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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCTGAGGGAGAATATGCTGTCAGAGAAAGTACATCAAAGATTAAAATTTTCAGCAAAAATTTCCAGgtttgtacttttttaaaaactttgtttcctctctaatctcgtgcaatcttgttctgtgtgtaatgaaccaacaagttcttgctatttcttaaaaggaaaa...

Basic information

species Glycine max
transcript GLYMA15G01680.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os02g11840.1 (Oryza sativa), 5'ss of exon 3
GTCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCTGAGGGAGAATATGCTGTCAGAGAAAGTACATCAAAGATTAAAATTTTCAGCAAAAATTTCCAGgtttgtacttttttaaaaactttgtttcctctctaatctcgtgcaatcttgttctg--tgtgtaatg-aaccaacaagttcttgctatttcttaaaaggaaaa
 ||||| || || ||||| ||||||||||||||   ||| ||||||||||||||||||||||| || || | ||| || || | ||| |||||||||||||||||||||          |||  |||  |   ||   | || ||     ||   |    |  |||| ||       | |      |||| ||    |   | 
ATCATTCGGGTCTGCACTTGAATTTGTTTGGTCAGTTGATGGAGAATATGCTGTCAGAGAAAGCACGTCGAGGATAAAGATATACAGTAAAAATTTCCAGgtttgtactaccactgtcccttcttttaat---tatctttgtacatcagagtaggggtccttcaatgcaatgtgtgggctagaaaaatttattgggtgtgcac

upper sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 12
GTCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCTGAGGGAGAATATGCTGTCAGAGAAAGTACATCAAAGATTAAAATTTTCAGCAAAAATTTCCAGgtttgtacttttttaaaaactttgtttcctctctaatctcgtgcaatcttgttctgtgtgtaatgaaccaacaagttcttgctatttcttaaaaggaaaa-
 ||||| || || ||||| ||||||||||||||   ||| |||||||| |||||||||||||| || || | ||| || || | ||| |||||||||||||||||||||          | || |||    | |  |        |   |        |  |||| |       |  || |  |  | |||  |||     
ATCATTCGGGTCTGCACTTGAATTTGTTTGGTCACTTGATGGAGAATACGCTGTCAGAGAAAGCACCTCGAGGATAAAGATATACAGTAAAAATTTCCAGgtttgtactgcccactgccccttcttttaattatcgttgtacatcagagtaggggtccttcaatgcaatgtgtggggctagaaaaat-ttagtaggtgtgc

upper sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 12
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 12
GTCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCTGAGGGAGAATATGCTGTCAGAGAAAGTACATCAAAGATTAAAATTTTCAGCAAAAATTTCCAGgtttgtacttttttaaaaactttgtttcctctc-taatctcgtgcaatcttgttctgtgtgtaatgaaccaacaagttcttgctatttcttaaaaggaaaa----
||||||||| || ||| |||| ||||||||||| || || ||||| |||||| |||| |||||||||||||  || || |||||||| |||   || ||||||||  |    || |        |||||| |  | |  | |  || |     | |  ||||       |  |||    |  | | |    | || | |      
GTCATTTGGATCTGCATTGGAGTTTGTTTGGTCATCAGAAGGAGAGTATGCTATCAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAGgtttggcccacattgattgtagcctttccttttatgaatttgatcagtaaaactgta-gtgtttcatttcttcaa----tcaccactctggagaatgcaccatct

upper sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G124886_T02 (Zea mays), 5'ss of exon 12
GTCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCTGAGGGAGAATATGCTGTCAGAGAAAGTACATCAAAGATTAAAATTTTCAGCAAAAATTTCCAGgtttgtacttttttaaaaactttgtttcctctctaatctcgtgcaatctt--gttctgtgtgtaatgaaccaa--caagttcttgctatttcttaaaaggaaaa
 |||||||| || ||||| ||||||||||||||  |||| |||||||||||  |||||||||| || |||| ||| || |||| ||| ||||||||||||||||||     | ||| |  ||    | ||| ||  |    ||   | ||  ||| | | | ||  |    |   |    |||  | |   | |  | ||    
ATCATTTGGGTCTGCACTTGAATTTGTTTGGTCAACTGATGGAGAATATGCCATCAGAGAAAGCACCTCAAGGATAAAGATTTACAGTAAAAATTTCCAGgtttgtttcaatataacatattccccttctccctggtacaatgttttgtttagttatatctataccgctgtaggcctgtctctaacaaacacctgtaggg----

upper sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G141587_T05 (Zea mays), 5'ss of exon 12
GTCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCTGAGGGAGAATATGCTGTCAGAGAAAGTACATCAAAGATTAAAATTTTCAGCAAAAATTTCCAGgtttgtacttttttaaaaactttgtttcctctctaatctcgtgcaatcttgttctgtgtgtaatgaaccaacaagttcttgctatttcttaaaaggaaaa
 |||||||| || ||||| ||||||||||||||  |||| |||||||||||  |||||||||| || || | ||| || || | ||| |||||||||||||||||      | ||| |  |||   | ||  ||      |   ||||| |||   || |   ||| |     ||                         
ATCATTTGGGTCTGCACTTGAATTTGTTTGGTCAACTGATGGAGAATATGCCATCAGAGAAAGCACCTCGAGGATAAAGATATACAGTAAAAATTTCCAGgtttgcctcgatataacatatttcacttcttcctgga---gcataatct-gttaactg-gagctgatcttttcag-------------------------

upper sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G095348_T03 (Zea mays), 5'ss of exon 12
GTCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCTGAGGGAGAATATGCTGTCAGAGAAAGTACATCAAAGATTAAAATTTTCAGCAAAAATTTCCAGgtttgtacttttttaaaaactttgtttcctctctaatctcgtgcaa---tcttgttctgtgtgtaatgaaccaacaagttcttgctatttcttaaaaggaaaa
||||||||| || |||||||||||||||||||| || || |||||||||||  | || |||||||||||||  || || |||||||| |||   || |||||   | ||  ||||     ||  ||  ||||||| ||   |||||   |||  ||   |   |||| |   ||    | | |    |||   |   | ||| 
GTCATTTGGATCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAGgt--attctagtttagtttattgtttctctctcta-tcagatgcaagtttctcatttcttccataattacgtaaaccttacctctggtttggcatctgtaaac

upper sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 12
lower sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 12
GTCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCTGAGGGAGAATATGCTGTCAGAGAAAGTACATCAAAGATTAAAATTTTCAGCAAAAATTTCCAGgtttgtacttttttaaaaactttgtttcctctctaatctcgtgcaatcttgttctgtgtgtaatgaaccaacaagttcttgctatttcttaaaaggaaaa-----
 |||||||| || |||||||||||||||||||| || || |||||||||||  | || |||||||||||||  || || |||||||  |||   || |||||   |  | |  |  |   ||| ||   | |||| | |  |     |||  || |  || ||    |  |    |||      || | ||||            
ATCATTTGGGTCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAATAAATCGTTTCAGgtacatggtctgctttag--tttattgtttttcta-tatattaattgcttaatcag-atgcaaatttctcatttcttcc-atagttacctaaacattgcctctgg

upper sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 12
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 5'ss of exon 12
GTCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCTGAGGGAGAATATGCTGTCAGAGAAAGTACATCAAAGATTAAAATTTTCAGCAAAAATTTCCAGgtttgtacttttttaaaaactttgtttcctctctaatctcgtgcaatcttgt-tctgtgtgtaatgaaccaacaagttcttgctatttcttaaaaggaaaa----------------------------------------
|||||||||||| | |||||||||||||||||| || ||||| || | ||| || ||||||||  |||||||||||||||| || ||||||||||||||||||| ||  | |||     || | |   ||      |   || ||| | ||| ||| ||  |  || |  |  |  || ||| || |  | |    || |                                         
GTCATTTGGTTCTGGACTGGAATTTGTTTGGTCATCCGAGGGGGAGTGTGCGGTTAGAGAAAGCTCATCAAAGATTAAAATATTTAGCAAAAATTTCCAGgtttctaaatctttt---tctctctgatctaagccgttctgttcaaccctgtatctatggttgttgga--agta--ttattgatactggtcatggagatagctatattcggatctggctcattcagaaaatacattttcag

upper sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 12
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 16
GTCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCTGAGGGAGAATATGCTGTCAGAGAAAGTACATCAAAGATTAAAATTTTCAGCAAAAATTTCCAGgtttgtactt--ttttaaaaactttgtttcctctctaatctcgtgcaa---tcttgttctgtgtgt-----------------aatgaaccaacaagttct--tgctatttcttaaaaggaaaa
||||||||| || || || |||||||||||||| ||||| || ||  |||||||||| |||||  |  ||||||| || || |||||||| |||||||||||||||| ||  ||||   |  ||  ||| |   || ||    |  ||   | ||||| | |||||                 |||  || |||   | ||  | |  ||  ||||   | |  
GTCATTTGGCTCTGCGCTAGAATTTGTTTGGTCATCTGATGGGGAGCATGCTGTCAGGGAAAGCTCGACAAAGATCAAGATCTTCAGCAAGAATTTCCAGgtttgtaattccttttggcacgttccttttccgactgattaactctaaagcttttgttttttgtgtcttattctgttatctgaaatacactaacctatgctgatacccttgtttaatttgcag-

upper sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 12
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 12
GTCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCTGAGGGAGAATATGCTGTCAGAGAAAGTACATCAAAGATTAAAATTTTCAGCAAAAATTTCCAGgtttg-tacttttttaaaaactttgtttcctctctaatctcgtgcaatcttgttctgtgtgtaatgaaccaacaagttcttgctatttcttaaaaggaaaa-----------------------------------
 || ||||| || |  ||||||||||||||||| |||||||| |||| ||| || ||||||||  |||||||||| || || ||||| ||||||||||||||||| || | |  | |   | ||  |  |   ||| | |  || | | |  ||||  |  | | |||    ||  | ||||| ||      |      |                                    
ATCTTTTGGGTCTGGCCTGGAATTTGTTTGGTCATCTGAGGGGGAATGTGCGGTTAGAGAAAGCTCATCAAAGATAAAGATATTCAGTAAAAATTTCCAGgtttgctattctcattatggccttact--catactattttgttggagtatgattctagggttgaagaaattgcagatgcttgcaatagagacagctattactggcttattatattaataaaaggtggtgttttcag

upper sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 12
GTCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCTGAGGGAGAATATGCTGTCAGAGAAAGTACATCAAAGATTAAAATTTTCAGCAAAAATTTCCAGgtttgtacttttttaaaaactttgtttcctctctaatctcgtgcaatcttgttctgtgtgta-atgaaccaacaagttcttgc-tatttcttaaaaggaaaa----
||| |||||||| ||| |||||||||| ||||| || || || |||||||||||||||||||||||||||||| |||| |||||||| || |||||||||||||||      |      ||||||||| ||||| ||        ||   || |  | | || ||  |    || ||   ||  | | | |      |||||    
GTCTTTTGGTTCGGCATTGGAATTTGTATGGTCATCAGATGGTGAATATGCTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAGgtttgtgtcccctc-----ctttgtttc-tctctgatgagaatagattaggtgcaatatatatatatatatgcatgtgtgtgtgtgtgtgtgctgctgaaaacatt

upper sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 12
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 5'ss of exon 12
GTCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCTGAGGGAGAATATGCTGTCAGAGAAAGTACATCAAAGATTAAAATTTTCAGCAAAAATTTCCAGgtttgtacttttttaaaaactttgtttcctctctaatctcgtgcaatcttgttctgtgtgtaatgaaccaacaagttcttgctatttcttaaaaggaaaa---
 |||||||| ||||| ||||||||||||||||| || || | |||||||||||| || ||||||||||||| |||||| |||||||||||||  ||||||||||  |   ||| |||   |   ||  | |       |  ||    ||| ||||    | ||   | |||   | |  |  | || |  |   |   |    
ATCATTTGGCTCAGCGCTGGAATTTGTTTGGTCATCAGATGCAGAATATGCTGTGAGGGAAAGTACATCAAGGATTAAGATTTTCAGCAAAACATTCCAGgttttgatcctttcaaagtttagattctcacgacttattgatgggggctt-ttctccaagcaaattagcaat--gcttcttttgttgcaaagttgtttatctt

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCTGAGGGAGAATATGCTGTCAGAGAAAGTACATCAAAGATTAAAATTTTCAGCAAAAATTTCCAGgtttgtacttttttaaaaactttgtttcctctctaatctcgtgcaatcttgttctgtgtgtaatgaaccaacaagttcttgctatttcttaaaaggaaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaggaaa