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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttaatctttttctctatcgaatcatgctattctccaccgaatgcacatacttctgcttccgccacctttcttgatgatgtttctggctgcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTGGAGAATGATGATGGAGGGAACCCTGCTTTGCTTGGTAGCTGTAATGACC

Basic information

species Zea mays
transcript GRMZM2G099980_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G099980_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os12g01170.1 (Oryza sativa), 3'ss of exon 1
ttttaatctttttctctatcgaatcatgctattctccaccgaatgcacatacttctgcttccgccacctttcttgatgatgtttctggct---gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGT---GGAGAATGATGATGGAGGGAACCCTGCTTTGCTTGGTAGCTGTAATGACC
  |      | |||  | || |       ||   | ||    || |  | ||  || ||    |||     | ||||  ||| |    ||   || ||| |||||||||||||||||||| ||||| || ||||| |||||||||||| ||||   ||||||||||||||| ||||| || ||||||||||||||||| ||||   
--tgtgctctcttcagtttcaagaaccattacattacattacatacgaaaacc-ctcctattaccataaggcgtgatcttgtcttgcactcttgcttgagtagGCTGAGCTAAGAGCAAGTGTGTTCGAGGCCATAGAAGAGGAGGATAGGGTAGTGGAGAATGATGATGGTGGGAATCCCGCTTTGCTTGGTAGCTGCAATG---
















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|211054006|gb|FL385558.1|FL385558
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211452567|gb|FL415951.1|FL415951
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211080223|gb|FL420001.1|FL420001
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCG-CAAKATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211466208|gb|FL385420.1|FL385420
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211267129|gb|FL426695.1|FL426695
EST:     GCTCGTCWACCCGCACCCTCGAGAAGAAGGGCGTCCTCG-CAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: GCTCGTC-ACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211203962|gb|FL369985.1|FL369985
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|32910631|gb|CF015443.1|CF015443
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGCTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211084387|gb|FL369936.1|FL369936
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211042377|gb|FL397272.1|FL397272
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCG-CAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211330509|gb|FL416285.1|FL416285
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGC-AAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211501608|gb|FL378289.1|FL378289
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCG-CAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211449691|gb|FL381423.1|FL381423
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211020467|gb|FL418619.1|FL418619
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211022189|gb|FL381966.1|FL381966
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211029303|gb|FL370358.1|FL370358
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGC-AAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211159520|gb|FL378584.1|FL378584
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCG-CAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211523925|gb|FL381024.1|FL381024
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211204242|gb|FL383411.1|FL383411
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGC-AAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211194591|gb|FL404838.1|FL404838
EST:     CGCTCGTCACCCGCANBCTCGAGAAGAAGGGCGTCCTCG-CAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211282200|gb|FL376831.1|FL376831
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGC-AAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211512095|gb|FL429021.1|FL429021
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGC-AAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211057059|gb|FL391378.1|FL391378
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211376378|gb|FL377798.1|FL377798
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211269442|gb|FL420605.1|FL420605
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|78109085|gb|DV527502.1|DV527502
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211186922|gb|FL380831.1|FL380831
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGC-AAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTKAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211147508|gb|FL408670.1|FL408670
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGC-AAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211212936|gb|FL424466.1|FL424466
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|33103991|gb|CF063951.1|CF063951
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211471762|gb|FL410798.1|FL410798
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCG-CAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211323555|gb|FL394717.1|FL394717
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCG-CAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211276957|gb|FL388228.1|FL388228
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCG-CAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|108953992|gb|EC364964.1|EC364964
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211051698|gb|FL411698.1|FL411698
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGC-AAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211355668|gb|FL392110.1|FL392110
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGC-AAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211186886|gb|FL377630.1|FL377630
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211490263|gb|FL376582.1|FL376582
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
EST: gi|211269439|gb|FL420602.1|FL420602
EST:     CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGG                         GCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG
genomic: CGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 765

ATTTCAGGCCGGGATGGACGACTACGCCCGGGAGATGATGGAGCTCAAGACGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTGGAGAATGATGATGGAGGGAACCCTGCTTTGCTTGGTAGCTGTAATGACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 300

ATTTCAGGCCGGGATGGACGACTACGCCCGGGAGATGATGGAGCTCAAGACGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTGGAGAATGATGATGGAGGGAACCCTGCTTTGCTTGGTAGCTGTAATGACC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 223

ATTTCAGGCCGGGATGGACGACTACGCCCGGGAGATGATGGAGCTCAAGACGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTGGAGAATGATGATGGAGGGAACCCTGCTTTGCTTGGTAGCTGTAATGACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 317

ATTTCAGGCCGGGATGGACGACTACGCCCGGGAGATGATGGAGCTCAAGACGCTCGTCACCCGCACCCTCGAGAAGAAGGGCGTCCTCGCCAAGATTAGGgttcgtactt ... gcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTGGAGAATGATGATGGAGGGAACCCTGCTTTGCTTGGTAGCTGTAATGACC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacatacttctgcttccgccacctttcttgatgatgtttctggctgcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTGGAGAATGATGATGGAGGGAACCCTGCTTTGCTTGGTAGCTGTAATGACC
                         tcttgat  putative branch site (score: 317)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttaatctttttctctatcgaatcatgctattctccaccgaatgcacatacttctgcttccgccacctttcttgatgatgtttctggctgcatgactagGCTGAGCTAAGAGCAAGCGTGTTTGAAGCCATTGAAGAGGAGGATCGGGTGGAGAATGATGATGGAGGGAACCCTGCTTTGCTTGGTAGCTGTAATGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - catgcta
- - - - - - - - - - - - - - - - -ctccacc
- - - - - - - - - - - - - - - - - - - - gaatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgtt