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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGTAACACGAGAATGGACACTTGAGGGAGGTGCACTAGTTCTTGCTGATAGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatataccatttgtatttggatgtcctgtgctatttaaatttctgtattaccaaaaatgtaattttcttctgattgtttcag

Basic information

species Zea mays
transcript GRMZM2G139894_T02
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G139894_T02 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os11g29380.1 (Oryza sativa), 5'ss of exon 11
CAGTAACACGAGAATGGACACTTGAGGGAGGTGCACTAGTTCTTGCTGATAGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatataccatttgtatttggatgtcctgtgctatttaa-atttctgtattaccaaaa-atgtaattttcttctgattgtttcag
|||||||||| ||||||||||||||||| ||||||||||| ||||||||||| ||||| ||||| |||||||| ||||| |||||||| |||||||||||||||| | ||  |     ||||||||    |||||| || |  |||| |||  ||       | |  || ||  ||| ||||||||||
CAGTAACACGGGAATGGACACTTGAGGGTGGTGCACTAGTGCTTGCTGATAGAGGCATATGCCTTATTGATGAATTTGATAAGATGAACGATCAAGATAGgtatg-tgtaatacc---atttggataatgtgtgcttttaagcatttatgttctattgccctaagatatctttctcttattgtttcag

upper sequence: GRMZM2G139894_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA17G03920.1 (Glycine max), 5'ss of exon 10
CAGTAACACGAGAATGGACACTTGAGGGAGGTGCACTAGTTCTTGCTGATAGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatataccat-ttgtatttggatgtcctgtgctatttaaatttctgtattac-caaaaatgtaattttcttctgattgtttcag---------------------------
|||| ||| | || ||||| ||||| || || ||||| ||||| ||||| |  || ||||| || ||||||||||||||||||||||||||||| |||||||| || |  | || ||||| ||   ||   | | ||| ||| |||  |  | ||| |    |  | || | |     | | |    |                           
CAGTCACAAGGGAGTGGACTCTTGAAGGGGGAGCACTTGTTCTAGCTGACAAAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGATCAGGATAGgtaagaaaatcaatcttgtaattatttgaattttcctaattacattgttaaactacaccttcacatgatatacaaa-aactatccttgaccattaatttatatttttgttaccag

upper sequence: GRMZM2G139894_T02 (Zea mays), 5'ss of exon 11
lower sequence: GLYMA07G36680.1 (Glycine max), 5'ss of exon 10
CAGTAACACGAGAATGGACACTTGAGGGAGGTGCACTAGTTCTTGCTGATAGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatataccat-ttgtatttggatgtcctgtgctatttaaatttctgtatt--accaaaaatgtaattttcttctgattgtttcag
|||| ||| | || ||||| ||||| || || || || ||||| ||||| || || ||||| || |||||||||||||||||||||||||| || |||||||| || |    |  |||||  |   ||   | |  || ||| |||  | |  |  | ||  ||| ||  ||| |  |  |  |  |||
CAGTCACAAGGGAGTGGACTCTTGAAGGGGGGGCGCTTGTTCTAGCTGACAGAGGAATTTGTCTTATTGATGAGTTTGACAAGATGAATGACCAGGATAGgtaagaaaattgaccttgtaaatccttgagttttcttaattacattattatccttgatcattaatttatatttatatttttgttaccag

upper sequence: GRMZM2G139894_T02 (Zea mays), 5'ss of exon 11
lower sequence: Vv01s0150g00390.t01 (Vitis vinifera), 5'ss of exon 10
CAGTAACACGAGAATGGACACTTGAGGGAGGTGCACTAGTTCTTGCTGATAGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatg---atatac-catttgtatttggatg-tcctgtgctatttaaatttctgtattac-caaaaatgtaattttcttctgattgtttcag
| || ||||| |||||||||||||| ||||| || || ||||| || ||||  || || || || |||||||||||||||||||||||||||||||| ||||| |   || ||      | ||||| | |  | |  | |  |  |||  | ||||| |    || | | || ||| |      | ||    
CTGTCACACGCGAATGGACACTTGAAGGAGGGGCTCTTGTTCTAGCAGATAAAGGAATCTGTCTAATTGATGAGTTTGACAAGATGAATGATCAAGACAGgtaaggaaatgtatgtgcgtatattttggtacttcaatcccttgcaaaaatttgtatcatgtgaacaagaaagtttatatcctctattag--

upper sequence: GRMZM2G139894_T02 (Zea mays), 5'ss of exon 11
lower sequence: PP1S28_266V6.1 (Physcomitrella patens), 5'ss of exon 10
CAGTAACACGAGAATGGACACTTGAGGGAGGTGCACTAGTTCTTGCTGATAGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtat--------------gatataccatttgtatttggatgtcctgtgctatttaaatttctgtattaccaaaaat--gtaattttcttctgattgtttcag------------------------------------------
| |||||| | || |||||  | || |||||||| || || || |||||  | || || || || ||||||||||| ||||||||||| |||||||| ||||                |||  |   ||  ||      |||  |    |  || ||  |||  ||| ||||   |  | ||    || ||   |||                                               
CTGTAACAAGGGAGTGGACTTTGGAAGGAGGTGCCCTTGTACTAGCTGACCGTGGTATATGTCTTATTGATGAGTTCGACAAGATGAACGATCAAGACAGgtgcagtccctttctggagatgcatttttcataaccatttgta-tacagttcttgaaactctcaattgccaagccttagaaaaacgctccttgatgtgctgctatttcatctgaagactttgtgtgaaattcgattttgtttag

upper sequence: GRMZM2G139894_T02 (Zea mays), 5'ss of exon 11
lower sequence: EFJ31227 (Selaginella moellendorffii), 5'ss of exon 7
CAGTAACACGAGAATGGACACTTGAGGGAGGTGCACTAGTTCTTGCTGATAGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatataccatttgtatttggatgtcctgtgctatttaaatttctgtattaccaaaaatgtaattttcttctgattgtttcag
| ||||| || || |||||| | || || || ||  | ||  | || ||| | || || ||||||||||||||||||||||| |||||||| ||||| ||||||  || ||     |  ||   ||||| |   |      | ||| |                                      
CTGTAACTCGCGAGTGGACATTAGAAGGCGGCGCCTTGGTCTTGGCCGATCGTGGAATCTGCCTCATTGATGAGTTTGACAAAATGAATGACCAAGACAGgtattttaaac-gcagggcttacaatgtcttactcgggagtattttttcag-----------------------------------

upper sequence: GRMZM2G139894_T02 (Zea mays), 5'ss of exon 11
lower sequence: EFJ17122 (Selaginella moellendorffii), 5'ss of exon 9
CAGTAACACGAGAATGGACACTTGAGGGAGGTGCACTAGTTCTTGCTGATAGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatataccatttgtatttggatgtcctgtgctatttaaatttctgtattaccaaaaatgtaattttcttctgattgtttcag
| ||||| || || |||||| | || || || ||  | ||  | || ||| | || || ||||||||||||||||||||||| |||||||| ||||| ||||||  || ||     |  ||    |||| |   |      | ||| |                                      
CTGTAACTCGCGAGTGGACATTAGAAGGCGGCGCCTTGGTCTTGGCCGATCGTGGAATCTGCCTCATTGATGAGTTTGACAAAATGAATGACCAAGACAGgtattttaaac-gcagggcttacattgtcttactcgggagtattttttcag-----------------------------------

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|211351173|gb|FL066633.1|FL066633
EST:     AGGGGCATTTGCCTCATTGACGAGTTTGACMAGATGAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAAAGTATCAGTATATCAAAAGC
genomic: AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
EST: gi|211174125|gb|FL130962.1|FL130962
EST:     AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
genomic: AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
EST: gi|32932509|gb|CF037321.1|CF037321
EST:     AGGGGCATTTGCCTCATTGACGAGTTTGACAAGATGAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
genomic: AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
EST: gi|211172448|gb|FL130949.1|FL130949
EST:     AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
genomic: AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
EST: gi|211174123|gb|FL130960.1|FL130960
EST:     AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
genomic: AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
EST: gi|211174124|gb|FL130961.1|FL130961
EST:     AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
genomic: AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
EST: gi|211172450|gb|FL130951.1|FL130951
EST:     AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
genomic: AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
EST: gi|32943927|gb|CF048746.1|CF048746
EST:     GAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
genomic: GAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
EST: gi|30306555|gb|CD001228.1|CD001228
EST:     AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
genomic: AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
EST: gi|29544563|gb|CB604943.1|CB604943
EST:     AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
genomic: AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
EST: gi|211174122|gb|FL130959.1|FL130959
EST:     AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
genomic: AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
EST: gi|29544433|gb|CB604813.1|CB604813
EST:     AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAG                         GGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC
genomic: AGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatata ... attgtttcagGGTAAGTATTCATGAAGCTATGGAGCAACAGAGTATCAGTATATCAAAAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGTAACACGAGAATGGACACTTGAGGGAGGTGCACTAGTTCTTGCTGATAGGGGCATTTGCCTCATTGATGAGTTTGACAAGATGAATGATCAAGATAGgtatgatataccatttgtatttggatgtcctgtgctatttaaatttctgtattaccaaaaatgtaattttcttctgattgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG