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'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCAGGGGTCAGGTCTCATTATTTGATTGGTCCAGGTCAACATCACTAGCTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAAgtaactaacttgacctgttgcctttttgacctataatttgaagatgcatatttgtttacttctctaaaaatgtactgttcaatattagttatgtgcatta...

Basic information

species Zea mays
transcript GRMZM5G825854_T02
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825854_T01 (Zea mays), 5'ss of exon 21
lower sequence: LOC_Os08g34970.1 (Oryza sativa), 5'ss of exon 21
TCTCAGGGGTCAGGTCTCATTATTTGATTGGTCCAGGTCAACATCACTAGCTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAAgtaactaacttgacctgttgcctttttgacctataatttgaagatgcatatttgtttacttctctaaaaatgtactgttcaata-ttagttatgtgcatta-
 |||||||| |||||||| |||||||||||||| |||||||||||||| |||||||| |||||||| |||||| ||||||||||||||||||||||||||||||| | ||||| ||| |  ||  | |   | |  |||     |  |  |      |  | | ||    |  | |  ||| || ||  |    |  |||  
CCTCAGGGGGCAGGTCTCGTTATTTGATTGGTCAAGGTCAACATCACTTGCTAGGACGTTTTCTCCCCGTGTTCTGGAGAACCAAATTGATGCCAGAAAAgtaaccatcttgaactgatagctgatagttatttctttttggcctaaaagtaaaaaaaaatgtttatg--ttaatttctcattagttgatctcataaattca
















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|37383203|gb|CF628592.1|CF628592
EST:     CTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAA                         GAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
genomic: CTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAAgtaactaact ... tctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
EST: gi|32832225|gb|CD971903.1|CD971903
EST:     CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAA                         GAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
genomic: CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAAgtaactaact ... tctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
EST: gi|86468964|gb|DY235334.1|DY235334
EST:     CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAA                         GAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
genomic: CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAAgtaactaact ... tctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
EST: gi|93281266|gb|EB673530.1|EB673530
EST:     AACCAAATTGATGCCAGAAAA                         GAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
genomic: AACCAAATTGATGCCAGAAAAgtaactaact ... tctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
EST: gi|60348401|gb|DN215374.1|DN215374
EST:     CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAA                         GAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
genomic: CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAAgtaactaact ... tctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
EST: gi|32929996|gb|CF034808.1|CF034808
EST:     CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAA                         GAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
genomic: CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAAgtaactaact ... tctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
EST: gi|6102001|gb|AW126471.1|AW126471
EST:     CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAA                         GAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
genomic: CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAAgtaactaact ... tctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
EST: gi|32931787|gb|CF036599.1|CF036599
EST:     CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAA                         GAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCTATA
genomic: CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAAgtaactaact ... tctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
EST: gi|60348441|gb|DN215414.1|DN215414
EST:     CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAA                         GAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
genomic: CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAAgtaactaact ... tctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
EST: gi|60341619|gb|DN208592.1|DN208592
EST:     CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAA                         GAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
genomic: CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAAgtaactaact ... tctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
EST: gi|149104240|gb|EE289676.2|EE289676
EST:     CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAA                         GAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA
genomic: CTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAAgtaactaact ... tctatttcagGAGTTGGAGAAAAGCCTTAAAGCTACCTGTGAAGAGTTTATAATGTCCATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTCAGGGGTCAGGTCTCATTATTTGATTGGTCCAGGTCAACATCACTAGCTAGGACCTTTTCTCCTCGTGTTTTGGAGAACCAAATTGATGCCAGAAAAgtaactaacttgacctgttgcctttttgacctataatttgaagatgcatatttgtttacttctctaaaaatgtactgttcaatattagttatgtgcatta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA