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'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agttattgtcttctccagccttccattgagctgaaatgaatctatttattgccatcttatccagaggtttctctcatcattattttttttggggttgtagTTTATTCGTGAGTACACTGGCAAAGTCGATGAACTAGTGAAGGACAAAATTGAAGCACAAAATGAAGTGAAGGCTAAAGAGCAAGAAGAAAAGGATGTAG

Basic information

species Glycine max
transcript GLYMA14G06340.1
intron # 28
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 28
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 28
agttattgtcttctccagccttccattgagctgaaatgaatctatttattgccatcttatccagaggtttctctcatcattattttttttggggttgtagTTTATTCGTGAGTACACTGGCAAAGTCGATGAACTAGTGAAGGACAAAATTGAAGCACAAAATGAAGTGAAGGCTAAAGAGCAAGAAGAAAAGGATGTAG
       || |  |    || | |||     ||  |     ||||| |||       ||   | || ||||  | |  |  |   ||  |  |  || |||| ||||| ||||||||  |||| || ||||| |||||||||||||  |||||| |||| |||||||| | |||||||||| | |||||||| ||| | |
-------gtatcttgtttccgttcatgtgtttggga-----ctattcatt-------tacgaacagttttccataacaacaaagcttgcttcgtgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 28
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 28
agttattgtcttctccagccttccattgagctgaaatgaatctatttattgccatcttatccagaggtttctctcatcattattttttttggggttgtagTTTATTCGTGAGTACACTGGCAAAGTCGATGAACTAGTGAAGGACAAAATTGAAGCACAAAATGAAGTGAAGGCTAAAGAGCAAGAAGAAAAGGATGTAG
       || |  |    || | |||     ||  |     ||||| |||       ||   | || ||||  | |  |  |   ||  |     || |||| ||||| ||||||||  |||| || ||||| |||||||||||||  |||||| |||| |||||||| | |||||||||| | |||||||| ||| | |
-------gtatcttgtttccgttcatgtgtttggga-----ctattcatt-------tacgtacagttttccataacaacaaagcttgcttcatgtgcagTTCATTCGGGAGTACACAAGCAAGGTTGATGAGCTAGTGAAGGACAGGATTGAATCACAGAATGAAGTAAGGGCTAAAGAGAAGGAAGAAAAAGATCTTG

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 28
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 28
agttattgtcttctccagccttccattgagctgaaatgaat------ctatttattgccatcttatccagaggtttctctcatcattattttttttggggttgtagTTTATTCGTGAGTACACTGGCAAAGTCGATGAACTAGTGAAGGACAAAATTGAAGCACAAAATGAAGTGAAGGCTAAAGAGCAAGAAGAAAAGGATGTAG
  || ||  | |     |       | |||||  | | | |      | |||  |    || ||||   | |||  || || | ||  ||   |||    ||  ||||||| || |||||| | |||||||| |||||||| || ||||||||  | ||||| |  |||||||| |||||||||||| | ||||| ||||||||| 
--ttgttagcctgcatcgtagcgagtggagcttgattaattaatgaaccattcttcttgattttattttgtggtcactttc-taatctttcccttt---ctttcagTTTATCCGCGAGTACGCAGGCAAAGTTGATGAACTTGTTAAGGACAAGCTGGAAGCTCTTAATGAAGTTAAGGCTAAAGAGAAGGAAGAGAAGGATGTAA

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|7588895|gb|AW704681.1|AW704681
EST:     TAGCTTGGATGCACAATATGATTGACTTTGCCTTCCCATATCTATTGCAG                         TTTATTCGTGAGTACACTGGCAAAGTCGATGAACTAGTGAAGGACAAAATT
genomic: TAGCTTGGATGCACAATATGATTGACTTTGCCTTCCCATATCTATTGCAGgtttgcattt ... ggggttgtagTTTATTCGTGAGTACACTGGCAAAGTCGATGAACTAGTGAAGGACAAAATT
EST: gi|151406151|gb|EV275966.1|EV275966
EST:     TAGCTTGGATGCACAATATGATTGACTTTGCCTTCCCATATCTATTGCAG                         TTTATTCGTGAGTACACTGGCAAAGTCGATGAACTAGTGAAGGACAAAATT
genomic: TAGCTTGGATGCACAATATGATTGACTTTGCCTTCCCATATCTATTGCAGgtttgcattt ... ggggttgtagTTTATTCGTGAGTACACTGGCAAAGTCGATGAACTAGTGAAGGACAAAATT
EST: gi|254320762|gb|GR827211.1|GR827211
EST:     CACAATATGATTGACTTTGCCTTCCCATATCTATTGCAG                         TTTATTCGTGAGTACACTGGCAAAGTCGATGAACTAGTGAAGGACAAAATT
genomic: CACAATATGATTGACTTTGCCTTCCCATATCTATTGCAGgtttgcattt ... ggggttgtagTTTATTCGTGAGTACACTGGCAAAGTCGATGAACTAGTGAAGGACAAAATT
EST: gi|6719249|gb|AW306896.1|AW306896
EST:     TGCCTTCCCATATCTATTGCAG                         TTTATTCGTGAGTACACTGGCAAAGTCGATGAACTAGTGAAGGACAAAATT
genomic: TGCCTTCCCATATCTATTGCAGgtttgcattt ... ggggttgtagTTTATTCGTGAGTACACTGGCAAAGTCGATGAACTAGTGAAGGACAAAATT
EST: gi|7924533|gb|AW830559.1|AW830559
EST:     TAGCTTGGATGCACAATATGATTGACTTTGCCTTCCCATATCTATTGCAG                         TTTATTCGTGAGTACACTGGCAAAGTCGATGAACTAGTGAAGGACAAAATT
genomic: TAGCTTGGATGCACAATATGATTGACTTTGCCTTCCCATATCTATTGCAGgtttgcattt ... ggggttgtagTTTATTCGTGAGTACACTGGCAAAGTCGATGAACTAGTGAAGGACAAAATT
EST: gi|26047482|gb|CA784260.1|CA784260
EST:     TAGCTTGGATGCACAATATGATTGACTTTGCCTTCCCATATCTATTGCAG                         TTTATTCGTGAGTACACTGGCAAAGTCGATGAACTAGTGAAGGACAAAATT
genomic: TAGCTTGGATGCACAATATGATTGACTTTGCCTTCCCATATCTATTGCAGgtttgcattt ... ggggttgtagTTTATTCGTGAGTACACTGGCAAAGTCGATGAACTAGTGAAGGACAAAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattgccatcttatccagaggtttctctcatcattattttttttggggttgtagTTTATTCGTGAGTACACTGGCAAAGTCGATGAACTAGTGAAGGACAAAATTGAAGCACAAAATGAAGTGAAGGCTAAAGAGCAAGAAGAAAAGGATGTAG
                                     ttttttttg  CT-rich tract
                            tcatcattattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agttattgtcttctccagccttccattgagctgaaatgaatctatttattgccatcttatccagaggtttctctcatcattattttttttggggttgtagTTTATTCGTGAGTACACTGGCAAAGTCGATGAACTAGTGAAGGACAAAATTGAAGCACAAAATGAAGTGAAGGCTAAAGAGCAAGAAGAAAAGGATGTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - -cttctcc
- - - - - - - - - ccttcca
- - - - - - - - - - - - - - agctgaa
- - - - - - - - - - - - - - - - - - - - - - - - -tgccatc