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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatataatttttttcttgttagtactgcagttttctatattcagtgtcattgaaagaattgcccaacacttcttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTGCTTGGTGGTACCCTTGTTCCATACTACCTTGAAGAGACAGCAAATTGGG

Basic information

species Glycine max
transcript GLYMA01G03260.3
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G03260.3 (Glycine max), 3'ss of exon 6
lower sequence: AT1G70580.2 (Arabidopsis thaliana), 3'ss of exon 6
----------gtaatataatttt---tttcttgttagtactgcag-ttttctatattcagtgtcattgaaagaattg--cccaacacttctta-ttgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTGCTTGGTGGTACCCTTGTTCCATACTACCTTGAAGAGACAGCAAATTGGG
            | |  |  ||    |||||||    |  |  || |||| ||   |  || | || | |  |  ||  | |||   |||||  ||| |||||| |||||||||| ||||| || ||||||||||| || || ||  ||||| | |||||||| |||||||| ||||| ||||||||| | | ||| ||||
ttgatggctaagagttcagattcagatttcttgcagatggtataggttttttaggcttggt-ttatagtagcatctggtcacaagttttcttggttggcagATTCTGGTTCCAGTTCCACAGTATCCACTCTACTCGGCTACTATATCTCTGTTAGGTGGTACTCTTGTTCCTTACTATCTTGAAGAGTCTGAAAACTGGG
















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|19053398|gb|BM732065.1|BM732065
EST:     AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCGCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGGgtaatataat ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|120529201|gb|EH257335.1|EH257335
EST:     AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGGgtaatataat ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|14205452|gb|BG839130.1|BG839130
EST:     AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGGgtaatataat ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|15285990|gb|BI469890.1|BI469890
EST:     AGGGGGTGATGCAAATATTAAATACTATCATCAGAGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGGgtaatataat ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|20498717|gb|BQ273647.1|BQ273647
EST:     AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGGgtaatataat ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|20814673|gb|BQ299151.1|BQ299151
EST:     AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGGgtaatataat ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|21887563|gb|BQ740776.1|BQ740776
EST:     AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGGgtaatataat ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|23052838|gb|BU577329.1|BU577329
EST:     AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGGgtaatataat ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|13481869|gb|BG511212.1|BG511212
EST:     AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGGgtaatataat ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|23056339|gb|BU577717.1|BU577717
EST:     AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGGgtaatataat ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|23064381|gb|BU579154.1|BU579154
EST:     AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGGgtaatataat ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|13480374|gb|BG509717.1|BG509717
EST:     AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGGgtaatataat ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|120491572|gb|EH219739.1|EH219739
EST:     AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGGgtaatataat ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|20498442|gb|BQ273372.1|BQ273372
EST:     AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGGgtaatataat ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|14205590|gb|BG839268.1|BG839268
EST:     AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGGgtaatataat ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|15285988|gb|BI469879.1|BI469879
EST:     AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGGgtaatataat ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
EST: gi|193430928|gb|FK393720.1|FK393720
EST:     AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGG                         ATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG
genomic: AGGGGGTGATGCAGATATTAAATACTATCATCAGAGGTCAAGACGATGGGgtaatataat ... ttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagttttctatattcagtgtcattgaaagaattgcccaacacttcttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTGCTTGGTGGTACCCTTGTTCCATACTACCTTGAAGAGACAGCAAATTGGG
                                         cttcttatt  CT-rich tract
     ttctatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatataatttttttcttgttagtactgcagttttctatattcagtgtcattgaaagaattgcccaacacttcttattgccagATTTTGGTTCCAGTCCCACAATACCCACTCTACTCAGCAACAATTGCTCTGCTTGGTGGTACCCTTGTTCCATACTACCTTGAAGAGACAGCAAATTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA