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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTCGGACGGGGATGGACGACTACGCCCGGGAGATGATGGAGCTGAAGACGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtacttaccacttctttccttcatttccacatcccttcattgatccggtgcctcacccacaccccaggatctagcttttcccgccctcccgtttgg...

Basic information

species Zea mays
transcript GRMZM2G151268_T04
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151268_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os12g01170.1 (Oryza sativa), 5'ss of exon 1
ATTTCGGACGGGGATGGACGACTACGCCCGGGAGATGATGGAGCTGAAGACGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtacttaccacttctttccttcatttccacatcccttcattgatccggtgcctcacccac-accccaggatctagcttttcccgccctcccgtttgg--
         |||||||||||||||||| ||||||||||||||||| |||||||||||||||||||||||||||||||||||||| ||||||||||| ||||| |  |    |||   || | ||||  |||  | | |   | ||  | |||   || || ||| ||    ||||||   | | || |||| || |  | |  
GGCGGAAGGGGGGATGGACGACTACGCGCGGGAGATGATGGAGCTCAAGACGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATCAGGgtacaaatcccccatccctcttcttctcttct-cttgctcacctttctgcgg-atctgactcactacttgcggatctcaatct-ccggcccgccggaattgct

upper sequence: GRMZM2G151268_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA20G38790.2 (Glycine max), 5'ss of exon 1
ATTTCGGACGGGGATGGACGACTACGCCCGGGAGATGATGGAGCTGAAGACGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtacttaccacttctttccttcatttccacatcccttcattgatccggtgcctcacccacaccccaggatctagcttttcccgccctcccgtttgg
 ||   ||  |  |||||||||||| |  |||| |||||||| |||||||| || ||||| ||||| ||||||||||| ||||| || |||| |||  | || ||||| ||||      || | |||     | |||| |||| |  |              |  |  |   || |   ||||    | |          
GTTCGAGAGAGAAATGGACGACTACACGAGGGAAATGATGGACCTGAAGACACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTTGCCAGGATCCGTgtgcgtacataccttagggtttcctcaccgt-agatccattcaattctttcaacttagggttattcttccatattttttttttttgtctcag--------

upper sequence: GRMZM2G151268_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA10G44070.2 (Glycine max), 5'ss of exon 1
ATTTCGGACGGGGATGGACGACTACGCCCGGGAGATGATGGAGCTGAAGACGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtacttaccacttctttccttcatttccacatcccttcattgatccggtgcctcacccacaccccaggatctagcttttcccgccctcccgtttgg-
       |  |  |||||||| ||| |  |||| |||||||| |||||||| || ||||| ||||| ||||||||||| ||||| ||||||| |||  | || | |||  |||      || | || |  | |   | |  | | |||||  |     |  | || |  ||| |    |||       | |   || |   
GAGAAACAGAGAAATGGACGATTACACGAGGGAAATGATGGACCTGAAGACACTGGTCACTCGCACTCTCGAGAAGAAAGGCGTCCTCGCCAGGATCCGTgtacatacacaccttagggtttcctcttcccaattcctcaccgtagatccatt---caattctcaacttagggttattcttccgttttctttttgtctcag

upper sequence: GRMZM2G151268_T02 (Zea mays), 5'ss of exon 1
lower sequence: Vv13s0067g03320.t01 (Vitis vinifera), 5'ss of exon 1
ATTTCGGACGGGGATGGACGACTACGCCCGGGAGATGATGGAGCTGAAGACGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtacttaccacttctttccttcatttccacatcccttcattgatccggtgcctcacccacaccccaggatctagcttttcccgccctcccgtttgg-------
|  |    | | ||||||||||||| | || ||||||||||| || ||||| || ||||| || ||||| |||||||| ||||| |||||||||||  ||||    | || ||  | ||||    |  ||   | | | ||   |    |  |  | |||||| | | | |  | | | ||   |     | |  |  |        
AGCTGTTGCAGAGATGGACGACTACACTCGAGAGATGATGGACCTCAAGACCCTTGTCACTCGAACCCTAGAGAAGAAAGGCGTCCTCGCCAAGATCCGGgt----attttcctttcctttttacctctttttccttcattttcttccgccttttcccacccagatctcggcgttttgttt---caaattttcaatacgagaaacga

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|22935937|gb|BU572212.1|BU572212
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGTGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211533622|gb|FL412539.1|FL412539
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGC-AAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|29945213|gb|CB815527.1|CB815527
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211305553|gb|FL417499.1|FL417499
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGC-AAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211029306|gb|FL370361.1|FL370361
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGC-AAGAT-ACG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211511056|gb|FL378831.1|FL378831
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGC-AAGATTAGG                         GCTGAGCTAAGAGCAAGTGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|32864387|gb|CF004069.1|CF004069
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211355840|gb|FL403701.1|FL403701
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCG-CAAGATTAGG                         GCTGAGCTAAGAGCAAGTGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211317656|gb|FL416767.1|FL416767
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCG-CAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211533628|gb|FL412545.1|FL412545
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|60399944|gb|DN232751.1|DN232751
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211156585|gb|FL395419.1|FL395419
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211036668|gb|FL370397.1|FL370397
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCG-CAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211191821|gb|FL384737.1|FL384737
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGC-AAGATTAGG                         GCTGAGCTAAGAGCAAGTGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211254949|gb|FL427088.1|FL427088
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGTGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|21432197|gb|BQ547687.1|BQ547687
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGTGTGTTTGAAGCCATTGAAGAGGTTTATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|9952754|gb|BE639217.1|BE639217
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211163025|gb|FL401335.1|FL401335
EST:     GCTCGTCACCCTGCACCCTCGAGAAGAAGGGCGTTCTCG-MAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: GCTCGTCACCC-GCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211403469|gb|FL414956.1|FL414956
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGC-AAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211076740|gb|FL399053.1|FL399053
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|67042990|gb|CO469245.1|CO469245
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211537120|gb|FL426924.1|FL426924
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGC-AAGATTAGG                         GCTGAGCTAAGAGCAAGTGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTCGGACGGGGATGGACGACTACGCCCGGGAGATGATGGAGCTGAAGACGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTTCTCGCCAAGATTAGGgttcgtacttaccacttctttccttcatttccacatcccttcattgatccggtgcctcacccacaccccaggatctagcttttcccgccctcccgtttgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG