Skip to another splice site:
1  
 5'  3'   
2  
 5'  3'   
3  
 5'  3'   
4  
 5'  3'   
5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgaggtctgtttcatttgcatcttataacttgatatataaaaggtcctgatacctgataatatgacctgtataacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTTGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT

Basic information

species Glycine max
transcript GLYMA16G05460.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G05460.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g52860.1 (Oryza sativa), 3'ss of exon 3
gtttgaggtctgtttcatttgcatcttataacttgatatata-aaaggtcctgatacctgataatatgacctgtataac-ataaaaatgttctttcttg--cagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTTGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT
|| | | || | | || | || || | || | | || | | | || | || | | | || || ||| || || |||| || |||||||||||||| || ||||||||||||||||| ||||||| |||||||| | || || ||| |||||||| ||| | ||| |
---tggcatg-gcaccaatgagtttttgtttgtttatttttatgagagctatgctgtcatgttatttcttctatgcatccattgaatatttccatcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACAAGCACGCTGTTCCTGTTCCGAAGTCTGAGTGCAGCAAGTCTTTCCAATT

upper sequence: GLYMA16G05460.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os06g10810.1 (Oryza sativa), 3'ss of exon 3
---gtttgaggtctg-tttcatttgcatcttataacttgatatataaaaggtcctgatacctgataatatgacctgtataacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTTGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT
| ||| | || | |||| | | ||| | ||| | | ||||| | || | ||| ||| |||| | | |||| ||||||||||||||||| || ||||||||||||||||| | ||||| ||||| || | || || ||| ||||| | |||| | || |
tctggttgttttttggtatcataagaaatatatcttgccaaataccttctctatttctacctttagacattattattatttt-taataatgatatact---cagATACAATGATGAAGTTTGCATCCTTTGAGACCATTGTTGAACAAATCTACAAGCATGCTGTTCCTGTCCCGAAGTCAGAGTGTAGCAAATCATTCCAGTT

upper sequence: GLYMA16G05460.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G152827_T01 (Zea mays), 3'ss of exon 3
-gtttgaggtctgtttcatttgcatcttataacttgatatataaaaggtcctgatacctgataatatgacct-gtataacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTTGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT
|||| ||| | || | | |||| || | || | | | | |||| ||| || | | | | | | | ||||| || ||||||||||||||||| ||||||||||| |||||||| ||||| ||||| || | || || ||| |||||||| ||| || |
aatttggtagttgtattatatat-ttttatctattctcgttcaagccatattctcatattataagctgaactcacccatcgcccttgtatgatgtat-gcagATACCATGATGAAGTTTGCTTCCTTTGAGACCATCGTTGAGCTTATCTACAAGCATGCTGTGCCTGTTCCGAAGTCTGAGTGCAGCAAGACTACCCAGTT

upper sequence: GLYMA16G05460.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G015401_T01 (Zea mays), 3'ss of exon 3
-gtttgaggtctgtttcatttgcatcttataacttgatatataaaaggtcctgatacctgataatatg-acctgtataacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTTGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT
|||| ||| | || | | |||| || | | || | | | | |||| || || | | | | | | | ||||| || ||||||||||||||||| ||||||||||| |||||||| ||||| ||||| || | || || ||| |||||||| ||| || |
catttggtagttgtattatatat-ttttatctattcttgttcaagccatattctcatattataagctgtactcacccatcgcccttgtatgatgtat-gcagATACCATGATGAAGTTTGCTTCCTTTGAGACCATCGTTGAGCTTATCTACAAGCATGCTGTGCCTGTTCCGAAGTCTGAGTGCAGCAAGACTACCCAGTT

upper sequence: GLYMA16G05460.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G060630_T01 (Zea mays), 3'ss of exon 3
--gtttgaggtctgtttcatttgcatcttataacttgatatataaaaggtcctgatacctgataatatg-acctgtataacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTTGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT
|||| | ||| | || | | |||| || || || | | || | |||| || || | | | | | | | ||||| || ||||||||||||||||| ||||||||||| |||||||| || || |||||||| | || || ||| |||||||| ||| || |
taatttggtatttgtattatat--aatttatttattatcatgcaagccatattcttatgttataagctgtactcacctgttgcactcgtatgatgtat-gcagATACCATGATGAAGTTTGCTTCCTTTGAGACCATCGTTGAGCTTATATACAAGCACGCTGTGCCTGTTCCGAAGTCTGAGTGCAGCAAGACTACCCAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtcctgatacctgataatatgacctgtataacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTTGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT
                          gtataac  putative branch site (score: 3)
 tgttctttctt  putative PPT
 tataacataaaaatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgaggtctgtttcatttgcatcttataacttgatatataaaaggtcctgatacctgataatatgacctgtataacataaaaatgttctttcttgcagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTTGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - -gtctgtt
- - - - - - - -catttgc
- - - - - - - - - - - - - - - - - - - - - - - - - tgatacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaaaa