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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATTGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAATCTGGAACTTCTggtatgtatgttgtggcacattgctgaagtagtttttgcttgtaatgtggttgggaagatgttaattggagctgtgttaattca

Basic information

species Glycine max
transcript GLYMA17G37820.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G37820.1 (Glycine max), 5'ss of exon 5
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 5'ss of exon 5
CAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATTGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAATCTGGAACTTCTggtatgtatgttgtg-gcacattgctgaagtagtttttgcttgtaatgtggttgggaa---gatgttaattggagctgtgttaattca-------------------------------------------------------------
||||| ||||| |||||||| ||||| || || |||||||||||||| ||||| ||| | || ||||| | ||||| || || |||||||||||||| ||||| | | || | ||| || |||| | | | | | | | | | | ||| | | ||| || |
-AAGGAGAAGAAGATTCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAAGATCTCATTAAGAACCTTGGGACCATTGCCAAATCTGGAACTTCAGgtattactcctttgtactgatttctcttaaagttat-gtgtattctcttgctaaaactttagtattatctatttgtttgtaaagagaattttaccaagtgccatttaacttaaacttgagtgataccaattccttgaaatttttgcag

upper sequence: GLYMA17G37820.1 (Glycine max), 5'ss of exon 5
lower sequence: GRMZM2G399073_T03 (Zea mays), 5'ss of exon 5
CAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATTGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAATCTGGAACTTCTggtat-gtatgtt-----gt--ggcacattgctgaagt--agtttttgcttgtaatgtggttgggaagatgttaattggagctg-tgttaattca---------------------------------------------
|| || |||||||| ||||| ||||| || || |||||||||||||| ||||||||| | || || || | || || || || || ||||| ||||| ||||| || | || || ||| ||| || | | | | |||| || ||| | ||| || || || | |||| ||||
-AAAGAGAAGAAAATCCTCTCCATTCGGGATAGGGGTATTGGTATGACCAAGGAGGATCTTATTAATAACCTTGGAACCATTGCTAAGTCTGGCACTTCAGgtattgttttttcatctgtcaggctgatttgtgcaatccaatatttgtttaatatgataatctgaatat-ttgtttaatattactgttctttcatcttatgctttcaaataatttgaattgtttgcaatttttttgcag

upper sequence: GLYMA17G37820.1 (Glycine max), 5'ss of exon 5
lower sequence: AT4G24190.2 (Arabidopsis thaliana), 5'ss of exon 5
CAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATTGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAATCTGGAACTTCTggtatgtatgttgtggcacattgctgaagtagtttttgcttgtaatgtggttgggaagatgtta-attggagctgtgttaattca-----
|| | ||||| ||||| || ||||||||| | || ||||||||||| ||||| || || || ||||| | || || ||||||||||||||||| || |||| || || || | | || || | | || | ||| | | || | ||| | || |
-AAAGCCAAGAAGATTCTTTCTATTCGAGACCGGGGAATTGGTATGACTAAGGAAGACTTAATCAAGAACCTTGGTACCATAGCAAAATCTGGAACGTCAGgtacgttacttatgtggtgatac----gttgtcctgcataatagtatggatcaataaattccatatttctaagatcttgcctttcgcag

upper sequence: GLYMA17G37820.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 5'ss of exon 5
CAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATTGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAATCTGGAACTTCTggtatgtatgttgtggcacattgctgaagtagtttttgcttgtaatgtg--gttgggaagatgttaattggagctgtgttaattca-----------------
|||||||||||||| || |||||||| || |||||||| |||||||| ||||| ||||| || ||||| || || ||||| |||||||||||||| || ||||| | | || || | | | | ||| | || | | || ||| || | | | | | |||||| |
-AAGGAAAAGAAAATCCTGTCAATTCGTGATAGAGGTATAGGTATGACAAAGGATGATTTAATCAAGAACTTAGGAACAATCGCAAAATCTGGAACGTCAGgtatctttattttgcaatgtctaatatcttgttctgaaatgaattctgaagtttggggtttaatgaattattgaatattaatttatattttcttttatatag

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|208261680|gb|GE060035.1|GE060035
EST:     AGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAATCTGGAACTTCT                         GCATTTGTTGAGAAGATGCAAACAAGTGGAGATCTCAATCTG
genomic: AGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAATCTGGAACTTCTggtatgtatg ... tgttaattcaGCATTTGTTGAGAAGATGCAAACAAGTGGAGATCTCAATCTG
EST: gi|298170585|gb|HO019209.1|HO019209
EST:     AGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAATCTGGAACTTCT                         GCATTTGTTGAGAAGATGCAAACAAGTGGAGATCTCAATCCGATTGGGCAG
genomic: AGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAATCTGGAACTTCTggtatgtatg ... tgttaattcaGCATTTGTTGAGAAGATGCAAACAAGTGGAGATCTCAATCTGATTGGGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGGAAAAGAAAATTCTCTCAATTCGAGACAGAGGTATTGGTATGACGAAGGAGGATTTGATAAAGAATTTGGGGACAATAGCAAAATCTGGAACTTCTggtatgtatgttgtggcacattgctgaagtagtttttgcttgtaatgtggttgggaagatgttaattggagctgtgttaattca

- - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA