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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAGTGCTTGATTATTCACGAAATAGTAGGCATTTATTGGTGACAGCTGGAGATGATGGTTCTGTGCATCTTTGGGATACAACTGCAAAGTCTCCTAAGgtatcagaattcggggttctgctgatgttatacttattctttggttgttcaagtgttataaagttaaccgctaaaataaaaataagatgcagccttcaag...

Basic information

species Zea mays
transcript GRMZM2G088261_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G088261_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os09g09470.1 (Oryza sativa), 5'ss of exon 4
GAGAGTGCTTGATTATTCACGAAATAGTAGGCATTTATTGGTGACAGCTGGAGATGATGGTTCTGTGCATCTTTGGGATACAACTGCAAAGTCTCCTAAGgtatcagaattcgg--ggttctgctgatgttatacttattctttggttgttcaagtgttataaagttaaccgctaaaataaaaataagatgcagccttcaag
|||||| ||||| |||||||| |||||||||||| ||||||||||||| ||||||||||||||||||||||| ||||||||||||||||   |||| |||||| |  || |     | | ||||| | |||  || | | ||  ||||  ||     | | ||  |   ||  |   ||| || |   |   |   |  || 
GAGAGTCCTTGACTATTCACGTAATAGTAGGCATATATTGGTGACAGCAGGAGATGATGGTTCTGTGCATCTCTGGGATACAACTGCAAGAACTCCAAAGgtacctaaagtacattgatgctgctta-gttgaacatctcctagggttcatcttaaatca-aagctatgccatttttatataatttgaacaaaagatagaat

upper sequence: GRMZM2G088261_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv18s0001g02820.t01 (Vitis vinifera), 5'ss of exon 4
GAGAGTGCTTGATTATTCACGAAATAGTAGGCATTTATTGGTGACAGCTGGAGATGATGGTTCTGTGCATCTTTGGGATACAACTGCAAAGTCTCCTAAGgtatcaga---attcggggttctgctgatgttatacttattctttggttgttcaagtgttataaagttaaccgctaaaataaaaataagatgcagccttcaag
 |||||||||||||||||||||| |||| | ||  | |||||||| ||||| |||||||| ||  | ||||| |||||||||||||   |    || |||||     |    |||     | |    ||   | |   ||   ||||   |  ||   ||| |  | |||    |||  || |      | |     ||    
AAGAGTGCTTGATTATTCACGAATTAGTCGACACCTTTTGGTGACTGCTGGTGATGATGGGTCAATACATCTGTGGGATACAACTGGTCACAGCCCAAAGgttcgtaacatgttctatagtttatgaataagaaatacatatgttgggaatgaaaaccttagatggctaaa---taagttatatcctttaggatatgtttggt
















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|71443925|gb|DR824975.1|DR824975
EST:     AAGTCGCCTAAG                         GTTTCATGGCTGAAGCAACATTCTGCACCCACAAGTGGTGTTTGTATTTCA
genomic: AAGTCTCCTAAGgtatcagaat ... tgttgtgcagGTTTCATGGCTGAAGCAACATTCTGCACCCACAAGTGGTGTTTGTATTTCA
EST: gi|71445853|gb|DR826903.1|DR826903
EST:     GAGATGATGGTTCTGTGCATCTTTGGGATACAACTGCAAAGTCTCCTAAG                         GTTTCATGGCTG
genomic: GAGATGATGGTTCTGTGCATCTTTGGGATACAACTGCAAAGTCTCCTAAGgtatcagaat ... tgttgtgcagGTTTCATGGCTG
EST: gi|93282883|gb|EB675147.1|EB675147
EST:     GAGATGATGGTTCTGTGCATCTTTGGGATACAACTGCAAAGTCTCCTAAG                         GTTTCATGGCTGAAGNCA-CATTCTGCACC
genomic: GAGATGATGGTTCTGTGCATCTTTGGGATACAACTGCAAAGTCTCCTAAGgtatcagaat ... tgttgtgcagGTTTCATGGCTGAAG-CAACATTCTGCACC
EST: gi|71443926|gb|DR824976.1|DR824976
EST:     CAACTGCAAAGTCTCCTAAG                         GTTTCATGGCTGAAGCAACATTCTGCACCCACAAGTGGTGTTTGTATTTCA
genomic: CAACTGCAAAGTCTCCTAAGgtatcagaat ... tgttgtgcagGTTTCATGGCTGAAGCAACATTCTGCACCCACAAGTGGTGTTTGTATTTCA
EST: gi|76280382|gb|DV019950.1|DV019950
EST:     GAGATGATGGTTCTGTGCATCTTTGGGATACAACTGCAAAGTCTCCTAAG                         GTTTCATGGCTGAAGCAACATTCTGCACCCACAAGTGGTGTTTGTATTTCA
genomic: GAGATGATGGTTCTGTGCATCTTTGGGATACAACTGCAAAGTCTCCTAAGgtatcagaat ... tgttgtgcagGTTTCATGGCTGAAGCAACATTCTGCACCCACAAGTGGTGTTTGTATTTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAGTGCTTGATTATTCACGAAATAGTAGGCATTTATTGGTGACAGCTGGAGATGATGGTTCTGTGCATCTTTGGGATACAACTGCAAAGTCTCCTAAGgtatcagaattcggggttctgctgatgttatacttattctttggttgttcaagtgttataaagttaaccgctaaaataaaaataagatgcagccttcaag

- - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataaa