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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataactagttagctatgcacatttaagatattttaagtcttctctttcagaggatcctgaaagttatgaaccctggatagtcaatgataaataaac...

Basic information

species Zea mays
transcript GRMZM2G165357_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 5'ss of exon 4
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaa-ataactagttagctatgcacatttaagatattttaagtcttctctttcagaggatcctgaaagttatgaaccctggatagtcaatgataaataaac
|||||||| || || ||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||||| |||||||||||||     ||    |   |      | || |   | | |   |     ||   |    |   | |  | ||  ||   |      ||||   |  | ||| 
GTCATTGTCGCAGACAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATCGGACACCCAAGATTTGAGCTAATCCGTCATGgtattgctacattctcagtgcatttagttcatgaactattgttacatactagtaataaagttttactgctagcaagttttttcgttcaaaatttgagaaa-

upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G06990.1 (Glycine max), 5'ss of exon 4
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataactagttagctatgcacatttaagatattttaagtcttctctttcagaggatcctgaaagttatgaaccctggatagtcaatgataaataaac-----
|||||||||||||||||||  |||||||| ||||| |||||||| || || |||||||| || |||||||| ||||| || |||||||||| |  || | ||     | |  ||| ||  | |      |||  |   | | |   |   | |  | ||  |   || |   |  || |||  |   |     
GTCATTGTTGCTGATAACTACTTCACTGGATCAAAGGACAACCTCAAAAAATGGATTGGTCATCCAAGATTCGAGCTTATTCGTCATGgtatactac-attttttcgtac-tattcaacgtgtcaactatcta-taaattaaattgttgggcatatgataga--gtgaaggttagattatattttgtctcatt

upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA13G40960.1 (Glycine max), 5'ss of exon 5
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaa---taac--tagttagctatgcacatttaagatattttaagtcttctctttcag-aggatc-ctgaaagttatgaaccctggatagtcaa-tgataaataaac
|| ||||||||||| ||||  |||||||| || || |||||||| || || ||||| || || |||||||||||||| ||||||||||||| |   |||   | |||  ||||  ||  | ||     || || |  || | ||  | || ||| |    || | | ||   | | | ||||| || |        
GTAATTGTTGCTGACAACTACTTCACTGGATCCAAGGACAACCTCAAAAAATGGATAGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatagtctaatctttgtttactatcaactatcaaaggcattaaaattgtcacattaggcagtatctccttgagcttttaaatttagtttgtcaactggt--------

upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA12G06980.2 (Glycine max), 5'ss of exon 3
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataactagttagctatgcacatttaagatattttaagtct----tctctttcagaggatcctgaaagttatgaaccctggatagtcaatgataaataaac
|||||||||||||| ||||| |||||||| || ||||||||||| || || ||||||||||| |||||||| ||||| || ||||||||||  ||| |     | | |   ||||  |   |||   || ||    |   ||| |  |  |  |   | || |      |   |   |||||   |  |   
GTCATTGTTGCTGACAACTTCTTCACTGGATCTAAAGACAACCTTAAAAAATGGATTGGCCATCCAAGATTCGAGCTAATTCGTCATGgta--taattttactgttctcttcattgcaatcattcacagactgggattaatttgatggtttattctcaattgttctaaatcagtcaccaatgtagagcag--

upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA11G15010.1 (Glycine max), 5'ss of exon 4
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaa---taactagttagctatgcacatttaag-atattttaagtcttctctttcagaggatcctgaaa-gttatgaaccctggatagtcaatgataaataaac
|||||||||||||| ||||  |||||||| || ||||||||||| || |  ||||||||||| |||||||||||||| || |||||||||| |   | |||| |    |     || | |   | | |||  |  |  | |    |   || || ||  ||| | || |     |   |||||   |  |   
GTCATTGTTGCTGACAACTACTTCACTGGATCTAAAGACAACCTTAAAAGATGGATTGGCCATCCAAGATTTGAGCTAATTCGTCATGgtataattttactattctcttcattgcaatcattcacagtttgggattaatttgatggtttattctcaattgttctaaatc---agttaccaatgtagagcag--

upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA11G15020.1 (Glycine max), 5'ss of exon 4
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaat---aactagttagctatgcacatttaagatattttaagtcttctctttcagaggatcctgaaagttatgaaccctggatagtcaatgataaataaac-
|||||||||||||| ||||  |||||||| ||||| |||||||| || || |||||||| || |||||||||||||| ||||||||||||| |    |  | |||  |||| ||  ||    |   | |||   ||   ||   | | ||  ||| ||   ||||   | |||  |  ||  |   | |   
GTCATTGTTGCTGACAACTACTTCACTGGATCAAAGGACAACCTCAAAAAATGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgtatactccattttgtttactattcaacttctcaaccatctaaaaattaaattattgtgcata-tgatagac-tgaagattagattat--attttgtctcattt

upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA15G04500.2 (Glycine max), 5'ss of exon 5
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataactagttagctatgcacatt-taagatattttaagtct-tctctttcagaggatcctgaaagttatgaaccctggatagtcaatgataaataaac
|||||||||||||| ||||  |||||||| || || || ||||| || ||||||||||| || |||||||||||||| |||||||||||||  ||     | | || ||   | | | |  |||      ||  |  | || | |   ||         ||| ||    | |  | | ||||  ||    
GTCATTGTTGCTGACAACTACTTCACTGGATCCAAGGATAACCTCAAAAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCATGgta--tagtctttcatctttgtttactgtcaactatcaactatcaatgccattaaaattgtcacatgttagatgcactaaagttttttattgatttatcttt

upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 5'ss of exon 3
------------GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgta-aataactagttagctatgcacatttaagatattttaagtcttctctttcagaggatcctgaaagttatgaaccctg-gatagtcaatgataaataaac
            || || ||||| ||||| |  ||||| || ||||||||||| || ||||| |||||||| || |||||||||||||| || |||||||||| | || ||  |||  ||  || | |||       ||||  ||  |    || |  |       | |  | |  | || |||  |    |          
GAAAAGAATGAAGTAATCGTTGCGGATAATTACTTCACAGGATCAAAAGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTAATTCGTCATGgtatagtatcttcttaattaatcaaactta------cttaatactcattaaccaaaacaatgcattaatactcattcttgtgattttttcag----------

upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT5G59290.2 (Arabidopsis thaliana), 5'ss of exon 3
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataactagttagctatgcacatttaagatattttaagtcttctctttcagaggatcctgaaagttatgaaccctggatagtcaatgataaataaac--
||  ||||||||||||||| ||||||||| |||||||| ||||| ||||||||||| || ||||| || ||||| || || ||||| ||||             ||  |    ||    |   | |   | |||   |  | | |||||  |   |  ||| | ||   | |    ||     |||||  
GTGGTTGTTGCTGATAACTATTTCACTGGCTCAAAAGAAAACCTCAAGAAGTGGATCGGTCACCCCAGGTTTGAACTTATTCGTCACGgtatggtctcgagactctcagtttgttgttaagcgtcttcttgttcatgtcaacaagatcc--atcatcgtgatctctatttggaatttgggctttaaacag

upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 5'ss of exon 4
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgta----------aataactagttagctatgcacatttaagatattttaagtcttctctttcagaggatcctgaaagttatgaaccctggatagtcaatgataaataaac
|| |||||||||||||||| ||||||||||||||| |||||||| |||||||||||||| || |||||||||||||| |||||||| ||||          | |  || | | | |      ||| |  ||    ||  || | |||||      ||||    |  | |      ||| |  | ||            
GTGATTGTTGCTGATAACTATTTCACTGGTTCAAAGGACAACCTTAAGAAGTGGATTGGTCATCCAAGATTTGAGCTTATCCGTCACGgtatggttttgaaattctctggcttgttgctgctattgagaatggaatat-tcctgtcttttgttctatccatttatattttggttttgggt--ttaacag---------

upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 5'ss of exon 4
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataactagttagctatgcacatttaagatattttaagtcttctctttcagaggat-cctgaaagttatga-accctggatagtcaatgataaataaac
|| |||||||| |||||||  ||||| ||||| || ||||| || ||||| |||||||| || |||||||||||||| || ||||||||||| |   |  |    |     ||||| |  | | | |  | | |   | |      |   || || ||  || | ||       | |||  | | |    
GTAATTGTTGCCGATAACTACTTCACCGGTTCTAAGGACAATCTCAAGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtaagttttttatctttttactccattttat-tttatcacatatgcatatgcgtcatttgtttggaatttgggatatcccttcagatgaatcctgattggt-

upper sequence: GRMZM2G165357_T02 (Zea mays), 5'ss of exon 3
lower sequence: Vv13s0019g00840.t01 (Vitis vinifera), 5'ss of exon 4
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataactagttagctatgcacatttaagatattttaagtcttctctttcagaggatcctgaaagttatgaaccctggatagtcaatga-taaataaac
|| ||||||||||||||||  |||||||| || ||||| ||||||| ||| |||||||| || |||||||||||||| || ||||||||||     ||  || ||| ||    |  ||| |      | ||    || | | | |    |    || | |  |  |   |  |  |||  |  ||    
GTGATTGTTGCTGATAACTACTTCACTGGATCTAAAGATAACCTGAGGAAATGGATTGGTCATCCAAGATTTGAGCTTATTCGTCATGgtattattctcatttgctttgtcattacaaggtggacacaatcaggactgttaaacgcctttccttgtcaagttctttatttgctggatgggttcatgtc-

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|32829264|gb|CD968942.1|CD968942
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|149070503|gb|EE158907.2|EE158907
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|211182716|gb|FL410032.1|FL410032
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|32787712|gb|CD936614.1|CD936614
EST:     AACCTGAAGAAGTGGATTGGCCACCCAAGNATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: AACCTGAAGAAGTGGATTGGCCACCCAAG-ATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|32829447|gb|CD969125.1|CD969125
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|149082965|gb|EE172201.2|EE172201
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|60394382|gb|DN227252.1|DN227252
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|32797525|gb|CD949761.1|CD949761
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|149070980|gb|EE159385.2|EE159385
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|32914071|gb|CF018883.1|CF018883
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|71444250|gb|DR825300.1|DR825300
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|32796729|gb|CD948965.1|CD948965
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|60339871|gb|DN206844.1|DN206844
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|32799379|gb|CD951615.1|CD951615
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|32798044|gb|CD950280.1|CD950280
EST:     CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|15100352|gb|BI396143.1|BI396143
EST:     GAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
genomic: GAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTATCACCTTGCTT
EST: gi|211283078|gb|FL322113.1|FL322113
EST:     CAACCTGAAGAAGTGGATTGGCCACTCAAGATTTGAGCTCATCCGTCATG                         ATGTCACCGAGCCGCTTCTT
genomic: CAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataact ... tttgttttagATGTCACCGAGCCGCTTCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCATTGTTGCTGATAACTTTTTCACTGGTTCAAAAGACAACCTGAAGAAGTGGATTGGCCACCCAAGATTTGAGCTCATCCGTCATGgtaaataactagttagctatgcacatttaagatattttaagtcttctctttcagaggatcctgaaagttatgaaccctggatagtcaatgataaataaac

- - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA