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

gtgcctctgtagtttgaaactatatattccatgttctcctgttgaggcagaaatatttttttttatatattatactggttcattttttcctggctgcagCTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGATGAAGTTTCCATTATCAAAGTGCTTCCAAAAGAATTTTCTTGGAGCACA

Basic information

species Zea mays
transcript GRMZM2G057037_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057037_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os09g24570.1 (Oryza sativa), 3'ss of exon 5
gtgcctctgtagt-ttgaaactatatattccatgttctcctgttgaggcagaaatatttttttttatatattatactggttcattttttcctggctgcagCTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGATGAAGTTTCCATTATCAAAGTGCTTCCAAAAGAATTTTCTTGGAGCACA
|||| | || ||| | | | |  ||||||     ||  | | ||        | | ||   |||||  |||       ||| |  ||||  |   || ||||| |||||||||||||||||||||||||| ||||||||| || |||||| ||||||||| ||  ||||||| || |||||| ||||||| |||||||||
gtgcttttggagtctcggagcactatatttttaatttccattttcc------actgttgaattttaagtat------agtttacctttttgta-ttgtagCTCCTTTGAAGAAATTTTTGATGTGGATCATTTTATCAACACCTTAAAAGCTGAAGTTTCAATAGTCAAAGTTCTCCCAAAAAAATTTTCCTGGAGCACA
















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|211458005|gb|FL008444.1|FL008444
EST:     ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGAT-CAAG                         CTCATTTGAAGAAAT
genomic: ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAGgtgcctctgt ... ctggctgcagCTCATTTGAAGAAAT
EST: gi|71330647|gb|DR802098.1|DR802098
EST:     ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAG                         CTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGA
genomic: ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAGgtgcctctgt ... ctggctgcagCTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGA
EST: gi|71449457|gb|DR830507.1|DR830507
EST:     ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAG                         CTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGA
genomic: ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAGgtgcctctgt ... ctggctgcagCTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGA
EST: gi|148946102|gb|EC891397.2|EC891397
EST:     ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAG                         CTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGA
genomic: ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAGgtgcctctgt ... ctggctgcagCTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGA
EST: gi|148971509|gb|EE022208.2|EE022208
EST:     ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAG                         CTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGA
genomic: ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAGgtgcctctgt ... ctggctgcagCTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGA
EST: gi|76925903|gb|DV170641.1|DV170641
EST:     ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAG                         CTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGA
genomic: ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAGgtgcctctgt ... ctggctgcagCTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGA
EST: gi|31359449|gb|CD443806.1|CD443806
EST:     ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGGTTGGAAGGATTCAAG                         CTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGA
genomic: ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAGgtgcctctgt ... ctggctgcagCTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGA
EST: gi|211460521|gb|FL008449.1|FL008449
EST:     ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAG                         CTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGA
genomic: ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAGgtgcctctgt ... ctggctgcagCTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGA
EST: gi|76932287|gb|DV172995.1|DV172995
EST:     ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAG                         CTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGA
genomic: ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAGgtgcctctgt ... ctggctgcagCTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGA
EST: gi|71426736|gb|DR807786.1|DR807786
EST:     ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAG                         CTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGA
genomic: ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAGgtgcctctgt ... ctggctgcagCTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGA
EST: gi|51592502|gb|CV071648.1|CV071648
EST:     ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAG                         CTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGA
genomic: ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAGgtgcctctgt ... ctggctgcagCTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGA
EST: gi|149076222|gb|EE164820.2|EE164820
EST:     ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAG                         CTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGA
genomic: ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAGgtgcctctgt ... ctggctgcagCTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGA
EST: gi|74236036|gb|DT643950.1|DT643950
EST:     ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAG                         CTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCCTAAAAG
genomic: ACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAGgtgcctctgt ... ctggctgcagCTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCC-TAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggcagaaatatttttttttatatattatactggttcattttttcctggctgcagCTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGATGAAGTTTCCATTATCAAAGTGCTTCCAAAAGAATTTTCTTGGAGCACA
                                  ttcattttttcct  CT-rich tract
      aaatatttttttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcctctgtagtttgaaactatatattccatgttctcctgttgaggcagaaatatttttttttatatattatactggttcattttttcctggctgcagCTCATTTGAAGAAATTTTTGATGTGGATCACTTTATCAACTCCCTAAAAGATGAAGTTTCCATTATCAAAGTGCTTCCAAAAGAATTTTCTTGGAGCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA