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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatattttttgcttcacattttaataaataatataatatggtaaacatcgctatatttttattaaaacagacatacacagatacactgccatttatgcttatgcaacagtttttactttgcagAACGACATAACATGGCATGAAGACAATTGGGACAATCATGACAGCAAATTTCTTGCATTCAC

Basic information

species Glycine max
transcript GLYMA06G10540.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G10540.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv18s0001g06520.t01 (Vitis vinifera), 3'ss of exon 21
gtaatattttttgcttcacattttaataaataatataatatggtaaacatcgctatatttttattaaaacagacatacacagatacactgccatttatgcttatgcaacagtttttactttgcagAACGACATAACATGGCATGAAGACAATTGGGACAATCATGACAGCAAATTTCTTGCATTCAC
        ||||| || |  | |  ||  ||| | || | |  |  |  | ||    | | |||     ||   || ||  | | | || |  || |||||| || |      ||||   ||||||| ||  | ||||||||||| ||||| ||||||||| |||| |||||||| |||||||||||
------ccttttggttaat-tatagatccatattttatttttatgcatgttgcc---tgtctat-----catctat-cattgtttctctacttttaatgcttgtgaa------ttta---tgcagAAAGATGTGACATGGCATGAGGACAACTGGGACAATTATGAGAGCAAATTCCTTGCATTCAC
















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|208120541|gb|GD917984.1|GD917984
EST:     AGTACAGGCATGCACATGAAGTATTCAATCATGAAAGTTTTCTCAGCAAG                         AACGACATAACATGGCATGAAGACAATTGGGACAATCATGACAACAAATTT
genomic: AGTACAGGCATGCACATGAAGTATTCAATCATGAAAGTTTTCTCAGCAAGgtaatatttt ... tactttgcagAACGACATAACATGGCATGAAGACAATTGGGACAATCATGACAGCAAATTT
EST: gi|208148902|gb|GD949356.1|GD949356
EST:     AGTACAGGCATGCACATGAAGTATTCAATCATGAAAGTTTTCTCAGCAAG                         AACGACATAACATGGCATGAAGACAATTGGGACAATCATGACAACAAATTT
genomic: AGTACAGGCATGCACATGAAGTATTCAATCATGAAAGTTTTCTCAGCAAGgtaatatttt ... tactttgcagAACGACATAACATGGCATGAAGACAATTGGGACAATCATGACAGCAAATTT
EST: gi|208298702|gb|GE095051.1|GE095051
EST:     AGTACAGGCATGCACATGAAGTATTCAATCATGAAAGTTTTCTCAGCAAG                         AACGACATAACATGGCATGAAGACAATTGGGACAATCATGACAACAAATTT
genomic: AGTACAGGCATGCACATGAAGTATTCAATCATGAAAGTTTTCTCAGCAAGgtaatatttt ... tactttgcagAACGACATAACATGGCATGAAGACAATTGGGACAATCATGACAGCAAATTT
EST: gi|193509752|gb|FK470758.1|FK470758
EST:     AGTACAGGCATGCACATGAAGTATTCAATCATGAAAGTTTTCTCAGCAAG                         AACGACATAACATGGCATGAAGACAATTGGGACAATCATGACAGCAAATTT
genomic: AGTACAGGCATGCACATGAAGTATTCAATCATGAAAGTTTTCTCAGCAAGgtaatatttt ... tactttgcagAACGACATAACATGGCATGAAGACAATTGGGACAATCATGACAGCAAATTT
EST: gi|208061591|gb|GD857163.1|GD857163
EST:     AGTACAGGCATGCACATGAAGTATTCAATCATGAAAGTTTTCTCAGCAAG                         AACGACATAACATGGCATGAAGACAATTGGGACAATCATGACAGCAAATTT
genomic: AGTACAGGCATGCACATGAAGTATTCAATCATGAAAGTTTTCTCAGCAAGgtaatatttt ... tactttgcagAACGACATAACATGGCATGAAGACAATTGGGACAATCATGACAGCAAATTT
EST: gi|208208486|gb|GE008477.1|GE008477
EST:     CATGCACATGAAGTATTCAATCATGAAAGTTTTCTCAGCAAG                         AACGACATAACATGGCATGAAGACAATTGGGACAATCATGACAGCAAATTT
genomic: CATGCACATGAAGTATTCAATCATGAAAGTTTTCTCAGCAAGgtaatatttt ... tactttgcagAACGACATAACATGGCATGAAGACAATTGGGACAATCATGACAGCAAATTT
EST: gi|193728840|gb|FK663786.1|FK663786
EST:     AGTACAGGCATGCACATGAAGTATTCAATCATGAAAGTTTTCTCAGCAAG                         AACGACATAACATGGCATGAAGACAATTGGGACAATCATGACAGCAAATTT
genomic: AGTACAGGCATGCACATGAAGTATTCAATCATGAAAGTTTTCTCAGCAAGgtaatatttt ... tactttgcagAACGACATAACATGGCATGAAGACAATTGGGACAATCATGACAGCAAATTT
EST: gi|193732865|gb|FK668194.1|FK668194
EST:     AGTACAGGCATGCACATGAAGTATTCAATCATGAAAGTTTTCTCAGCAAG                         AACGACATAACATGGCATGAAGACAATTGGGACAATCATGACAGCAAATTT
genomic: AGTACAGGCATGCACATGAAGTATTCAATCATGAAAGTTTTCTCAGCAAGgtaatatttt ... tactttgcagAACGACATAACATGGCATGAAGACAATTGGGACAATCATGACAGCAAATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agacatacacagatacactgccatttatgcttatgcaacagtttttactttgcagAACGACATAACATGGCATGAAGACAATTGGGACAATCATGACAGCAAATTTCTTGCATTCAC
                                         tttttacttt  CT-rich tract
                                         tttttacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatattttttgcttcacattttaataaataatataatatggtaaacatcgctatatttttattaaaacagacatacacagatacactgccatttatgcttatgcaacagtttttactttgcagAACGACATAACATGGCATGAAGACAATTGGGACAATCATGACAGCAAATTTCTTGCATTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA