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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGTTGCTGAAGACCTGGCTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgctacataggataaaaaaacgtcacattcctgttgtcaaaacttaaaaaacctactgcggtgtctcaaatatgttattcgtgtgttgcag

Basic information

species Zea mays
transcript GRMZM2G085747_T02
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085747_T01 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os10g35960.1 (Oryza sativa), 5'ss of exon 18
CGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGTTGCTGAAGACCTGGCTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgctacataggataaaaaaacgtcacattcctgttgtcaaaacttaaaaaacctactgcggtgtctcaaatatgttatt---cgtgtgt-tgcag
||||||||||||||| |||||||||||||||||||||| |||||| ||||| |||||| | |||||||| |   ||||||| ||   ||| ||| | ||||||| ||   | | |  ||         ||| || ||||  ||  ||  ||       | | |  || |||| |||| ||| |||   | |||||   |||
CGCACGTGTCGGCGCCGCAGTCGTCCGTGCCGCTGTTGATGAAGATCTGGCCGAGGGGCGTTGTGATGTAGACGCTAGGGACCTCAAGAGCATGACTGAGgtactgcatcatacataatt--------tcaaatccctgaagttgaattttttg----ccagtttggcgtctgaaatgtgtcattttacatgtgtgcacag
















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|211281985|gb|FL018038.1|FL018038
EST:     CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAG                         TCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
genomic: CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgct ... tgtgttgcagTCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
EST: gi|4647288|gb|AI622363.1|AI622363
EST:     CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAG                         TCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
genomic: CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgct ... tgtgttgcagTCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
EST: gi|32933889|gb|CF038701.1|CF038701
EST:     CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAG                         TCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACC
genomic: CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgct ... tgtgttgcagTCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACC
EST: gi|71758667|gb|DR956604.1|DR956604
EST:     CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAG                         TCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
genomic: CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgct ... tgtgttgcagTCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
EST: gi|211281986|gb|FL018039.1|FL018039
EST:     CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAG                         TCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
genomic: CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgct ... tgtgttgcagTCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
EST: gi|86470645|gb|DY237015.1|DY237015
EST:     CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAG                         TCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
genomic: CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgct ... tgtgttgcagTCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
EST: gi|4730607|gb|AI649773.1|AI649773
EST:     CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAG                         TCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
genomic: CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgct ... tgtgttgcagTCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
EST: gi|76919652|gb|DV167818.1|DV167818
EST:     CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAG                         TCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAAC
genomic: CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgct ... tgtgttgcagTCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
EST: gi|50334197|gb|CO529323.1|CO529323
EST:     CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAG                         TCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
genomic: CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgct ... tgtgttgcagTCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
EST: gi|113701975|gb|EE679479.1|EE679479
EST:     CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAG                         TCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
genomic: CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgct ... tgtgttgcagTCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
EST: gi|74232917|gb|DT640831.1|DT640831
EST:     CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAG                         TCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
genomic: CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgct ... tgtgttgcagTCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
EST: gi|40303330|gb|CK347717.1|CK347717
EST:     CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAG                         TCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
genomic: CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgct ... tgtgttgcagTCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
EST: gi|211050465|gb|FL475129.1|FL475129
EST:     CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAG                         TCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
genomic: CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgct ... tgtgttgcagTCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
EST: gi|213169886|gb|FM184059.1|FM184059
EST:     CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAG                         TCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
genomic: CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgct ... tgtgttgcagTCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
EST: gi|211281987|gb|FL018040.1|FL018040
EST:     CTGAAGGTTGTTGTGATGTGGGTCCTAGGGAGCTTGGGAGCATGTCAGAG                         TCGGAAGCAGTGGACTACGTCG
genomic: CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgct ... tgtgttgcagTCGGAAGCAGTGGACTACGTCG
EST: gi|4647287|gb|AI622362.1|AI622362
EST:     CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAG                         TCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
genomic: CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgct ... tgtgttgcagTCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
EST: gi|74232916|gb|DT640830.1|DT640830
EST:     CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAG                         TCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
genomic: CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgct ... tgtgttgcagTCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
EST: gi|74238357|gb|DT646271.1|DT646271
EST:     CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAG                         TCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
genomic: CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgct ... tgtgttgcagTCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
EST: gi|211326815|gb|FL454067.1|FL454067
EST:     CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAG                         TCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
genomic: CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgct ... tgtgttgcagTCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
EST: gi|78544875|gb|DV622373.1|DV622373
EST:     CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAG                         TCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
genomic: CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgct ... tgtgttgcagTCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
EST: gi|30032196|gb|CB834047.1|CB834047
EST:     CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAG                         TCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
genomic: CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgct ... tgtgttgcagTCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
EST: gi|20802365|gb|BQ293415.1|BQ293415
EST:     CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAG                         TCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
genomic: CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgct ... tgtgttgcagTCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
EST: gi|12971899|gb|BG267713.1|BG267713
EST:     CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAG                         TCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC
genomic: CTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgct ... tgtgttgcagTCGGAAGCAGTGGACTACGTCGCTCGGAAGATGTGGTACCCTATTTACAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCACGTGTCGGCGCAGCAGTCGTCCGTGCCGCTGTTGCTGAAGACCTGGCTGAGGGGTGCTGTGATGTGGGTCCTAGGGAGCTTGGGAGTATGTCAGAGgtacggcgctacataggataaaaaaacgtcacattcctgttgtcaaaacttaaaaaacctactgcggtgtctcaaatatgttattcgtgtgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT