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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgcttttgttccaactattagtatttttttatttcagagtttcagaacaaaatgatatctcgattcatgtgaaaaaactgtctatttattgtcactttttgtaaaattcag

Basic information

species Zea mays
transcript GRMZM2G116087_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116087_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g55870.1 (Oryza sativa), 5'ss of exon 5
GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgcttttgttccaactattagtatttttttatttcagagtttcagaaca----aaatgatatctcg-------------attcatgtgaaaaaactgtctattt------------attgtcactttttgtaaaattcag
|| ||||||||||| || |||||||| ||||||||||||||||| |||||||||||||| ||||||||||||| ||| || |||||||| || || |||| || ||||        || | | | |||||    |      |  | |    |  || | ||| |              | ||| | |||     |||||||             ||| |   | | ||  || |||||
GCGCTCTCCAAAAGAATTCACTATGGTAAGTTTGTGGCAGAGGCTAAGTTTCAAGAGTCTCCTGAAGCTTACATGCCTGCGATAATAGCACAGgtttgtg-ttctgttttgctgtataatctgtctttatcatgggaagcaaataaattccatgtgttttcttgtacattactttaggtacatatcaaagttgagtctattatgcaagcggctaattatttttatctgggaatttcag

upper sequence: GRMZM2G116087_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA01G06660.1 (Glycine max), 5'ss of exon 4
GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgcttttgttccaactattagtatttttttatttcagagtttcagaacaaaatgatatctcgattcatg-tgaaaaaactgtctatttattgtcactttttgtaaaattcag
|| ||||| ||||| ||||||||||| || ||||| || ||||| |||||||||||  |||||   |  ||     | |||||   |||  ||||     ||||||        |||  | || ||||   |     ||  |||     |  |||  |   ||  || ||  | |    || ||   |                      
GCTCTCTCAAAAAGAATCCACTATGGCAAATTTGTTGCTGAGGCAAAGTTTCAAGATGCCCCTTCTGAATATGTAGCTGCCATTGAAGCGAAAgt--aaacttttgcatacctgattcattttattttccattgtgattctagat----accatacttaattttctgatgctacattaatccatgcttcacag-----------------
















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|148961521|gb|EE012273.2|EE012273
EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
EST: gi|78125597|gb|DV543981.1|DV543981
EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
EST: gi|78089259|gb|DV517633.1|DV517633
EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
EST: gi|149086679|gb|EE176219.2|EE176219
EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
EST: gi|149086680|gb|EE176220.2|EE176220
EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAAACGGTGGAGCGTGC
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAA-CGGTGGAGCGTGC
EST: gi|78111571|gb|DV529968.1|DV529968
EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCAT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCAT
EST: gi|149029769|gb|EE154771.2|EE154771
EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
EST: gi|211039898|gb|FK958023.1|FK958023
EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
EST: gi|71762890|gb|DR960827.1|DR960827
EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
EST: gi|149033875|gb|EE155016.2|EE155016
EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTTTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
EST: gi|60356414|gb|DN223387.1|DN223387
EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
EST: gi|148952137|gb|EC897931.2|EC897931
EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAACG
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACG
EST: gi|31352097|gb|CD436454.1|CD436454
EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
EST: gi|211304785|gb|FL143334.1|FL143334
EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCA
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCA
EST: gi|71448582|gb|DR829632.1|DR829632
EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGTCAGCCATAATAGCCCCA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
EST: gi|78089260|gb|DV517634.1|DV517634
EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCNA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
EST: gi|149088482|gb|EE177591.2|EE177591
EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
EST: gi|94479717|gb|EB708675.1|EB708675
EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTAC-CGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTCTCACATA
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgcttttgttccaactattagtatttttttatttcagagtttcagaacaaaatgatatctcgattcatgtgaaaaaactgtctatttattgtcactttttgtaaaattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC