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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACCCAGAACTCATTTACCTGACAGACGGCGCCAGCAAAGGTGTGATGCAAATGCTGAATGCCATCATTAGAAACGAGAGGGATGGGgtatggttgttcttgaaagaaaaaaaaaacatatcttttccactgatggatgtgatgccacttctactgaagagcaaaggataatttcgttgatataaatcttctgtggcag

Basic information

species Zea mays
transcript GRMZM5G840582_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G840582_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os07g01760.1 (Oryza sativa), 5'ss of exon 4
TGACCCAGAACTCATTTACCTGACAGACGGCGCCAGCAAAGGTGTGATGCAAATGCTGAATGCCATCATTAGAAACGAGAGGGATGGGgtatggttgttcttgaaagaaaaaaaaaacatatcttttccactgatggatgtgatgccacttctactgaagagcaaa--------ggataatttcgttg--atataaatcttctgtggcag
||| |||||||| |||||||| ||||| || |||||||||||||||||||||||||||||| |||| || ||||| ||||| ||||||||||| || || ||         ||||   ||||   || | |||||  ||    ||| | ||||||||||||  ||            | |||     |  || |  | ||||  | ||||
TGATCCAGAACTTATTTACCTCACAGATGGTGCCAGCAAAGGTGTGATGCAAATGCTGAATACCATTATCAGAAATGAGAGAGATGGGgtatg-ttattattcctt-----aaaagctatat---ttgccctgattaattcagtgctatttctactgaagactaatttcaccccatctgattcaaccgagatgtgtaccttccttcgcag
















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|148974504|gb|EE025287.2|EE025287
EST:     AAGGTGTGATGCAAATGCTGGATGCCATCATTAGAAACGAGAGGGATGGG                         ATCTTGGTTTCTGTTCCTCAGTACC
genomic: AAGGTGTGATGCAAATGCTGAATGCCATCATTAGAAACGAGAGGGATGGGgtatggttgt ... tctgtggcagATCTTGGTTCCTGTTCCTCAGTACC
EST: gi|148974460|gb|EE025239.2|EE025239
EST:     AAGGTGTGATGCAAATGCTGAATGCCATCATTAGAAACGAGAGGGATGGG                         ATCTTGGTTCCTGTTCCTCAGTACCCACTTTATTCTGCT
genomic: AAGGTGTGATGCAAATGCTGAATGCCATCATTAGAAACGAGAGGGATGGGgtatggttgt ... tctgtggcagATCTTGGTTCCTGTTCCTCAGTACCCACTTTATTCTGCT
EST: gi|149070661|gb|EE159075.2|EE159075
EST:     AAGGTGTGATGCAAATGCTGAATGCCATCATTAGAAACGAGAGGGATGGG                         ATCTTGGTTCCTGTTCCTCAGTACCCACTTTATTCTGCTATCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATGCCATCATTAGAAACGAGAGGGATGGGgtatggttgt ... tctgtggcagATCTTGGTTCCTGTTCCTCAGTACCCACTTTATTCTGCTATCATTTCCCTC
EST: gi|91048303|gb|EB158721.1|EB158721
EST:     AAGGTGTGATGCAAATGCTGAATGCCATCATTAGAAACGAGAGGGATGGG                         ATCTTGGTTCCTGTTCCTCAGTACCCACTTTATTCTGCTATCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATGCCATCATTAGAAACGAGAGGGATGGGgtatggttgt ... tctgtggcagATCTTGGTTCCTGTTCCTCAGTACCCACTTTATTCTGCTATCATTTCCCTC
EST: gi|78112476|gb|DV530870.1|DV530870
EST:     AAGGTGTGATGCAAATGCTGAATGCCATCATTAGAAACGAGAGGGATGGG                         ATCTTGGTTCCTGTTCCTCAGTACCCACTTTATTCTGCTATCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATGCCATCATTAGAAACGAGAGGGATGGGgtatggttgt ... tctgtggcagATCTTGGTTCCTGTTCCTCAGTACCCACTTTATTCTGCTATCATTTCCCTC
EST: gi|149041122|gb|EE046896.2|EE046896
EST:     AAGGTGTGATGCAAATGCTGAATGCCATCATTAGAAACGAGAGGGATGGG                         ATCTTGGTTCCTGTTCCTCAGTACCCACTTTATTCTGCTATCATTTCCCTC
genomic: AAGGTGTGATGCAAATGCTGAATGCCATCATTAGAAACGAGAGGGATGGGgtatggttgt ... tctgtggcagATCTTGGTTCCTGTTCCTCAGTACCCACTTTATTCTGCTATCATTTCCCTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACCCAGAACTCATTTACCTGACAGACGGCGCCAGCAAAGGTGTGATGCAAATGCTGAATGCCATCATTAGAAACGAGAGGGATGGGgtatggttgttcttgaaagaaaaaaaaaacatatcttttccactgatggatgtgatgccacttctactgaagagcaaaggataatttcgttgatataaatcttctgtggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG