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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatgccgctgctcaacagactttttgatggaagatctgcaatcatttttgtggattgcatttacactcttttttttttgcctttttgggatgcag

Basic information

species Zea mays
transcript GRMZM5G845755_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G845755_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 5'ss of exon 7
GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatgccgctgctcaacagactttttgatggaagatctgcaatcatttttgtggattgcatttacactcttttttttttgcctttttgggatgcag
|||||||| |||||  | ||||||   || |||||||||||| | |||||||||||||| ||||| |||||||| ||||||||||| | |      |   |  | |     |   ||| |||| ||  | |  ||  | || |||  | ||      |||||||||    |             
GTACTTGGGACAGACAGCCTGAATTCATACTTGAACAAGTACCGTATTGAGCTTGACCCACAGCTTGAAGCCCTCGTTGGAAGgtata-tgaattacaatt--atatgtgatgcaatgcaagacctctagtt-ttaatatgaattaaaattttgacatttttttttcatatgcag---------
















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|6465600|gb|AW191195.1|AW191195
EST:     -ACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|5846756|gb|AI999839.1|AI999839
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|32846294|gb|CD985975.1|CD985975
EST:     ACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: ACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|194717129|gb|FK934282.1|FK934282
EST:     GTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: GTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|29945847|gb|CB815850.1|CB815850
EST:     AGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|60350778|gb|DN217751.1|DN217751
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|94476026|gb|EB704984.1|EB704984
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|61117730|gb|DN558691.1|DN558691
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|60354727|gb|DN221700.1|DN221700
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|32849734|gb|CD989415.1|CD989415
EST:     ACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATACAGACAACCAACACCT
genomic: ACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|4609748|gb|AI600587.1|AI600587
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|61117733|gb|DN558694.1|DN558694
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|61117731|gb|DN558692.1|DN558692
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|113626902|gb|DW790797.1|DW790797
EST:     TTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: TTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|113860692|gb|DW979642.1|DW979642
EST:     CTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAAAGCAGACAACCAACACCT
genomic: CTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|61117732|gb|DN558693.1|DN558693
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT
EST: gi|148990947|gb|EE032376.2|EE032376
EST:     AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAG                         GCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACCCCT
genomic: AACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatg ... tgggatgcagGCATAGCAGGAAACCCTGGACAAAGTTTATTAATGCAGACAACCAACACCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACTTGGAACAGATGGGCTGAATGTCTATTTGAACAAGTACAGAATTGAGCTTGACCCTCAGCTCGAAGCCCTTGTTGGAAGgtaaagtatgccgctgctcaacagactttttgatggaagatctgcaatcatttttgtggattgcatttacactcttttttttttgcctttttgggatgcag

- - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG