Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctacagatattgctaaatatattcattcagtgcaattggtctgtctgtcactcttacctgacgttatgtatttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAACAAGCTTCTCGAAGAAGCGTCCCGAAGGGGAAGCTCTGATAACATCACCG

Basic information

species Zea mays
transcript GRMZM5G829894_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G829894_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g05630.3 (Oryza sativa), 3'ss of exon 6
----------gtacctacagatattgctaaatatattcattcagtgcaattgg-----tctgtctgtcactct-tacctga--cgttatgtatttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAACAAGCTTCTCGAAGAAGCGTCCCGAAGGGGAAGCTCTGATAACATCACCG
            |  |   ||   | ||  |     |  |    ||| |||||     | | | ||| ||||  ||| |||  |   |  | | ||||||||||||||||| |||||| | |||||||||||| ||| |  | ||||| || | ||||||| | || |||| || |||||| ||| | |||||||||||||
gtaacaacagaaatttcttgagtctccttcacccgcttgtatgttgccattggcgccttatatatgttactcaatacatgaaacccaaattctatttccagGAAGCTGTTGACATGGTGAGGCCTATTCAGGATCCCGAACAGGCAGCGAAGAGGCTTCTCCAGGAGGCGTACCAAAGGGGTAGCGCCGATAACATCACCG
















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|60398848|gb|DN231664.1|DN231664
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|60398872|gb|DN231688.1|DN231688
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|60349103|gb|DN216076.1|DN216076
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|149001340|gb|EE038630.2|EE038630
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|60358725|gb|DN225698.1|DN225698
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|60359012|gb|DN225985.1|DN225985
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|60351393|gb|DN218366.1|DN218366
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|31909593|gb|CD650996.1|CD650996
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|60337634|gb|DN204607.1|DN204607
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|60351806|gb|DN218779.1|DN218779
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|9254746|gb|BE345214.1|BE345214
EST:     TGGGATGTTGTCCCTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: TGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|74238817|gb|DT646731.1|DT646731
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|60400081|gb|DN232888.1|DN232888
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|60341056|gb|DN208029.1|DN208029
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|60358897|gb|DN225870.1|DN225870
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|16925989|gb|BM079057.1|BM079057
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|149099178|gb|EE185204.2|EE185204
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAAGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|149106826|gb|EE188723.2|EE188723
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|32857745|gb|CD997426.1|CD997426
EST:     AATTCCTCATCTTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|32857201|gb|CD996882.1|CD996882
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTCTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|71326203|gb|DR799792.1|DR799792
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|18659317|gb|BM500274.1|BM500274
EST:     GGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: GGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|149099824|gb|EE185877.2|EE185877
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|60399036|gb|DN231852.1|DN231852
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|71442169|gb|DR823219.1|DR823219
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|5055824|gb|AI734711.1|AI734711
EST:     CTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: CTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|13491100|gb|BG517864.1|BG517864
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTTATTACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|78119894|gb|DV538278.1|DV538278
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|60341073|gb|DN208046.1|DN208046
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|21481348|gb|BQ578031.1|BQ578031
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|33096324|gb|CF056318.1|CF056318
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCCGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCTGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
EST: gi|149107349|gb|EE189228.2|EE189228
EST:     AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAG                         GAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC
genomic: AATTCCTCATCCTTGCTAGTGATGGACTCTGGGATGTTGTCACTAATGAGgtacctacag ... atttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcagtgcaattggtctgtctgtcactcttacctgacgttatgtatttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAACAAGCTTCTCGAAGAAGCGTCCCGAAGGGGAAGCTCTGATAACATCACCG
                               acctgac  putative branch site (score: 3)
                                            tatttttcc  putative PPT
                                       ttatgtattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacctacagatattgctaaatatattcattcagtgcaattggtctgtctgtcactcttacctgacgttatgtatttttccagGAAGCTGTTGCCATGGTCAAGCCTATTCAGGACCCCCAGGAAGCAGCAAACAAGCTTCTCGAAGAAGCGTCCCGAAGGGGAAGCTCTGATAACATCACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC