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'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctggtccatgtaacatttttttgatatggtccatgtaacattttttcattacgtcttgtggttatttacagctgagttcattttgtgctgctctgcagGTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTGAATGTGTATGCGTGCTTGGTCTGTGGAAAATATTTCCAAGGAAGAGGGT

Basic information

species Zea mays
transcript GRMZM2G091151_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os09g24250.1 (Oryza sativa), 3'ss of exon 1
atctggtccatgtaacatttttttgatatggtccatgtaacattttttcatt--------acgtcttgtggttatttacagctgagttcattttgtgctgctctgcagGTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTGAATGTGTATGCGTGCTTGGTCTGTGGAAAATATTTCCAAGGAAGAGGGT
          | | ||| | || ||  |   |   ||    | | | |||||        |  ||   || | ||| |  | ||  |  ||||||| || |  || |||| |||||||||||||| ||||||||||| ||||||||||| ||||| ||||| |||||||| || ||||| |||||||| |||| |||||||||||| |
-------atgttttacactcttctggcagaatgtgtgctggactgtatcattgatgggctatttcacatgttcattgattgttgtatatattttgt-ctacattgtagGTCCTTGATTTTGATTTTGAGAAGTTCTGCTCAATCTCCTTATCAAACTTGAACGTGTATGCATGTTTGGTTTGTGGAAAGTATTACCAAGGAAGAGGCT

upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA10G08500.2 (Glycine max), 3'ss of exon 2
atctggtccatgtaacatttttttgatatggtccatgtaacattttttcattacgtcttgtggttatttacagctgagttcattttg----tgctgctctgcagGTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTGAATGTGTATGCGTGCTTGGTCTGTGGAAAATATTTCCAAGGAAGAGGGT
                   | |||||  |      ||   |||| ||        | |||  | | ||||  ||  | || ||||||    || |  | |||||||| | ||||| || || || || ||||||||  ||||| |||||||||| ||||||||||| || ||||| || || || |||| |||||| |||||| 
------------------gtatttgacttatcttgtg---cattgttgagaagaattttgctgctgtttat-gcatatttaattttgatgatgtttgtgtgcagGTTTTGGATTTCGACTTTGAAAAATTCTGTTCTGTCTCCCTGTCAAATTTAAATGTGTATGCATGTTTGGTTTGCGGGAAGTATTACCAAGGGAGAGGGA

upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA13G22190.1 (Glycine max), 3'ss of exon 2
atctggtccatgtaacatttttttgatatggtccatgtaacattttttcattacgtcttgtggttatttacagctgagttcattttgtgctgctctgcagGTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTGAATGTGTATGCGTGCTTGGTCTGTGGAAAATATTTCCAAGGAAGAGGGT
         || | || | | ||  | || ||  |   || | |||| | |    | || ||  ||||||    |||  | || |||||      |||||||| | |||||||| || || || ||||||||  ||||| | || ||||| ||||||||||| || ||||| ||||| || |||| |||||| |||||  
-------gtatttgacttatcttatacattgttga--gaataattttgc-tgcttttttatgcatatttaattttga--tgatgttgtg------tgcagGTTTTGGATTTTGACTTTGAAAAATTCTGTTCTGTCTCCCTCTCGAATTTAAATGTGTATGCATGTTTGGTTTGTGGGAAGTATTACCAAGGGAGAGGAA

upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT4G22285.1 (Arabidopsis thaliana), 3'ss of exon 2
-------atctggtccatgtaacatttttttgat----atggtccatgtaacattttttcattacgtcttgtggttatttacagctgagttcattttgt--gctgctctgcagGTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTGAATGTGTATGCGTGCTTGGTCTGTGGAAAATATTTCCAAGGAAGAGGGT
       || |  |   |||||  |||  |  ||    ||| | |   |  | |  ||  || |    || ||||  |    | || |  |||| ||||  | ||   | |||||  | ||||||||||| |||| ||| || ||  | |||||||||||| ||||||||||||||||  | || ||||| || || |||||||||||| |  
gtaattaatttcttgattgtaatctttgatcaatggttatgtttctgctgtcttcattgtataatcgtttttggtgttgagtatctaaactcatgttgtatgttgaatttcagGTGTTGGATTTTGATTTTGAGAGGTTTTGCTCTGTGTCCTTGTCAAATCTGAATGTGTATGCGTGTCTTGTTTGTGGGAAGTACTTCCAAGGAAGAAGCC

upper sequence: GRMZM2G091151_T01 (Zea mays), 3'ss of exon 1
lower sequence: AT4G22350.2 (Arabidopsis thaliana), 3'ss of exon 1
------------------------atctggtccatgtaacatttttttgatatggtccatgt--aacatttt------ttcattacgtcttgtggtt---atttacagctgagttcattttgtgctgct--ctgcagGTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTGAATGTGTATGCGTGCTTGGTCTGTGGAAAATATTTCCAAGGAAGAGGGT
                         | |||| | |||||  | | |    ||||||  || |  ||  || |      |||||||  |     | ||   |||  |   | |  |||| |  |   | |   | |||||  | |||||||||||||||| ||| || ||  |||| ||||||||| ||||||||||||||||  | || ||||| || || || ||||||||| |  
gtatatcattgaccaatttcttgtgtttggtacttgtaatgtatctaatctatggtggatctttaagcttctgctaggttcattatattgctggtttgagattagcgtttaaactcatatcttatggttgatttcagGTGTTGGATTTTGATTTCGAGAGGTTTTGCTCTGTCTCATTGTCAAATCTGAATGTGTATGCGTGTCTTGTTTGTGGGAAGTACTTTCAAGGAAGAAGCC

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|211066153|gb|FL067272.1|FL067272
EST:     AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAG                         GTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
genomic: AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAGgtgtgcactt ... tgctctgcagGTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
EST: gi|211068894|gb|FL067283.1|FL067283
EST:     AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAG                         GTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
genomic: AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAGgtgtgcactt ... tgctctgcagGTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
EST: gi|211066159|gb|FL067278.1|FL067278
EST:     AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAG                         GTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
genomic: AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAGgtgtgcactt ... tgctctgcagGTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
EST: gi|211068890|gb|FL067279.1|FL067279
EST:     AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAG                         GTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
genomic: AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAGgtgtgcactt ... tgctctgcagGTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
EST: gi|211068893|gb|FL067282.1|FL067282
EST:     AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAG                         GTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
genomic: AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAGgtgtgcactt ... tgctctgcagGTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
EST: gi|211066145|gb|FL067264.1|FL067264
EST:     AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAG                         GTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
genomic: AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAGgtgtgcactt ... tgctctgcagGTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
EST: gi|211066155|gb|FL067274.1|FL067274
EST:     AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAG                         GTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTACTTGTCAAATTTG
genomic: AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAGgtgtgcactt ... tgctctgcagGTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
EST: gi|211066152|gb|FL067271.1|FL067271
EST:     AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAG                         GTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
genomic: AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAGgtgtgcactt ... tgctctgcagGTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
EST: gi|19821939|gb|BQ047963.1|BQ047963
EST:     AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAG                         GTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGNCAAATTTG
genomic: AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAGgtgtgcactt ... tgctctgcagGTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
EST: gi|211066151|gb|FL067270.1|FL067270
EST:     AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGNGAACAGACAG                         GTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
genomic: AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAGgtgtgcactt ... tgctctgcagGTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
EST: gi|211066150|gb|FL067269.1|FL067269
EST:     AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAG                         GTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
genomic: AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAGgtgtgcactt ... tgctctgcagGTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
EST: gi|211066157|gb|FL067276.1|FL067276
EST:     AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAG                         GTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
genomic: AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAGgtgtgcactt ... tgctctgcagGTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
EST: gi|211066147|gb|FL067266.1|FL067266
EST:     AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAG                         GTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
genomic: AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAGgtgtgcactt ... tgctctgcagGTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
EST: gi|211066156|gb|FL067275.1|FL067275
EST:     AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAG                         GTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG
genomic: AGGTAGAGCTGCGCCGGGACTGCCCATACCTCGACACCGTGAACAGACAGgtgtgcactt ... tgctctgcagGTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcattacgtcttgtggttatttacagctgagttcattttgtgctgctctgcagGTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTGAATGTGTATGCGTGCTTGGTCTGTGGAAAATATTTCCAAGGAAGAGGGT
                                            ctgctct  CT-rich tract
                  ttatttaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctggtccatgtaacatttttttgatatggtccatgtaacattttttcattacgtcttgtggttatttacagctgagttcattttgtgctgctctgcagGTTCTTGATTTTGATTTCGAGAAGTTCTGTTCAATCTCCTTGTCAAATTTGAATGTGTATGCGTGCTTGGTCTGTGGAAAATATTTCCAAGGAAGAGGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - -gtccatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acagctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcattt