCAGCAATGTCTACGCTTGAAATTGAAGCTCGAGA                         TGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGAC
genomic: AGTCCAATCGATATAGCAGCAATGTCTACGCTTGAAATTGAAGCTCGAGAgtaagtagtt ... cccttcgcagTGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGAC
EST: gi|213609045|gb|DB958814.1|DB958814
EST:     AGTCCAATCGATATAGCAGCAATGTCTACGCTTGAAATTGAAGCTCGAGA                         TGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGAC
genomic: AGTCCAATCGATATAGCAGCAATGTCTACGCTTGAAATTGAAGCTCGAGAgtaagtagtt ... cccttcgcagTGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGAC
EST: gi|193367431|gb|FK329541.1|FK329541
EST:     AGTCCAATCGATATAGCAGCAATGTCTACGCTTGAAATTGAAGCTCGAGA                         TGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGAC
genomic: AGTCCAATCGATATAGCAGCAATGTCTACGCTTGAAATTGAAGCTCGAGAgtaagtagtt ... cccttcgcagTGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttcttttttaaatttatgtgtcattttcaatttctgtttgccccttcgcagTGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGACTTTTCAGATGCTGCAGAACGAATGCCAGGTTTCTCTGAACACTGTTGAC
                                  tttctgtttgcccctt  CT-rich tract
       ttttttaaatttatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtagtttcatttgccaactcttgaaaatcgggaaatttaattttcttcgtttactgaatcacatgtttcaattttgtttgacgtctaattgaagctcgtttaatggttctttcgcacaatagatcttttttcttttttaaatttatgtgtcattttcaatttctgtttgccccttcgcagTGTCATCAAAATTGTGCTTCAGTTTTGCAAAGAGAATTCGTTGCATCAGACTTTTCAGATGCTGCAGAACGAATGCCAGGTTTCTCTGAACACTGTTGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG