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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcacctatgcaaattggtcatcttatacagaatagatttcaccttcttttttatgtgctaaaactgatccaaatggcattgcattgtctttttgaaacagCCCTTCAAGGACATGATCGAAGGGATGAGGGTGGACCTGAGAAAGTCAAGATACAATAACTTTGATGAGCTCTACCTTTACTGCTACTATGTTGCTGGGA

Basic information

species Glycine max
transcript GLYMA14G03500.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G03500.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os12g43130.1 (Oryza sativa), 3'ss of exon 3
-----------------gcacctatgcaaattggtcat------cttatacag---aatagatttcaccttcttttttatgtgc-taaaactgat--ccaaatggcattgcattgtctttttgaaacagCCCTTCAAGGACATGATCGAAGGGATGAGGGTGGACCTGAGAAAGTCAAGATACAATAACTTTGATGAGCTCTACCTTTACTGCTACTATGTTGCTGGGA
                 ||  || |  ||   ||  ||      ||| || |    | |||    ||     ||  | |   || |    |||||          | | |   | ||||||    |||||| ||||| |||||||| ||||| |||||| | |||||| | || ||||| || |  | |||||||||||||||||| ||||||||||| |||||||| |
gtacagccaacaaaaaagctactgtaaaagcaggatatgaagtgcttttaaaagttattagtacacagtaaattggtgacacgcatttgtctgatgtttctgcaccgtcgggatctcttttatttacagCCATTCAAAGACATGATTGAAGGAATGAGGCTTGACCTGTGGAAATCAAGGTATAGGAGCTTTGATGAGCTCTACCTCTACTGCTACTACGTTGCTGGCA

upper sequence: GLYMA14G03500.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G149317_T03 (Zea mays), 3'ss of exon 2
--------------------------------------gcacctatgcaaattggtc-atcttatacagaatagatttcacct-tcttttttatgtgctaaaa-ctgatccaaatggcattgcattgtct-----ttttgaaacagCCCTTCAAGGACATGATCGAAGGGATGAGGGTGGACCTGAGAAAGTCAAGATACAATAACTTTGATGAGCTCTACCTTTACTGCTACTATGTTGCTGGGA
                                       || |      ||    |  | |  |    |  | ||  |||||   |      | ||    | | |||   |   |  ||  |  || |||     ||||    ||||| ||||| |||||| || |||| |||||| |||||||| | ||||| || ||||  | ||| || ||||||||||| ||||||||||| || || || |
gtaaacccgtccgtccgtccatccatctatccatccatccagcagcaggaacaaatttaccacaagacgtctggaaatcaccggccacaaagacgtctggagatctgcatctgctaacaacgttttctctccctttttttccccagCCGTTCAAAGACATGGTCCAAGGAATGAGGCTGGACCTGTGGAAGTCGAGGTACATGACCTTCGACGAGCTCTACCTCTACTGCTACTACGTCGCCGGCA

upper sequence: GLYMA14G03500.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv12s0028g00960.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------------------------------------------gcacctatg-caaattggt--catcttat-acagaatagatttca-----ccttcttttttatg--tgctaaaactgatccaaatggcattgcattgtctttttgaaacagCCCTTCAAGGACATGATCGAAGGGATGAGGGTGGACCTGAGAAAGTCAAGATACAATAACTTTGATGAGCTCTACCTTTACTGCTACTATGTTGCTGGGA
                                                                               | || | ||   | | |||   |  || | |||||  | || | |     | |||| | | |||  |    ||||   |||| |||  | |  ||| ||||||| |  ||||||||||| |||||||| ||||| |||||  ||||||||||||| ||||||||||| | ||||||||||||||| || |||||||| ||||||||||| |
gtacatttatatgggctcaaaactgattcacccatcttgcattttagctgctaatcaacctatgaacacgcacacatatgaacatttgatgagtaggtagtacattgtgacagagcacatattatgggcctttctgtatcatgaatatataaacacttccacatgttaata-attttcttttt-atgcagCCCTTCAAAGACATGATAGAAGGAATGAGATTGGACCTGAGAAAATCAAGATACAACAGCTTTGATGAGCTCTATCTGTACTGCTATTATGTTGCTGGAA

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|192314403|gb|FK008401.1|FK008401
EST:     ATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCGGTTGATATTCAG                         CCCTTCAAGGACATGATCGAAGGGATGAGGGTGGACCTGAGAAAGTCAAGA
genomic: ATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCGGTTGATATTCAGgtactttaca ... tttgaaacagCCCTTCAAGGACATGATCGAAGGGATGAGGGTGGACCTGAGAAAGTCAAGA
EST: gi|192314402|gb|FK008400.1|FK008400
EST:     ATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCGGTTGATATTCAG                         CCCTTCAAGGACATGATCGAAGGGATGAGGGTGGACCTGAGAAAGTCAAGA
genomic: ATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCGGTTGATATTCAGgtactttaca ... tttgaaacagCCCTTCAAGGACATGATCGAAGGGATGAGGGTGGACCTGAGAAAGTCAAGA
EST: gi|9259258|gb|BE347466.1|BE347466
EST:     ATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCGGTTGATATTCAG                         CCCTTCAAGGACATGATCGAAGGGATGAGGGTGGACCTGAGAAAGTCAAGA
genomic: ATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCGGTTGATATTCAGgtactttaca ... tttgaaacagCCCTTCAAGGACATGATCGAAGGGATGAGGGTGGACCTGAGAAAGTCAAGA
EST: gi|151403755|gb|EV273565.1|EV273565
EST:     ATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCGGTTGATATTCAG                         CCCTTCAAGGACATGA
genomic: ATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCGGTTGATATTCAGgtactttaca ... tttgaaacagCCCTTCAAGGACATGA
EST: gi|51341598|gb|CO982915.1|CO982915
EST:     ATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCGGTTGATATTCAG                         CCCTTCAAGGACATGATCGAAGGGATGAGGGTGGACCTGAGAAAGTCAAGA
genomic: ATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCGGTTGATATTCAGgtactttaca ... tttgaaacagCCCTTCAAGGACATGATCGAAGGGATGAGGGTGGACCTGAGAAAGTCAAGA
EST: gi|192318813|gb|FK011427.1|FK011427
EST:     ATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCGGTTGATATTCAG                         CCCTTCAAGGACATGATCGAAGGGATGAGGGTGGACCTGAGAAAGTCAAGA
genomic: ATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCGGTTGATATTCAGgtactttaca ... tttgaaacagCCCTTCAAGGACATGATCGAAGGGATGAGGGTGGACCTGAGAAAGTCAAGA
EST: gi|9205460|gb|BE331684.1|BE331684
EST:     ATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCGGTTGATATTCAG                         CCCTTCAAGGACATGATCGAAGGGATGAGGGTGGACCTGAGAAAGTCAAGA
genomic: ATGATGCTGCCCTCTCACATACTGTCTCAAAGTACCCGGTTGATATTCAGgtactttaca ... tttgaaacagCCCTTCAAGGACATGATCGAAGGGATGAGGGTGGACCTGAGAAAGTCAAGA
EST: gi|193379581|gb|FK344005.1|FK344005
EST:     AAAGTACCCGGTTGATATTCAG                         CCCTTCAAGGACATGATCGAAGGGATGAGGGTGGACCTGAGAAAGTCAAGA
genomic: AAAGTACCCGGTTGATATTCAGgtactttaca ... tttgaaacagCCCTTCAAGGACATGATCGAAGGGATGAGGGTGGACCTGAGAAAGTCAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttttatgtgctaaaactgatccaaatggcattgcattgtctttttgaaacagCCCTTCAAGGACATGATCGAAGGGATGAGGGTGGACCTGAGAAAGTCAAGATACAATAACTTTGATGAGCTCTACCTTTACTGCTACTATGTTGCTGGGA
                                      ttgtcttttt  CT-rich tract
                                           tttttgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcacctatgcaaattggtcatcttatacagaatagatttcaccttcttttttatgtgctaaaactgatccaaatggcattgcattgtctttttgaaacagCCCTTCAAGGACATGATCGAAGGGATGAGGGTGGACCTGAGAAAGTCAAGATACAATAACTTTGATGAGCTCTACCTTTACTGCTACTATGTTGCTGGGA

- -cctatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cattgca