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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtatatatgatgatgataatgagttatctgtgagtgctggatgaagttttgaagtgatgggtttatttatgaatgaacacagGGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTACCATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTTCATGGAGCAATA

Basic information

species Zea mays
transcript GRMZM5G840582_T03
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G840582_T03 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os07g01760.1 (Oryza sativa), 3'ss of exon 11
-------------gtatgtgtatatatgatgatgataatga--gttatctgtgagtgctggatgaagttttgaagtgatgggtttatttatgaatgaacacagGGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTACCATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTTCATGGAGCAATA-
             |   |   || |   | |||   | |||   || | |||| ||  |  || |     | || |||||  |   ||  ||    |   |||||||||||||||  |||| || ||||| ||||| ||||| ||| | ||| |||||||| | ||||||||||||||||||||| | ||||||||| || || 
gacttgtcttcttgataggaaatctgaaaagatatcactgacgattttttgtgtgta-tatataagtaagtaaactgatgcatg-gttggtgtgc-actgcagGGTGTTCCACCTGAGGACGACCATCCTGCCAGCTGAGGAGGACATGCCTGCCATCATGACCAGCTTCAAGAAGTTCAACGACAC-TTTCATGGATCAGTAC
















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|78112475|gb|DV530869.1|DV530869
EST:     GCAACGGGGATTTCCACTGTTCCGGGATCTGGTTTTGGGCAGAAGGAAGG                         GGTGTTCCCCCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTAC
genomic: GCAACGGGGATTTCCACTGTTCCGGGATCTGGTTTTGGGCAGAAGGAAGGgtatgtgtat ... atgaacacagGGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTAC
EST: gi|32803697|gb|CD955933.1|CD955933
EST:     GATCCGGTTTTGGGCAGAAGGAAGG                         GGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTAC
genomic: GATCTGGTTTTGGGCAGAAGGAAGGgtatgtgtat ... atgaacacagGGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTAC
EST: gi|32793206|gb|CD945442.1|CD945442
EST:     GATCTGGTTTTGGGCAGAAGGAAGG                         GGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTAC
genomic: GATCTGGTTTTGGGCAGAAGGAAGGgtatgtgtat ... atgaacacagGGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTAC
EST: gi|5740535|gb|AI948225.1|AI948225
EST:     GCAACGGGGATTTCCACTGTTCCGGGATCTGGTTTTGGGCAGAAGGAAGG                         GGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTAC
genomic: GCAACGGGGATTTCCACTGTTCCGGGATCTGGTTTTGGGCAGAAGGAAGGgtatgtgtat ... atgaacacagGGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTAC
EST: gi|32850940|gb|CD990621.1|CD990621
EST:     GCAACGGGGATTTCCACTGTTCCGGGATCTGGTTTTGGGCAGAAGGAAGG                         GGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTAC
genomic: GCAACGGGGATTTCCACTGTTCCGGGATCTGGTTTTGGGCAGAAGGAAGGgtatgtgtat ... atgaacacagGGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTAC
EST: gi|7238269|gb|AW573536.1|AW573536
EST:     GCAACGGGGATTTCCACTGTTCCGGGATCTGGTTTTGGGCAGAAGGAAGG                         GGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTAC
genomic: GCAACGGGGATTTCCACTGTTCCGGGATCTGGTTTTGGGCAGAAGGAAGGgtatgtgtat ... atgaacacagGGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTAC
EST: gi|110203147|gb|EC885044.1|EC885044
EST:     GCAACGGGGATTTCCACTGTTCCGGGATCTGGTTTTGGGCAGAAGGAAGG                         GGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTAC
genomic: GCAACGGGGATTTCCACTGTTCCGGGATCTGGTTTTGGGCAGAAGGAAGGgtatgtgtat ... atgaacacagGGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTAC
EST: gi|91054117|gb|EB164535.1|EB164535
EST:     GCAACGGGGATTTCCACTGTTCCGGGATCTGGTTTTGGGCAGAAGGAAGG                         GGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTAC
genomic: GCAACGGGGATTTCCACTGTTCCGGGATCTGGTTTTGGGCAGAAGGAAGGgtatgtgtat ... atgaacacagGGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTAC
EST: gi|5917498|gb|AW054301.1|AW054301
EST:     GCAACGGGGATTTCCACTGTTCCGGGATCTGGTTTTGGGCAGAAGGAAGG                         GGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTAC
genomic: GCAACGGGGATTTCCACTGTTCCGGGATCTGGTTTTGGGCAGAAGGAAGGgtatgtgtat ... atgaacacagGGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTAC
EST: gi|5928965|gb|AW056257.1|AW056257
EST:     GCAACGGGGATTTCCACTGTTCCGGGATCTGGTTTTGGGCAGAAGGAAGG                         GGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTAC
genomic: GCAACGGGGATTTCCACTGTTCCGGGATCTGGTTTTGGGCAGAAGGAAGGgtatgtgtat ... atgaacacagGGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTAC
EST: gi|7227753|gb|AW566394.1|AW566394
EST:     GCAACGGGGATTTCCACTGTTCCGGGATCTGGTTTTGGGCAGAAGGAAGG                         GGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTAC
genomic: GCAACGGGGATTTCCACTGTTCCGGGATCTGGTTTTGGGCAGAAGGAAGGgtatgtgtat ... atgaacacagGGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtgagtgctggatgaagttttgaagtgatgggtttatttatgaatgaacacagGGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTACCATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTTCATGGAGCAATA
                                  tttatttatgaatgaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgtatatatgatgatgataatgagttatctgtgagtgctggatgaagttttgaagtgatgggtttatttatgaatgaacacagGGTGTTCCACCTTCGGACAACTATCCTTCCAGCCGAGGAAGACTTCCCTACCATCATGTCGAGCTTCAAGAAGTTCAACGACTCATTTCATGGAGCAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA