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'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAGGCCGAAGACCTTCGTCTAAAGGAGAAAAGGAGACGAGAACATGAGgtttgcaacatgcttatgaagtgatgtttggattatgtattgataatgtgcatgaggtttgtttatactgacattctcttatctttgttttacag

Basic information

species Zea mays
transcript GRMZM2G420865_T02
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G420865_T01 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os12g29660.1 (Oryza sativa), 5'ss of exon 16
GAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAGGCCGAAGACCTTCGTCTAAAGGAGAAAAGGAGACGAGAACATGAGgtttgcaacatgcttatgaa-gtgatgtttggattatgtattgataatgtgcatgaggtttgtttatactgacattct--cttatcttt-gttttacag
|||||   |  ||| ||||||||||  |||||||||||||| ||| || | || ||||| |||||||| |||||||||| |||| | || | ||||||       |||||||||||  || | |||| || |    ||| |||||  ||||||||||  ||    |||  || |   ||||||||   | |||||
GAATCCACGAGTCAAGGTAAGAGTAATTCTGGAGTTATTAGCGCTCAGCAAGCTGAAGATCTTCGTCTGAAGGAGAAAAAGAGAAGGGAGCGTGAGgt-------atgcttatgaacatgttatttgaatga---gttggtaatgcccatgaggttttctttagttgatgttttattttatcttttactctacag
















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|211343050|gb|FL472500.1|FL472500
EST:     AAAGGAGAAAAGGAGACGAGAACATGAG                         AAGAATCTACCAAGGAAGAAGCGCCGAAGATTGGAGGCCCAGCGTGAGATG
genomic: AAAGGAGAAAAGGAGACGAGAACATGAGgtttgcaaca ... tgttttacagAAGAATCTACCAAGGAAGAAGCGCCGAAGATTGGAGGCCCAGCGTGAGATG
EST: gi|78090028|gb|DV518402.1|DV518402
EST:     AGAAGGCCGAAGACCTTCGTTTAAAGGAGAAAAGGAGACGAGAACATGAG                         AAGAATTTACCAAGGAAGAAGCGCCGAAGATTGGAGGCCCAGCGTGAGATG
genomic: AGAAGGCCGAAGACCTTCGTCTAAAGGAGAAAAGGAGACGAGAACATGAGgtttgcaaca ... tgttttacagAAGAATCTACCAAGGAAGAAGCGCCGAAGATTGGAGGCCCAGCGTGAGATG
EST: gi|37373944|gb|CF623297.1|CF623297
EST:     AGAAGGCCGAAGACCTTCGTCTAAAGGAGAAAAGGAGACGAGAACATGAG                         AAGAATCTACCAAGGAAGAAGCGCCGAAGATTGGAGGCCCAGCGTGAGATG
genomic: AGAAGGCCGAAGACCTTCGTCTAAAGGAGAAAAGGAGACGAGAACATGAGgtttgcaaca ... tgttttacagAAGAATCTACCAAGGAAGAAGCGCCGAAGATTGGAGGCCCAGCGTGAGATG
EST: gi|60396007|gb|DN228877.1|DN228877
EST:     AGAAGGCCGAAGACCTTCGTCTAAAGGAGAAAAGGAGACGAGAACATGAG                         AAGAATCTACCAAGGAAGAAGCGCCGAAGATTGGAGGCCCAGCGTGAGATG
genomic: AGAAGGCCGAAGACCTTCGTCTAAAGGAGAAAAGGAGACGAGAACATGAGgtttgcaaca ... tgttttacagAAGAATCTACCAAGGAAGAAGCGCCGAAGATTGGAGGCCCAGCGTGAGATG
EST: gi|37398106|gb|CF636362.1|CF636362
EST:     AGAAGGCCGAAGACCTTCGTCTAAAGGAGAAAAGGAGACGAGAACATGAG                         AAGAATCTACCAAGGAAGAAGCGCCGAAGATTGGAGGCCCAGCGTGAGATG
genomic: AGAAGGCCGAAGACCTTCGTCTAAAGGAGAAAAGGAGACGAGAACATGAGgtttgcaaca ... tgttttacagAAGAATCTACCAAGGAAGAAGCGCCGAAGATTGGAGGCCCAGCGTGAGATG
EST: gi|40337352|gb|CK371422.1|CK371422
EST:     AGAAGGCCGAAGACCTTCGTCTAAAGGAGAAAAGGAGACGAGAACATGAG                         AAGAATCTACCAAGGAAGAAGCGCCGAAGATTGGAGGCCCAGCGTGAGATG
genomic: AGAAGGCCGAAGACCTTCGTCTAAAGGAGAAAAGGAGACGAGAACATGAGgtttgcaaca ... tgttttacagAAGAATCTACCAAGGAAGAAGCGCCGAAGATTGGAGGCCCAGCGTGAGATG
EST: gi|60344195|gb|DN211168.1|DN211168
EST:     AGAAGGCCGAAGACCTTCGTCTAAAGGAGAAAAGGAGACGAGAACATGAG                         AAGAATCTACCAAGGAAGAAGCGCCGAAGATTGGAGGCCCAGCGTGAGATG
genomic: AGAAGGCCGAAGACCTTCGTCTAAAGGAGAAAAGGAGACGAGAACATGAGgtttgcaaca ... tgttttacagAAGAATCTACCAAGGAAGAAGCGCCGAAGATTGGAGGCCCAGCGTGAGATG
EST: gi|60341880|gb|DN208853.1|DN208853
EST:     AGAAGGCCGAAGACCTTCGTCTAAAGGAGAAAAGGAGACGAGAACATGAG                         AAGAATCTACCAAGGAAGAAGCGCCGAAGATTGGAGGCCCAGCGTGAGATG
genomic: AGAAGGCCGAAGACCTTCGTCTAAAGGAGAAAAGGAGACGAGAACATGAGgtttgcaaca ... tgttttacagAAGAATCTACCAAGGAAGAAGCGCCGAAGATTGGAGGCCCAGCGTGAGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATCTTTGGATCACGGTAAGAGTACCTCTGGAGTTATTAGTGCTAAGAAGGCCGAAGACCTTCGTCTAAAGGAGAAAAGGAGACGAGAACATGAGgtttgcaacatgcttatgaagtgatgtttggattatgtattgataatgtgcatgaggtttgtttatactgacattctcttatctttgttttacag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA