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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggcaaataggagcagtcaagtcattaagaatgctttttatatgatacctctcttttatgtttgggctatggcttttaactgattttttttttatgctagATTGGGGATGAGACGTTTATAATAGCAGCTCTCATGGCTATGCGTCACCCTAAGTCAATTGTCTTGTCTGGTGCGCTCAGTGCTCTGATTATAATGACA

Basic information

species Glycine max
transcript GLYMA09G38640.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G38640.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G151863_T01 (Zea mays), 3'ss of exon 3
--------------tggcaaataggagcagtcaagtcattaagaatgctttt---tatatgatacctctcttttatgtttgggctatgg---------------------cttttaactg----attttttttttatgct-----agATTGGGGATGAGACGTTTATAATAGCAGCTCTCATGGCTATGCGTCACCCTAAGTCAATTGTCTTGTCTGGTGCGCTCAGTGCTCTGATTATAATGACA
              ||  |  |||||| | |  |||     | |  || | |   ||  || |  |   ||    ||  | |||| ||                      |||  | |||    ||||||||| | ||||     ||||||| |||||||| || || || || || || ||||| ||||| ||||| ||||||||||| ||||||||||| ||   ||| ||   | | ||||||
gtactgattagtgatgtgagctaggaggatttgagtttcggaaatggcctctgtgtacctgctgtcctactgcattgccttggctgtgagatttggatgtgtggctgtttcttcgagctgttcaattttttttctttgctgatgtagATTGGAGATGAGACATTCATCATTGCTGCGCTGATGGCGATGCGGCACCCCAAGTCAATTGTGTTGTCTGGTGCACTATCTGCGCTTTATGTGATGACA

upper sequence: GLYMA09G38640.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G36290.1 (Arabidopsis thaliana), 3'ss of exon 4
tggcaaataggagcagtcaagtcattaagaatgctttttatatgatacctctcttttatgtttg-ggctatggcttt-taactgattttttttttatgctagATTGGGGATGAGACGTTTATAATAGCAGCTCTCATGGCTATGCGTCACCCTAAGTCAATTGTCTTGTCTGGTGCGCTCAGTGCTCTGATTATAATGACA
                ||  ||   |    ||| ||      |     |  | |||  | || | || ||  ||||  |   || ||  | || |||| |||||||||||||| || ||||||||||| ||  | ||||||||||| || |||||  | | ||| || |||||||| |||   ||| || || | ||||| 
--------------gttcgtgtgtgttgatatgattcaagcttagggtcaatttttagttttagtggttagagcttaatctttgtttcgtattatatgttagATTGGGGATGAAACTTTTATAATAGCGGCATTGATGGCTATGCGACATCCTAAAGCTACTGTTTTATCTGGTGCACTCTCAGCTTTGTTTGTTATGACT

upper sequence: GLYMA09G38640.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0023g00380.t01 (Vitis vinifera), 3'ss of exon 3
tggcaaataggagcagtcaagtcattaagaatgctttttatatgatacctctcttttatgtttgggct--atggct-tttaactgattttttttttatgctagATTGGGGATGAGACGTTTATAATAGCAGCTCTCATGGCTATGCGTCACCCTAAGTCAATTGTCTTGTCTGGTGCGCTCAGTGCTCTGATTATAATGACA
|    |    ||||  ||||    |||     |   | ||| |    |   | | |||| ||||      |||  | ||| | ||||  |  | ||||  |||||||| ||||| || ||||||||||||||||| ||||| ||| | |||||||| |||||||| || |||||||||||||||||| ||||| ||||||| 
ttattatagtgagcc-tcaaactgttactgtggtactgtatgtttaccagttttgttatatttgcatctgatgaatgttttattgataatggtgttat--tagATTGGAGATGAAACATTTATAATAGCAGCTCTTATGGCAATGAGACACCCTAAATCAATTGTTTTATCTGGTGCGCTCAGTGCTTTGATTGTAATGACG

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|18735262|gb|BM528663.1|BM528663
EST:     GATCCTTGTCAGTGAG                         ATTGGGGATGAGACGTTTATAATAGCAGCTCTCATGGCTATGCGTCACCCT
genomic: GATCCTTGTCAGTGAGgttagcttaa ... tttatgctagATTGGGGATGAGACGTTTATAATAGCAGCTCTCATGGCTATGCGTCACCCT
EST: gi|208096471|gb|GD892164.1|GD892164
EST:     GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAG                         ATTGGGGATGAGACGTTTA
genomic: GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAGgttagcttaa ... tttatgctagATTGGGGATGAGACGTTTA
EST: gi|192297697|gb|FG992775.1|FG992775
EST:     GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAG                         ATTGGGGATGAGACGTTTATAATAGCAGCTCTCATGGCTATGCGTCACCCT
genomic: GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAGgttagcttaa ... tttatgctagATTGGGGATGAGACGTTTATAATAGCAGCTCTCATGGCTATGCGTCACCCT
EST: gi|26045883|gb|CA783315.1|CA783315
EST:     GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAG                         ATTGGGGATGAGACGTTTATAATAGCAGCTCTCATGGCTATGCGTCACCCT
genomic: GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAGgttagcttaa ... tttatgctagATTGGGGATGAGACGTTTATAATAGCAGCTCTCATGGCTATGCGTCACCCT
EST: gi|21889576|gb|BQ742789.1|BQ742789
EST:     GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAG                         ATTGGGGATGAGACGTTTATAATAGCAGCTCTCATGGCTATGCGTCACCCT
genomic: GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAGgttagcttaa ... tttatgctagATTGGGGATGAGACGTTTATAATAGCAGCTCTCATGGCTATGCGTCACCCT
EST: gi|151405478|gb|EV275292.1|EV275292
EST:     GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAG                         ATTGGGGATGAGACGTTTATAATAGCAGCTCTCATGGCTATGCGTCACCCT
genomic: GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAGgttagcttaa ... tttatgctagATTGGGGATGAGACGTTTATAATAGCAGCTCTCATGGCTATGCGTCACCCT
EST: gi|26269289|gb|CA820352.1|CA820352
EST:     GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAG                         ATTGGGGATGAGACGTTTATAATAGCAG
genomic: GACTCTTCGACGCATTTTTCGCGAGTTTTTCGATGATCCTTGTCAGTGAGgttagcttaa ... tttatgctagATTGGGGATGAGACGTTTATAATAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacctctcttttatgtttgggctatggcttttaactgattttttttttatgctagATTGGGGATGAGACGTTTATAATAGCAGCTCTCATGGCTATGCGTCACCCTAAGTCAATTGTCTTGTCTGGTGCGCTCAGTGCTCTGATTATAATGACA
                                      ttttttttttatgct  CT-rich tract
                            ttttaactgatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggcaaataggagcagtcaagtcattaagaatgctttttatatgatacctctcttttatgtttgggctatggcttttaactgattttttttttatgctagATTGGGGATGAGACGTTTATAATAGCAGCTCTCATGGCTATGCGTCACCCTAAGTCAATTGTCTTGTCTGGTGCGCTCAGTGCTCTGATTATAATGACA

- - - - - - gcagtca
- - - - - - - - - - - - - - gaatgct