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

GGATGCTTCCGACAAAATTTGACGGTTGTAACAATATATGCATCTCTTGGTGAGGATGCATTGGTGCATTCACTAAACGAGgtactgtgaatttggtgtactgttatacaatttttttgaaggggtcatcttctcttggactctatccagctgaaaactattctgtatgcaattacatgtc...

Basic information

species Zea mays
transcript GRMZM2G079236_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G079236_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g25310.2 (Oryza sativa), 5'ss of exon 3
GGATGCTTCCGACAAAATTTGACGGTTGTAACAATATATGCATCTCTTGGTGAGGATGCATTGGTGCATTCACTAAACGAGgtactgtgaatttggtgtactgttatacaatttttttgaaggggtcatcttctcttggactctatccagctga-aaactattctgta--tgcaattacatgtc-------
|||||||| ||||||||| | || |||||||| || |||||||||||||| ||||||||| ||||||||||||| || |||||||     || ||  |   | || | || | ||| ||         |    ||||  | | ||||||  ||  |||||| |   |   | |  || | | |        
GGATGCTTTCGACAAAATCTAACAGTTGTAACTATCTATGCATCTCTTGGCGAGGATGCACTGGTGCATTCACTGAATGAGgtacaacccatatgtggcttttttgtgcagtatttatg---------ttcattcttataat-tatccacttgggaaactagtacattcctaccgtttcttttttttcttt
















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|211182985|gb|FL309802.1|FL309802
EST:     CAATATATGCATCTCTTGGTGAGGATGCATTGGTGCATTCACTAAACGAG                         ACACAGGTTTCAACTCTGATATGTGATTCGAAGCAACTTAAGAAAATACCT
genomic: CAATATATGCATCTCTTGGTGAGGATGCATTGGTGCATTCACTAAACGAGgtactgtgaa ... tgaatttcagACACAGGTTTCAACTCTGATATGTGATTCGAAGCAACTTAAGAAAATACCT
EST: gi|211296212|gb|FL366279.1|FL366279
EST:     CAATATATGCATCTCTTGGTGAGGATGCATTGGTGCATTCACTAAACGAG                         ACACAGGTTTCAACTCTGATATGTGATTCGAAGCAACTTAAGAAAATACCT
genomic: CAATATATGCATCTCTTGGTGAGGATGCATTGGTGCATTCACTAAACGAGgtactgtgaa ... tgaatttcagACACAGGTTTCAACTCTGATATGTGATTCGAAGCAACTTAAGAAAATACCT
EST: gi|211295628|gb|FL337561.1|FL337561
EST:     CAATATATGCATCTCTTGGTGAGGATGCATTGGTGCATTCACTAAACGAG                         ACACAGGTTTCAACTCTGATATGTGATTCGAAGCAACTTAAGAAAATACCT
genomic: CAATATATGCATCTCTTGGTGAGGATGCATTGGTGCATTCACTAAACGAGgtactgtgaa ... tgaatttcagACACAGGTTTCAACTCTGATATGTGATTCGAAGCAACTTAAGAAAATACCT
EST: gi|211388360|gb|FL321726.1|FL321726
EST:     CAATATATGCATCTCTTGGTGAGGATGCATTGGTGCATTCACTAAACGAG                         ACACAGGTTTCAACTCTGATATGTGATTCGAAGCAACTTAAGAAAATACCT
genomic: CAATATATGCATCTCTTGGTGAGGATGCATTGGTGCATTCACTAAACGAGgtactgtgaa ... tgaatttcagACACAGGTTTCAACTCTGATATGTGATTCGAAGCAACTTAAGAAAATACCT
EST: gi|211059386|gb|FL366070.1|FL366070
EST:     CAATATATGCATCTCTTGGTGAGGATGCATTGGTGCATTCACTAAACGAG                         ACACAGGTTTCAACTCTGATATGTGATTCGAAGCAA
genomic: CAATATATGCATCTCTTGGTGAGGATGCATTGGTGCATTCACTAAACGAGgtactgtgaa ... tgaatttcagACACAGGTTTCAACTCTGATATGTGATTCGAAGCAA
EST: gi|211393326|gb|FL307372.1|FL307372
EST:     CAATATATGCATCTCTTGGTGAGGATGCATTGGTGCATTCACTAAACGAG                         ACACAGGTTTCAACTCTGATATGTGAATCGAAGCAACTTAAGAAAATACCT
genomic: CAATATATGCATCTCTTGGTGAGGATGCATTGGTGCATTCACTAAACGAGgtactgtgaa ... tgaatttcagACACAGGTTTCAACTCTGATATGTGATTCGAAGCAACTTAAGAAAATACCT
EST: gi|211067248|gb|FL339519.1|FL339519
EST:     CAATATATGCATCTCTTGGTGAGGATGCATTGGTGCATTCACTAAACGAG                         ACACAGGTTTCAACTCTGATATGTGATTCGAAGCAACTTAAGAAAATACCT
genomic: CAATATATGCATCTCTTGGTGAGGATGCATTGGTGCATTCACTAAACGAGgtactgtgaa ... tgaatttcagACACAGGTTTCAACTCTGATATGTGATTCGAAGCAACTTAAGAAAATACCT
EST: gi|211043811|gb|FL339055.1|FL339055
EST:     CAATATATGCATCTCTTGGTGAGGATGCATTGGTGCATTCACTAAACGAG                         ACACAGGTTTCAACTCTGATATGTGATTCGAAGCAACTTAAGAAAATACCT
genomic: CAATATATGCATCTCTTGGTGAGGATGCATTGGTGCATTCACTAAACGAGgtactgtgaa ... tgaatttcagACACAGGTTTCAACTCTGATATGTGATTCGAAGCAACTTAAGAAAATACCT
EST: gi|211234600|gb|FL315445.1|FL315445
EST:     CAATATATGCATCTCTTGGTGAGGATGCATTGGTGCATTCACTAAACGAG                         ACACAGGTTTCAACTCTGATATGTGATTCGAAGCAACTTAAGAAAATACCT
genomic: CAATATATGCATCTCTTGGTGAGGATGCATTGGTGCATTCACTAAACGAGgtactgtgaa ... tgaatttcagACACAGGTTTCAACTCTGATATGTGATTCGAAGCAACTTAAGAAAATACCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGCTTCCGACAAAATTTGACGGTTGTAACAATATATGCATCTCTTGGTGAGGATGCATTGGTGCATTCACTAAACGAGgtactgtgaatttggtgtactgttatacaatttttttgaaggggtcatcttctcttggactctatccagctgaaaactattctgtatgcaattacatgtc

- - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG