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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTGgtaaatttatcttccaatagcatgttttggtacaaacatttcactacaatatcaaaatatgcagactagtttgatttctgaatctttcctctatag

Basic information

species Zea mays
transcript AC203754.4_FGT008
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC203754.4_FGT008 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os05g38150.1 (Oryza sativa), 5'ss of exon 12
CTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTGgtaaatttatcttccaatagcatgttttggtacaaacatttcactac--aatatcaaaatatgcagactagtt-tgatttctga--------atctttcctctatag
||| ||||||| ||||||||||||||||||||||| || |||||||| || || ||||||||| | ||||||||||| ||||||||||| ||||||||||||||  | ||  ||    |  | ||   ||    ||  |  ||    || |  |  | |     ||  ||   ||||||||        || |  || ||  ||
CTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTGgtaaattc-tgtttgaacttaagttcttaccactcttatggctttattggatgttgagtttttttttctttttgctatttctgacattccatatttccccactgcag

upper sequence: AC203754.4_FGT008 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA14G07120.1 (Glycine max), 5'ss of exon 10
CTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTGgtaaatttatcttccaatagcatgttttggtacaaacatt--tcactacaatatcaaaatatg--cagactagtttgatttctgaatctttcctctatag----
||  |||| ||||||||||| || ||||||||||||||||| || || ||||| ||||||||||  || ||||| || |||||| | ||||| ||||||||   |||  | |      ||||||   || |  |||   |   |||  |||  || |  |        | ||||||| || ||  |||  || |       
CTGGATGACGTAATTGATCTGGTGATTCCAAGAGGCAGCAACAAACTTGTTTCTCAAATCAAGAGTTCCACTAAAATTCCTGTTTTAGGTCACGCTGgtaagactattatgct----tatgtttaaatataggcataaatttttactctatttaatttggactgtgtgattttgattcctcaagtttttttcaagtcaatt

upper sequence: AC203754.4_FGT008 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA03G12240.1 (Glycine max), 5'ss of exon 13
CTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTGgtaaatttatcttccaatagcatgttttggtacaaacatttcactacaatatcaaaatatgcagactagtttgatttctgaatctttcctctatag
||| |||||||||| ||||| ||  | || |||||||| |||||||| ||||| |||||||||  |||||| || || ||||||||||||||||||||||| |||  ||||||     || |  |  |    |    | | || |    |    | |    |||   ||  ||     || |||  | |  ||
CTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTGgtaatttt--cttccatataaatttcctattttgtag---ttagtaaatagcctctctttttttactgaatttgtt-----atttttgttatgcag

upper sequence: AC203754.4_FGT008 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA02G41850.1 (Glycine max), 5'ss of exon 10
CTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTGgtaaatttatcttcc--aatagcatgttttggtacaaacatttcactacaatatcaaaa---tatgcagactagtttgatttctgaatctttcctctatag
||  |||||||||| ||||| || ||||||||||||||||| || || ||||| || |||||||  || ||||| || |||||| | ||||||||||||||   |||  | |  ||| |||  |||   |   |   | | | |    |  |  ||   | | ||   |  ||   |  ||  || |||    |  | 
CTGGATGATGTAATCGATCTGGTGATTCCAAGAGGCAGCAACAAACTTGTTTCTCAGATCAAGAGTTCCACTAAAATTCCTGTTTTAGGTCATGCTGgtaagactattatgcttaatggcacttttactttggactgtgtgattttggtccctcaagttttttcaagttgattaagtccctctatttttgaaattaa-

upper sequence: AC203754.4_FGT008 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA01G24530.1 (Glycine max), 5'ss of exon 14
CTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTGgtaaatttatcttccaatagcatgttttggtacaaacatttcactacaatatcaaaatatgcagactagtttgatttctgaatctttcctctatag
||| |||||||||| ||||| ||  | || |||||||| |||||||| ||||| |||||||||  |||||| || || |||||||||||||||||||||||   | |  | | |||  |  |||        | ||||   |  | |    | ||| ||    |  ||||| ||     | ||   | |  ||
CTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTGgtaa---tgttcttccata-taaatttc-------atattt---tgtagttagtatataggctttattttttgaatttgtttttttcattatgcag

upper sequence: AC203754.4_FGT008 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA07G16510.1 (Glycine max), 5'ss of exon 10
CTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTGgtaaatttatcttccaatagcatgttttggtacaaacatttcactacaatatcaaaatatgcagactagtttgatttctgaatctttcctctatag
                |||||||  | || |||||||| |||||||| || || |||||||||    |||| ||||| |||||||||||||||||||||||  |    ||   ||  | | |||| |   ||       | |||||  |   | | |  | | | |||   ||| | |  |            
----------------ATCTTGTGGTCCCCAGAGGCAGTAATAAGCTTGTCTCTCAAATCAAGGGTACAACAAAGATTCCTGTTCTTGGTCATGCTGgtaatatatgatttacatttcctatttttgattaa------tattacaaagtaggattttataaaattgttatttttgtcatgcag----------

upper sequence: AC203754.4_FGT008 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA18G40770.1 (Glycine max), 5'ss of exon 14
CTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTGgtaaatttatcttccaatagcatgttttggtacaaacatttcactacaatatcaaaatatgcagactagtttgatttctgaatctttcctctatag
                |||||||  | || |||||||| || || || ||||| |||||||||   || || ||||| |||||||||||||||||||||||  |    ||   ||  | | |||| | |   | ||||||    |  ||   | ||    |  || |||  |     |               
----------------ATCTTGTGGTCCCCAGAGGCAGTAACAAACTTGTTTCTCAAATCAAGGATTCCACAAAGATTCCTGTTCTTGGTCATGCTGgtaatatatgatttacatttcctatttttg-attgatatttcaaagtaggattttattaaattg-ttatttttgtcatgcag--------------

upper sequence: AC203754.4_FGT008 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA18G03830.1 (Glycine max), 5'ss of exon 13
CTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTGgtaa-atttatcttcc-aata-gcatgt----tttggtacaa-acatttcactacaatatcaaaatatgcagac-tagtttgatttctgaatctttcctctatag
 |  |||||||||||||||| || ||||||||||||||||| || || ||  | || |||||||  || ||||| || ||||| || |||||||| ||||| |  | ||| |  || | ||| |      ||  |   | |   |  |      | |||||| |    | | ||    |    |   ||  | |  | |   
TTGGATGATGTAATTGATCTAGTGATTCCAAGAGGCAGCAACAAACTTGTCACTCAGATCAAGAGTTCCACTAAAATTCCTGTCCTGGGTCATGCAGgtaagacctttctgcttaacatgcaagaaatgcttaatgtgatatggtaaatccttttgtcaaaagaatttgccataacaaggccacattattgtccaaccag--

upper sequence: AC203754.4_FGT008 (Zea mays), 5'ss of exon 12
lower sequence: AT3G55610.2 (Arabidopsis thaliana), 5'ss of exon 13
CTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTGgtaaatttatct-tccaatagcatgttttggtacaaacatttcactacaatatcaaaatatgcagactagtttgatttctgaatctttcctctatag
||| |||| || ||||||||||| || |||||||||||||| ||||| ||||| ||||| || |  || || || ||||| || || || ||||||||||  |||||   | || |  |||   |  || |  |  ||  | |    ||   | |    ||   | | ||  ||| ||  | |||||       
CTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTTTCTCAAATAAAAAACTCGACGAAAATCCCAGTGCTAGGCCATGCTGgtatgtttataagttcagttccat---taagttcttaagttggattggcctagagaga---aca---tggcttattttttgggtgtttccag-----

upper sequence: AC203754.4_FGT008 (Zea mays), 5'ss of exon 12
lower sequence: Vv08s0007g01060.t01 (Vitis vinifera), 5'ss of exon 13
CTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTGgtaaatttatcttccaatagcatgttttggtacaaacatttcactacaatatcaaaatatgcagactagtttgatttctgaatctttcctctatag
||| ||||||| || |||||||| || || ||||||||||| || || ||||| |||||||||   |||||||| ||||||||||||||||||||||||||  | |  |   | |       |||   | || |     ||||  |  |   | |||   |  |  ||| |                      
CTTGATGATGTCATAGATCTTGTGATCCCTAGAGGCAGCAACAAACTCGTTTCTCAAATCAAGGATTCAACTAAAATCCCTGTTCTTGGTCATGCTGgtaagataaattgtgactctttaaattt---ataatctgcaaacta-gaggttttattatagtgtttgctttcag---------------------

upper sequence: AC203754.4_FGT008 (Zea mays), 5'ss of exon 12
lower sequence: Vv13s0019g02360.t01 (Vitis vinifera), 5'ss of exon 13
CTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTGgtaaatttatcttccaatagcatgttttggtacaaacatttcactacaatatcaa-aatatgcagactagtttgatttctgaatctttcctctatag-------------------------------------------------
||| ||||||| || || ||||| || ||||||||||||||||| || ||||| ||||| |||   ||||| || || |||||||| || ||||||||||   | |    | ||       ||  | | | |    || | || |||||||| | |||   |   |   || |     ||| ||   | ||| |                                                 
CTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTGgtatgatgacagactaaa-----cttaagatgctatttattta-tataatatcaacagtatat-gctcaacctggtcaaacaattttctttttatgggaagaacaatgtctgcatttagaattaaagatacagcatttgctctcag

upper sequence: AC203754.4_FGT008 (Zea mays), 5'ss of exon 12
lower sequence: EFJ29127 (Selaginella moellendorffii), 5'ss of exon 13
CTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTGgtaaatttatcttccaatagcatgttttggtacaaacatttcactacaatatcaaaatatgcagactagtt-tgatttctgaatctttcctctatag
||| | ||||| ||||| || || || |||||||| |||||||| || |||||||||||||||   || || || || ||||| || || ||||| ||||   |  | ||    | ||||       | | ||  |||  |       ||  | |  | |  ||  || |||    || |     | |      
CTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCGgtatgctacttttgtcctcgcat-------tgcgaaagtttgtcc------tcgcattgcgaaagctgtttctgacacatggaaaaccctttag---

upper sequence: AC203754.4_FGT008 (Zea mays), 5'ss of exon 12
lower sequence: EFJ17662 (Selaginella moellendorffii), 5'ss of exon 13
CTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTGgtaaa-----tttatcttccaatagcatgttttggtacaaacatttcacta--caatatcaaaatatgcagactagtttgatt--tctgaatctttcctctatag
||| | ||||| ||||| || || || |||||||| |||||||| || |||||||||||||||   || || || || ||||| || || ||||| ||||       ||| || ||  || ||     || || |   | || |   |     |    | | ||| | |    |||   |  | |    | |  ||   |||
CTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCGgtatgctacttttgtcctcgcattgcgaaaatttgtcctcgcgttgcgaaagctgtttctgacacatggaaaaccttttagatggtatctgccatgtctacgtag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTGgtaaatttatcttccaatagcatgttttggtacaaacatttcactacaatatcaaaatatgcagactagtttgatttctgaatctttcctctatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG