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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtcttttatagcttgcactcttgccattttgcttttaaaaaataaaaactatcaccgaggaaatttaccctttgtgtagtcctttcaaagaaagtcttagagtttgataccatgcaaaaattatgaattggtattaattttctgtctttcctatttttcattttattttacagGACGACTTTGAAGAATTTAGTGATGTTGATGAGTTATATAGTTCATTACCCTTAGACAAGGTGGAGTCACTTGAAGATATTGTTACAATTCCCCCTGGTC

Basic information

species Glycine max
transcript GLYMA16G26850.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G26850.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0007g07570.t01 (Vitis vinifera), 3'ss of exon 6
gtttgtcttttatagcttgcactcttgccattttgcttttaaaaaataaaaactatcaccgaggaaatttaccctttgtgtagtcctttcaaagaaagtcttagagtttgataccatgcaaaaattatgaattggtattaattttctgtctttcctatttttcattttattttacagGACGACTTTGAAGAATTTAGTGATGTTGATGAGTTATATAGTTCATTACCCTTAGACAAGGTGGAGTCACTTGAAGATATTGTTACAATT--CCCCCTGGTC
                                                                           | |  |  | |    ||  | | |   ||||||   |   |||      || || ||  |   ||| | | | | || |||     | | || ||||| ||||| ||||||||||||||||||||||| |||||  | || |  || || || |||||||||||||| |||||||||||| | |||||||||    | |  |  
-----------------------------------------------------------------------ataatggcttgctaccaataagaataatgagagagttgctttagatgtttgc-ttctgcatgagacataaatatttttgttgcct-----tgaattaatttttcagGAGGACTTTGAAGAATTTAGTGATGTAGATGACCTTTACAACTCTTTGCCATTAGACAAGGTGGAATCACTTGAAGATCTGGTTACAATTGGTGCTCCAG--
















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|193676081|gb|FK620067.1|FK620067
EST:     TGGATGACTATGTAGACCGTAATCAG                         GACGACTTTGAAGAATTTAGTGATGTTGATGAGTTATATAGTTCATTACCC
genomic: TGGATGACTATGTAGACCGTAATCAGgtttgtcttt ... tattttacagGACGACTTTGAAGAATTTAGTGATGTTGATGAGTTATATAGTTCATTACCC
EST: gi|193664139|gb|FK608747.1|FK608747
EST:     AGGTTAATGATGTCAAAGATTTCCTGGATGACTATGTAGACCGTAATCAG                         GAACGAACTTTGAAGAATTTAGTGATGTTGATG
genomic: AGGTTAATGATGTCAAAGATTTCCTGGATGACTATGTAGACCGTAATCAGgtttgtcttt ... tattttacagGA-CGA-CTTTGAAGAATTTAGTGATGTTGATG
EST: gi|193574663|gb|FK527492.1|FK527492
EST:     TGGATGACTATGTAGACCGTAATCAG                         GACGACTTTGAAGAATTTAGTGATGTTGATGAGTTATATAGTTCATTACCC
genomic: TGGATGACTATGTAGACCGTAATCAGgtttgtcttt ... tattttacagGACGACTTTGAAGAATTTAGTGATGTTGATGAGTTATATAGTTCATTACCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattatgaattggtattaattttctgtctttcctatttttcattttattttacagGACGACTTTGAAGAATTTAGTGATGTTGATGAGTTATATAGTTCATTACCCTTAGACAAGGTGGAGTCACTTGAAGATATTGTTACAATTCCCCCTGGTC
             tattaat  putative branch site (score: 2)
                   ttttctgtctttccta  CT-rich tract
                            tttcctatttttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtcttttatagcttgcactcttgccattttgcttttaaaaaataaaaactatcaccgaggaaatttaccctttgtgtagtcctttcaaagaaagtcttagagtttgataccatgcaaaaattatgaattggtattaattttctgtctttcctatttttcattttattttacagGACGACTTTGAAGAATTTAGTGATGTTGATGAGTTATATAGTTCATTACCCTTAGACAAGGTGGAGTCACTTGAAGATATTGTTACAATTCCCCCTGGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA