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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgtttatttattgtttcaatctggtgtgctttatagctccatgatgtgttctccagtatcgttgtttataaaatggtcaagagaaacttcttccc...

Basic information

species Zea mays
transcript GRMZM2G158479_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158479_T04 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os05g23620.1 (Oryza sativa), 5'ss of exon 6
GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgta--cctgtttatttattgtttcaatct--ggtgtgctttatagctccatgatgtgttctccagtatcgttgtttata-aaatggtcaagagaaacttcttccc
|||||||||||||| ||||||||||| || |||||||||||||| || | |||||||||||| ||||||||||||   ||  || | | |   ||  | ||  ||  |      | ||| | || | |||    |    |   |   | || |||   | ||||    |||      
GCAAGGCACAATGGCCAGAACTATGTGTTTGCTCTTCTTACTGGTTACCGTGATCCACCTGCCGGTGTTCAGgtaaatctcattctctgtcagttataccttaggcatttgcagttgctacttgctatgtgtatcgcccttaattcctttacaaacaataaagatgctcttg-----

upper sequence: GRMZM2G158479_T04 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA19G24620.2 (Glycine max), 5'ss of exon 5
GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgtttatttat-tgtttcaatctggtgtgctt--tatagctccatgatgtgttctccagtatcgttgtttataaaatggtcaagagaaacttcttccc
||  | ||||||||||||||||||||||| || ||||| ||||| |||| ||| |||||||||||||||   |||  |  || ||||| |       |||  | |  ||  || ||     | ||   || | |    | |     |  |||||| |        | | | |   
GCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTAACTGGTTATCGTGACCCACCTGCTGGTGTTTCAgtaagttcttttttatctaaagtcttctattttatttagtaaagtaattttataaatttttctaagttgactgatggaaaatgttaggccaccaatacct---

upper sequence: GRMZM2G158479_T04 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA16G06700.2 (Glycine max), 5'ss of exon 5
GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgtttatttattgtttcaatctggtgtgctttatagctccatgatgtgttctccagtatcgttgtttataaaatggtcaagagaaacttcttccc-----
||  | ||||||||||||||||||||||| || ||||| ||||| |||| ||| |||||||||||||||  ||||  |  || ||| || | | ||  |  | | ||||||   |   | | ||  | |     ||  ||| | |    |  |     | |  ||    | |     
GCCCGTCACAATGGTCAGAACTATGTTTTTGCCCTTCTGACTGGTTATCGTGACCCACCTGCTGGTGTTTCGgtaaattcttctttcttatcttaag-tcttctactttat---ttagtaaagtaattttatacatt-ttgctcagttgactgatggaaaatgctaggccaccaata

upper sequence: GRMZM2G158479_T04 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA05G07020.1 (Glycine max), 5'ss of exon 5
GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgtttatttattg---tttcaatctggtgtgctttatagctcca--tgatgtgttctccagtatcgttgt-ttataaaatggtcaagagaaacttcttccc
||  | |||||||||||||||||||| || || ||||| ||||| |||| ||| || ||||||||||||  ||||  |  || | ||||    |||  |  |  | ||||| || |||  |  |  ||     || |  |  ||||| |||||      |    |||  || | |   
GCTCGTCACAATGGTCAGAACTATGTGTTTGCACTTCTAACTGGTTATCGTGACCCTCCTGCTGGTGTTTCGgtaaattgttgtctattaacatttttaattattatgctt-attgctgtaacttttgcacattctaccaaagttgtcttatatgtcaattgctaga--ctacgt---

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|31356708|gb|CD441065.1|CD441065
EST:     ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgttt ... tgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|14244836|gb|BG842774.2|BG842774
EST:     TGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: TGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgttt ... tgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|67028963|gb|CO457712.1|CO457712
EST:     ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgttt ... tgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|16379087|gb|BI992745.1|BI992745
EST:     ATGTTTTCGCTCTTCTTACTGGATATCATGATCCCCCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgttt ... tgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|5055406|gb|AI734293.1|AI734293
EST:     ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgttt ... tgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|15323508|gb|BI478611.1|BI478611
EST:     ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgttt ... tgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|60338899|gb|DN205872.1|DN205872
EST:     ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgttt ... tgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|211036752|gb|FL261404.1|FL261404
EST:     ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgttt ... tgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|74245922|gb|DT653836.1|DT653836
EST:     ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgttt ... tgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|91054777|gb|EB165195.1|EB165195
EST:     ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTGTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgttt ... tgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|76283401|gb|DV022969.1|DV022969
EST:     GTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: GTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgttt ... tgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|16919521|gb|BM074230.1|BM074230
EST:     TGGTTTTCGCTCTTCTAACTGGATATCATGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: T-GTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgttt ... tgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|15590213|gb|BI674829.1|BI674829
EST:     ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgttt ... tgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|31356905|gb|CD441262.1|CD441262
EST:     ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgttt ... tgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|60396397|gb|DN229266.1|DN229266
EST:     ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgttt ... tgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|14243082|gb|BG840790.2|BG840790
EST:     ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgttt ... tgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|149097934|gb|EE183875.2|EE183875
EST:     ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgttt ... tgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|6012601|gb|AW062038.1|AW062038
EST:     ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgttt ... tgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|31354314|gb|CD438671.1|CD438671
EST:     ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgttt ... tgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|18163834|gb|BM333673.1|BM333673
EST:     GGATATCATGATCCACCTGCTGGTGTTCAG                         ATTCGTAAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: GGATATCATGATCCACCTGCTGGTGTTCAGgtacctgttt ... tgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|78075104|gb|DV503538.1|DV503538
EST:     ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgttt ... tgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|40303643|gb|CK348030.1|CK348030
EST:     ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAG                         ATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
genomic: ATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgttt ... tgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGCC
EST: gi|211323658|gb|FL286664.1|FL286664
EST:     TGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGGTGTTCAG                         ATTCGTGARGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGC
genomic: TGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGG-TGTTCAGgtacctgttt ... tgcatcctagATTCGTGAGGGTCTGCACTACAATCCCTACTTCCCTGGTGGTGCCATAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAAGGCACAATGGTCAGAACTATGTTTTCGCTCTTCTTACTGGATATCATGATCCACCTGCTGGTGTTCAGgtacctgtttatttattgtttcaatctggtgtgctttatagctccatgatgtgttctccagtatcgttgtttataaaatggtcaagagaaacttcttccc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagagaaa