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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCTTTAACAAGCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcatgctacatgataagttctttcccacttaatgggcttgattttccaacttgcttacattcctattgctgtgcttgcag

Basic information

species Zea mays
transcript GRMZM2G103812_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G103812_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g68770.1 (Oryza sativa), 5'ss of exon 5
TTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCTTTAACAAGCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcatg-ctacatgataagttctttcccactta-------atgggcttgattttccaacttgcttac---attcctattgctgtgcttgcag---------------
||||||||||||||||||||| ||||| ||||| ||||||||| | |||||||||||||| |||||||||||||| || |||||||| |||||||||||||||||| |||  || ||||  ||  |  || | | ||        |  | | |  || ||||| ||| |||     || || |   | ||||||||                
TTTACATGATCCATCAAAGGATACTGGGTATGTGGGCTGTGCTCTGACAAGCAACATGGTCAGATTTTTCAAGACTGCAGATGGATCATGGAGCCATGAGgtttgtccataactccatgccaatgttcttgctattttcttgtataaagccctatttgtccaatttgtttagttgtttactctccttatgcttgcatgacatgacatgacag

upper sequence: GRMZM2G103812_T02 (Zea mays), 5'ss of exon 5
lower sequence: Vv05s0029g00240.t01 (Vitis vinifera), 5'ss of exon 5
TTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCTTTAACAAGCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcatgctacatgataagttctttcccacttaatgggcttgattttccaacttgcttacattcctattgctgtgcttgcag--------------------------------------
  | |||||||| || || || || || | ||| || ||||| |||||||||||||||||| |||||||||||||| | ||||| || |||||||| ||||| ||   ||  ||  || |   |   ||||    |      | |    ||   | |||  |   |  |||||   |   |  ||                                       
CCTGCATGATCCTTCTAAAGATACAGGGTTTGTAGGTTGTGCCTTAACAAGCAACATGGTGCGATTTTTCAAGACCCCAGATGGGTCATGGAGCCACGAGgtatgcggataatatgtgtttcttcaattcctttgtttgaaaccttgcattttgaattgtattagtctctattaaggca-tgacaatccacaatatataatcactccctaatttacttatgaag
















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|6021033|gb|AW065961.1|AW065961
EST:     GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
genomic: GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
EST: gi|5895606|gb|AW036852.1|AW036852
EST:     GCAACATGGTGAGATTTTTCAAGGCCGCGGATGGATCGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
genomic: GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
EST: gi|85151683|gb|DW587480.1|DW587480
EST:     GCAACATGGTGAGATTTTTCAAGGCCGCGGATGGATCGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
genomic: GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
EST: gi|60344862|gb|DN211835.1|DN211835
EST:     ATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
genomic: ATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
EST: gi|38502601|gb|CF972461.1|CF972461
EST:     GCAACATGGTGAGATTTTTCAAGGCCGCGGATGGATCGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
genomic: GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
EST: gi|83279371|gb|DV943379.1|DV943379
EST:     GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
genomic: GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
EST: gi|32801957|gb|CD954193.1|CD954193
EST:     GCAACATGGTGAGATTTTTCAAGGCCGCGGATTGATCGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
genomic: GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
EST: gi|78076644|gb|DV505078.1|DV505078
EST:     GCAACATGGTGAGA-TTTTCAAGACCGCGGATGGATCGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
genomic: GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
EST: gi|31355194|gb|CD439551.1|CD439551
EST:     GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
genomic: GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
EST: gi|18172411|gb|BM347799.1|BM347799
EST:     GCAACATGGTGAGATTTTT-AAGACCGCGGATGGATCGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
genomic: GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
EST: gi|31354133|gb|CD438490.1|CD438490
EST:     CAACATGGTGAGATTTTTTCA-GACCGCGGATGGATCGTGGAGCCATGAG                         GGTGCTATCTCTGTGAAACCACTGAAG
genomic: CAACATGGTGAGATTTTT-CAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAG
EST: gi|60355186|gb|DN222159.1|DN222159
EST:     GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
genomic: GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
EST: gi|32941574|gb|CF046393.1|CF046393
EST:     GCAACATGGTGAGATTTTTCAAGGCCGCGGATGGATCGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCTGGAA
genomic: GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
EST: gi|31349415|gb|CD433772.1|CD433772
EST:     GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
genomic: GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
EST: gi|31360531|gb|CD444888.1|CD444888
EST:     GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
genomic: GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
EST: gi|6994143|gb|AW453357.1|AW453357
EST:     GCAACATGGTGAGATTTTCCAAGACCGCGGATGGATCGAGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
genomic: GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
EST: gi|67021527|gb|CO450276.1|CO450276
EST:     GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
genomic: GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
EST: gi|31362486|gb|CD446843.1|CD446843
EST:     CGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGA
genomic: CGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTG-AAACCACTGAAGGTCCGCAACTGGATTCTGCCGGA
EST: gi|32796562|gb|CD948798.1|CD948798
EST:     GCAACATGGTGAGATTTTTCAAGGCCGCGGATGGATCGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
genomic: GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
EST: gi|31355476|gb|CD439833.1|CD439833
EST:     GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
genomic: GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
EST: gi|31356060|gb|CD440417.1|CD440417
EST:     GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
genomic: GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
EST: gi|40334707|gb|CK368777.1|CK368777
EST:     GCAACATGGTGAGATTTTTCAAGGCCGCGGATGGATCGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
genomic: GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
EST: gi|14701287|gb|BI233705.1|BI233705
EST:     GCAACATGGTGAGATTTTTCAAGGCCGCGGATGGATCGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
genomic: GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
EST: gi|31348673|gb|CD433030.1|CD433030
EST:     GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
genomic: GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
EST: gi|67031397|gb|CO460146.1|CO460146
EST:     CAACATGGTGAGATTTTTTCAGGGCCGCG-ATGGATCGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAAC
genomic: CAACATGGTGAGATTTTT-CAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAAC
EST: gi|32865912|gb|CF005594.1|CF005594
EST:     GCAACATGGTGAGATTTTTCAAGGCCGCGGATGGATCGTGGAGCCATGAG                         GTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
genomic: GCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGCTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGAA
EST: gi|149005327|gb|EE039878.2|EE039878
EST:     ATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAG                         G-TGCTTATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGA
genomic: ATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcat ... gtgcttgcagGTTGC-TATCTCTGTGAAACCACTGAAGGTCCGCAACTGGATTCTGCCGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTACATGATCCATCAAAGGACACTGGCTATGTTGGCTGTGCTTTAACAAGCAACATGGTGAGATTTTTCAAGACCGCGGATGGATCGTGGAGCCATGAGgtttgttcatgctacatgataagttctttcccacttaatgggcttgattttccaacttgcttacattcctattgctgtgcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG