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

gtaattctttcatttggaaaaaaaacttgtttttctgttggtaattgacctcattttattgagatattgtccgatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT

Basic information

species Glycine max
transcript GLYMA14G06340.1
intron # 20
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 20
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 18
gtaatt-ctttcatttggaaaaaaaacttgtttttctgttggtaattgacctcattttattgagatattgtccgatgta-tttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
||| || || | | | | | || ||||| ||| |||| | | ||| | ||| | | | | |||| | | ||| ||| | | ||||||||||| || || || || || ||||| || ||||| |||| ||||| || ||||| || ||||||||||| || ||||| || ||||||||||||
gtagttactcttactcctgatg----ttggtatttcttaaggtggcataccttaat--attaa---atttctcaacatggcatgcattgatattaaattttctttatattc----atagTGAGGATCCAGATATCCATTTCAAATACATAGAAGCAGCTGCAAGAACTGGACAGATCAAAGAAGTTGAGCGTGTAACCAGAGAGTCTAATTTCTATGAT

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 20
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 20
gtaattctttcatttggaaaaaaaacttgtttttctgttggtaattgacctcattttattgagatattgtccgatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
| || | || |||| || | | | | |||| | | | || | |||| || | || || | | ||||| |||| | || | |||||||||||||| || || || ||||||||||| ||||| || |||||||||||||| ||||||||||||||||| || ||||| || || |||||||||
--------gtgatatagataaaa--tctgatctcgtttctgtaaacaagcacgattctt----gtattt----atatgcttatgtttaca-atgtttctctc-----tgtgcgatagTGAGGATCCTGAGATCCATTTCAAGTACATTGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTAACTAGAGAGTCTAACTTCTATGAT

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 20
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 20
gtaattctttcatttggaaaaaaaacttgtttttctgttggtaattgacctcattttattgagatattgtccgatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
|||||| | ||| | | | || | | | |||| | | | | | | | | | ||| || | |||| | | ||||| | ||| ||||||||||||| |||||||| |||||||| || ||||| || |||||||||||||| |||||||||||||||||||| ||||| || || || ||||||
gtaattttatca---------agatcctgctgtcattcctgtaaacaagcaccatgcagcaatttgtatttttatgacttac----aatgtct-tccctctgtgtgata-------gTGAGGATCCTGAGATTCACTTCAAGTACATCGAAGCAGCTGCCAAGACTGGTCAAATAAAGGAGGTTGAGCGTGTGACTAGAGAGTCTAACTTTTATGAT

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 20
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 20
gtaattctttcatttggaaaaaaaacttgtttttctgttggtaattgacctc-attttattgagatattgtccgatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
|||||| || | | | || ||||| ||||| | ||| || || | ||||| | ||| || || ||||| || |||| |||||||||||||||||||||||||||||| ||||| ||||| || || || || ||||| ||||| |||||||||||||||||||| |||||||||| |||||||||
gtaatttgtttagt--aaggaagaactttgctttctttaggtgcggtacatccaacttattttgtgattttcatatcgttttcttttg------gttc-----------atggaacagTGAGGATCCTGACATTCACTTCAAGTATATTGAAGCTGCTGCTAAAACTGGACAAATTAAGGAGGTTGAGCGTGTGACTCGAGAATCAAACTTCTATGAT

upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 20
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 20
------------------------------gtaattctttcatttggaaaaaaaacttgtttttctgt---tggtaattgacctcattttattgagatattgtccgatgtatttctgctgatgtatgttcctctaaataa----------tatggaacagTGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
| || ||| | || || |||| | || ||||| | || | |||| | | ||| | || ||| ||| | ||| | | ||| | || ||| ||||| ||||| || |||| |||||||||||||| |||||||||||||| ||||||||||| || || ||||| |||||||| || || |||||| |
gtgggaatttatgtcttttctttctttctgtttttttttttaattttaattttggcttggaatctggtatacggtaagcagattgatatgggtgagtttgggatgcatgaagttatgc--atgcacaatccgcctagtaaactatatctttttgtgtcagCGAGGACCCTGAGATCCACTACAAGTACATTGAGGCTGCAGCAAAGACTGGCCAAATCAAGGAAGTGGAACGTGTCACAAGAGAGTCCAACTTCTATCCT

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|208315625|gb|GE117789.1|GE117789
EST:     AGGTCATATGAGGGACTGTAC-TTTTCCTTGGATCATACTTGAGCTCCAG                         TGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGG
genomic: AGGTCATATGAGGGACTGTACTTTTTCCTTGGATCATACTTGAGCTCCAGgtaattcttt ... tatggaacagTGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatattgtccgatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT
                                   ctctaaa  putative branch site (score: 3)
 taaataatatggaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattctttcatttggaaaaaaaacttgtttttctgttggtaattgacctcattttattgagatattgtccgatgtatttctgctgatgtatgttcctctaaataatatggaacagTGAGGATCCTGACATTCACTTTAAGTACATTGAGGCAGCAGCAAAGACTGGTCAAATCAAGGAGGTTGAGCGTGTGACAAGAGAATCAAATTTCTATGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA