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'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACTTGACTGTGCAGTTCGTTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGAgtacgttagtttgttctattcccttcctcttgaacaatgatttgatgattatagcaactgggttttgtatggaatcttgtcattttcgtctgtactagtatggagttggacatgttttaccttatttgctaaagtatttctcttttgtgatttttttaatttacag

Basic information

species Zea mays
transcript GRMZM2G017086_T01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017086_T03 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 5'ss of exon 12
GTACTTGACTGTGCAGTTCGTTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGAgtacgttagtttgttctattcccttcctcttgaacaatgatttgatgattatagcaactgggttttgtatggaatcttgtcattttcgtctgtactagtatggagttggacatgttttaccttatttgctaaagtatttctcttttgtgatttttttaatttacag
|||||||||||||||||| ||||| |||||||||||||||||||||||||| ||||||||||||||||| ||| |||  ||| |    |      | |  |   |  || |   |  | ||||| |      ||||       | ||   | | ||       |||  |  | |                                                              
GTACTTGACTGTGCAGTTTGTTCGTTTCTTTTGGAAAAGGGAATCAAACCAGAAGGCAAAGATTTTACGGgtatgtttatttctcgagtaaaaaacatactcc-ctttggt---aaaactatagaacaacacttttaagcaagaactacacttctttacagtaacttttgagaa--------------------------------------------------------------

upper sequence: GRMZM2G017086_T03 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA07G01480.1 (Glycine max), 5'ss of exon 12
GTACTTGACTGTGCAGTTCGTTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGAgta-----cgttagtttgttctattcccttcctcttgaacaatgatttgatgattatagcaactgggttttgtatggaatcttgtcattttcg---tctgtactagtatggagttggacatgttttaccttatttgctaaagtatttctcttttgtgatttttttaatttacag
|||||||||||| ||||| || || ||||||||||| |||||||| ||||| ||||| |||||||| || |||     |  ||  |  || | |     |  | ||| | | | ||| | ||| |    ||| |     ||| | | | |  | |  |||  |   | | |  ||  |||   | |  | || || | || |                                          
GTACTTGACTGTTCAGTTTGTCCGTTTCTTTTGGAAGAGGGAATCCAACCAGAAGGCTAAGATTTTGCGGgtaaagctcactatctgcttttttgtgtgtgtttttggatagttatt-gttgagtcggacaaattatccttggaagaatttgtttgctttctgaaatttattttacaatgtcatcgtgcttggtt-atctcag-----------------------------------------

upper sequence: GRMZM2G017086_T03 (Zea mays), 5'ss of exon 12
lower sequence: GLYMA08G20900.1 (Glycine max), 5'ss of exon 12
GTACTTGACTGTGCAGTTCGTTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGAgtacg--tta--gtttgttctattcccttcctcttgaacaatgatttgatgattatagcaactgggttttgtatggaatcttgtcattttc--gtctgtactagtatggagttggacatgttttaccttatttgctaaagtatttctcttttgtgatttttttaatttacag
|||||||||||| ||||| || || ||||||||||| |||||||| ||||||||||| |||||||| || |||    | |  || | || | |     |  | ||| | | | |||    | ||  |  || |    || | | |   | ||  | || |   || | |   |  |||   | |  | || || | || |                                          
GTACTTGACTGTTCAGTTTGTCCGTTTCTTTTGGAAGAGGGAATCCAACCAAAAGGCTAAGATTTTGCGGgtagagctcactgtcttttttgtgtgtgtgtttttggatagttattgttgggttggacaaattatccttggaaagttttgtttgctttctaaagtttatttgacaatgtcatcgtgcttggtt-atctcag-----------------------------------------

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|33093217|gb|CF053211.1|CF053211
EST:     TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA                         AAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
genomic: TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGAgtacgttagt ... taatttacagAAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
EST: gi|5932702|gb|AW057063.1|AW057063
EST:     TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA                         AAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
genomic: TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGAgtacgttagt ... taatttacagAAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
EST: gi|32866635|gb|CF006317.1|CF006317
EST:     TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA                         AAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
genomic: TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGAgtacgttagt ... taatttacagAAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
EST: gi|32930058|gb|CF034870.1|CF034870
EST:     TTCGCTTC-TTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA                         AAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
genomic: TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGAgtacgttagt ... taatttacagAAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
EST: gi|33094822|gb|CF054816.1|CF054816
EST:     TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA                         AAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
genomic: TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGAgtacgttagt ... taatttacagAAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
EST: gi|6056638|gb|AW091043.1|AW091043
EST:     TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA                         AAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
genomic: TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGAgtacgttagt ... taatttacagAAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
EST: gi|5846961|gb|AW000040.1|AW000040
EST:     TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA                         AAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
genomic: TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGAgtacgttagt ... taatttacagAAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
EST: gi|12968043|gb|BG264990.1|BG264990
EST:     TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA                         AAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
genomic: TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGAgtacgttagt ... taatttacagAAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
EST: gi|32942933|gb|CF047752.1|CF047752
EST:     TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA                         AAAGTTGATTACCCACTGGTTTTTGATGTTTATGAATTTTGCTCTGATGAA
genomic: TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGAgtacgttagt ... taatttacagAAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
EST: gi|5901176|gb|AW042276.1|AW042276
EST:     TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA                         AAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
genomic: TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGAgtacgttagt ... taatttacagAAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
EST: gi|32933054|gb|CF037866.1|CF037866
EST:     TTCGCTTC-TTTGNAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA                         AAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
genomic: TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGAgtacgttagt ... taatttacagAAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
EST: gi|5296339|gb|AI783109.1|AI783109
EST:     TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA                         AAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
genomic: TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGAgtacgttagt ... taatttacagAAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
EST: gi|32934559|gb|CF039371.1|CF039371
EST:     TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA                         AAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
genomic: TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGAgtacgttagt ... taatttacagAAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
EST: gi|60352250|gb|DN219223.1|DN219223
EST:     AAAGATTTTACGA                         AAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
genomic: AAAGATTTTACGAgtacgttagt ... taatttacagAAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
EST: gi|32932375|gb|CF037187.1|CF037187
EST:     TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA                         AAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
genomic: TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGAgtacgttagt ... taatttacagAAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
EST: gi|32930666|gb|CF035478.1|CF035478
EST:     TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA                         AAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
genomic: TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGAgtacgttagt ... taatttacagAAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
EST: gi|74240014|gb|DT647928.1|DT647928
EST:     TCAAACCAAAAGGGCAAAGATTTTACGA                         AAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
genomic: TCAAACCAAAA-GGCAAAGATTTTACGAgtacgttagt ... taatttacagAAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA
EST: gi|33093538|gb|CF053532.1|CF053532
EST:     TTCGC-TCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGA                         AAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTNTGCTCTGATGAA
genomic: TTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGAgtacgttagt ... taatttacagAAAGTTGATTACCCACTGGAATTGGATGTTTATGAATTTTGCTCTGATGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACTTGACTGTGCAGTTCGTTCGCTTCTTTTGGAAAAGGGAATCAAACCAAAAGGCAAAGATTTTACGAgtacgttagtttgttctattcccttcctcttgaacaatgatttgatgattatagcaactgggttttgtatggaatcttgtcattttcgtctgtactagtatggagttggacatgttttaccttatttgctaaagtatttctcttttgtgatttttttaatttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG