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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTGAATGTAATAATCAATTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTGgtaagactgatcttatgatcctgtagctggtgcttgttgcaagtttcttcctgttacatatttttattttcctggctcagttatgaaaatactatttata...

Basic information

species Zea mays
transcript GRMZM5G876003_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G876003_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g38060.2 (Oryza sativa), 5'ss of exon 4
CAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTGAATGTAATAATCAATTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTGgtaagactgatcttatgatcctgtagctggtgcttgttgcaagtttcttcctgt-tacatatttttattttcctggctcagttatgaaaatactatttata----------
| |||||| ||||| || ||||| || || ||||| ||||| ||||||||||||||||||||||| | ||| || ||||| ||||| ||||||||||||||||||| || |      | | | ||         ||  |  |  || |  |  | |     ||||||||| ||||||  | | |||  ||||| ||| | |          
CGAGAGCAAATGTCGCATTGGCCAGAGCAACCAGTAAATGTTATAATCAATTGGTTGAAGAGTCATAGTGCATCTTGGACAGTTGCAGATTTTGGCTGTGgtaagaatgct-----aaacatttactctcaatatgccgacaccttttcacaatgttttcctttttatttccctggcataatcatggtaatacaattgacatcttgtctag
















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|76923220|gb|DV169382.1|DV169382
EST:     TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTG                         GCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
genomic: TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTGgtaagactga ... tattttccagGCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
EST: gi|74240435|gb|DT648349.1|DT648349
EST:     TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTG                         GCAATGCAGCAGTTGCAAAAAATCTGAAGAAC
genomic: TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTGgtaagactga ... tattttccagGCAATGCAGCAGTTGCAAAAAATCTGAAGAAC
EST: gi|31354696|gb|CD439053.1|CD439053
EST:     TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTG                         GCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
genomic: TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTGgtaagactga ... tattttccagGCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
EST: gi|60395258|gb|DN228127.1|DN228127
EST:     TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTG                         GCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
genomic: TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTGgtaagactga ... tattttccagGCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
EST: gi|78093364|gb|DV521738.1|DV521738
EST:     TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTG                         GCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
genomic: TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTGgtaagactga ... tattttccagGCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
EST: gi|78074349|gb|DV502783.1|DV502783
EST:     TCATGGACTGTTGCTGATTTTGGCTGTG                         GCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
genomic: TCATGGACTGTTGCTGATTTTGGCTGTGgtaagactga ... tattttccagGCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
EST: gi|71435218|gb|DR816268.1|DR816268
EST:     TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTG                         GCAATGCAGCAGTTGC
genomic: TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTGgtaagactga ... tattttccagGCAATGCAGCAGTTGC
EST: gi|71429033|gb|DR810083.1|DR810083
EST:     TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTG                         GCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
genomic: TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTGgtaagactga ... tattttccagGCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
EST: gi|78074350|gb|DV502784.1|DV502784
EST:     TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTG                         GCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
genomic: TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTGgtaagactga ... tattttccagGCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
EST: gi|76922748|gb|DV169154.1|DV169154
EST:     TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTG                         GCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
genomic: TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTGgtaagactga ... tattttccagGCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
EST: gi|74240434|gb|DT648348.1|DT648348
EST:     TCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTG                         GCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
genomic: TCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTGgtaagactga ... tattttccagGCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
EST: gi|74245743|gb|DT653657.1|DT653657
EST:     TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTG                         GCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
genomic: TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTGgtaagactga ... tattttccagGCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
EST: gi|148948106|gb|EC893615.2|EC893615
EST:     TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTG                         GCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
genomic: TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTGgtaagactga ... tattttccagGCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
EST: gi|74235314|gb|DT643228.1|DT643228
EST:     TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTG                         GCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
genomic: TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTGgtaagactga ... tattttccagGCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
EST: gi|149071083|gb|EE159484.2|EE159484
EST:     TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTG                         GCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
genomic: TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTGgtaagactga ... tattttccagGCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
EST: gi|91055947|gb|EB166365.1|EB166365
EST:     TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTG                         GCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
genomic: TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTGgtaagactga ... tattttccagGCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
EST: gi|149100899|gb|EE186995.2|EE186995
EST:     TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTG                         GCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
genomic: TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTGgtaagactga ... tattttccagGCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
EST: gi|78093365|gb|DV521739.1|DV521739
EST:     TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTG                         GCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
genomic: TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTGgtaagactga ... tattttccagGCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
EST: gi|78080458|gb|DV508870.1|DV508870
EST:     TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTG                         GCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
genomic: TTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTGgtaagactga ... tattttccagGCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
EST: gi|76923219|gb|DV169381.1|DV169381
EST:     CAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTG                         GCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC
genomic: CAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTGgtaagactga ... tattttccagGCAATGCAGCAGTTGCAAAAAATCTGAAGAACAAGGTTTTCTCCATTGATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGAGCAGATGTCACACTGGCCTGAACAGCCAGTGAATGTAATAATCAATTGGTTGAAGAGTCAGAATGCGTCATGGACTGTTGCTGATTTTGGCTGTGgtaagactgatcttatgatcctgtagctggtgcttgttgcaagtttcttcctgttacatatttttattttcctggctcagttatgaaaatactatttata

- - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT