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'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcacaccatctaccagttgaaatgcagtgagagcactttgtgagttgtataccaatgtttctcacgcttcacttagcatgtgatactgtttatgctcagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTACAAAATGCGTTGGACAACAATAAT

Basic information

species Zea mays
transcript GRMZM2G113873_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G113873_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g25940.2 (Oryza sativa), 3'ss of exon 4
-atcacaccatctaccagttgaa-atgcagtgagagcactttgtgagttgtataccaatgtttctcacgcttcacttagcatgtgatactgttt-atgctcagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTACAAAATGCGTTGGACAACAATAAT
 |  ||    | |   |  ||   |||   |  |  |  |||||   || || |  |||||||   |    |  |||| | | ||| ||  |||  ||  |||||||| || ||||| |||||||||||||||||||| ||||||||  |||| || ||||||
gaatacggtgtttggaatatgcctatgatctttgttccatttgt---ttatacataaatgtttacaatttgttgcttatcttatgacacaattttgtgtccagATGACCGTTATTAGACCTGCTGACATGGATGCTCTCCAAAATGCACTGGATAATAATAAT
















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|149076129|gb|EE164714.2|EE164714
EST:     GGAAAACAAGGATTTACATGGAAACTGAGCTCCCCAAGAGGGGAATTTCG                         ATGACTGTCATTAGGCCTGCTGACATGGATGCTCTACAAAATGCGTTGGAC
genomic: GGAAAACAAGGATTTACATGGAAACTGAGCTCCCCAAGAGGGGAATTTCGgtaataccat ... ttatgctcagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTACAAAATGCGTTGGAC
EST: gi|148936104|gb|EC880167.2|EC880167
EST:     GGAAAACAAGGATTTACATGGAAACTGAGCTCCCCAAGAGGGGAATTTCG                         ATGACTGTCATTAGGCCTGCTGACATGGATGCTCTACAAAATGCGTTGGAC
genomic: GGAAAACAAGGATTTACATGGAAACTGAGCTCCCCAAGAGGGGAATTTCGgtaataccat ... ttatgctcagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTACAAAATGCGTTGGAC
EST: gi|149102766|gb|EE288113.2|EE288113
EST:     GGAAAACAAGGATTTACATGGAAACTGAGCTCCCCAAGAGGGGAATTTCG                         ATGACTGTCATTAGGCCTGCTGACATGGATGCTCTACAAAATGCGTTGGAC
genomic: GGAAAACAAGGATTTACATGGAAACTGAGCTCCCCAAGAGGGGAATTTCGgtaataccat ... ttatgctcagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTACAAAATGCGTTGGAC
EST: gi|78110794|gb|DV529192.1|DV529192
EST:     GGAAAACAAGGATTTACATGGAAACTGAGCTCCCCAAGAGGGGAATTTCG                         ATGACTGTCATTAGGCCTGCTGACATGGATGCTCTACAAAATGCGTTGGAC
genomic: GGAAAACAAGGATTTACATGGAAACTGAGCTCCCCAAGAGGGGAATTTCGgtaataccat ... ttatgctcagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTACAAAATGCGTTGGAC
EST: gi|78086437|gb|DV514830.1|DV514830
EST:     GGAAAACAAGGATTTACATGGAAACTGAGCTCCCCAAGAGGGGAATTTCG                         ATGACTGTCATTAGGCCTGCTGACATGGATGCTCTACAAAATGCGTTGGAC
genomic: GGAAAACAAGGATTTACATGGAAACTGAGCTCCCCAAGAGGGGAATTTCGgtaataccat ... ttatgctcagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTACAAAATGCGTTGGAC
EST: gi|76010979|gb|DT938149.1|DT938149
EST:     GGAAAACAAGGATTTACATGGAAACTGAGCTCCCCAAGAGGGGAATTTCG                         ATGACTGTCATTAGGCCTGCTGACATGGATGCTCTACAAAATGCGTTGGAC
genomic: GGAAAACAAGGATTTACATGGAAACTGAGCTCCCCAAGAGGGGAATTTCGgtaataccat ... ttatgctcagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTACAAAATGCGTTGGAC
EST: gi|149030074|gb|EE286293.2|EE286293
EST:     GGAAAACAAGGATTTACATGGAAACTGAGCTCCCCAAGAGGGGAATTTCG                         ATGACTGTCATTANGCCTGCTGACATGGATGCTCTACAAAATGCGTTGGAC
genomic: GGAAAACAAGGATTTACATGGAAACTGAGCTCCCCAAGAGGGGAATTTCGgtaataccat ... ttatgctcagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTACAAAATGCGTTGGAC
EST: gi|29130696|gb|CB381400.1|CB381400
EST:     GGAAAACAAGGATTTACATGGAAACTGAGCTCCCCAAGAGGGGAATTTCG                         ATGACTGTCATTAGGCCTGCTGACATGGATGCTCTACAAAATGCGTTGGAC
genomic: GGAAAACAAGGATTTACATGGAAACTGAGCTCCCCAAGAGGGGAATTTCGgtaataccat ... ttatgctcagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTACAAAATGCGTTGGAC
EST: gi|93013670|gb|EB639190.1|EB639190
EST:     GGAAAACAAGGATTTACATGGAAACTGAGCTCCCCAAGAGGGGAATTTCG                         ATGACTGTCATTAGGCCTGCTGACATGGATGCTCT
genomic: GGAAAACAAGGATTTACATGGAAACTGAGCTCCCCAAGAGGGGAATTTCGgtaataccat ... ttatgctcagATGACTGTCATTAGGCCTGCTGACATGGATGCTCT
EST: gi|101401317|gb|EB822336.1|EB822336
EST:     GGAAAACAAGGATTTACATGGAAACTGAGCTCCCCAAGAGGGGAATTTCG                         ATGACTGTCATTAGGCCTGCTGACATGGATGCTCTACAAAATGCGTTGGAC
genomic: GGAAAACAAGGATTTACATGGAAACTGAGCTCCCCAAGAGGGGAATTTCGgtaataccat ... ttatgctcagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTACAAAATGCGTTGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtataccaatgtttctcacgcttcacttagcatgtgatactgtttatgctcagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTACAAAATGCGTTGGACAACAATAAT
              ttctcac  putative branch site (score: 2)
         aatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcacaccatctaccagttgaaatgcagtgagagcactttgtgagttgtataccaatgtttctcacgcttcacttagcatgtgatactgtttatgctcagATGACTGTCATTAGGCCTGCTGACATGGATGCTCTACAAAATGCGTTGGACAACAATAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA