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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCAAGACGCGCTGCAGTTCCTGGTCAGCTGGATGTCACGGTTCCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGGgtgagtcatgtcactcgctgccattgctgatccacagggacacacaccagctagctgtccaagagttttctttttttttatgcttcaatctgttcactttgcttgcttccacag

Basic information

species Zea mays
transcript GRMZM5G879749_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G879749_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g55130.1 (Oryza sativa), 5'ss of exon 4
CTCAAGACGCGCTGCAGTTCCTGGTCAGCTGGATGTCACGGTTCCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGGgtgagtcatgtcactcgctgccattgctgatccacagggacacacaccagctagctgtccaagagttttctttttttttatgcttcaatctgttcactttgcttgcttccacag
||||||| ||| |||||||| || |||| |||||||| || ||||| ||||| |||||||| ||||||||||| || ||||||||||| || ||| |    ||| |   |  |   ||  ||   |||     |  | || |  || || | ||  |  |  ||  | |          ||| ||  ||  || || |         
CTCAAGATGCGTTGCAGTTCTTGATCAGTTGGATGTCCCGCTTCCCACAGTATCGGCACCGGGATTTCTACATTGCTGGAGAAAGCTATGCTGgtaa--tgtgtaaactggcgatgtt--tgcatcaccatctctgaaacta-ttatctctgcatcatctgactactgtccatcaacaaaatttgcacaaatt-ctag---------
















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|94479697|gb|EB708655.1|EB708655
EST:     CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGG                         GCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
genomic: CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGGgtgagtcatg ... gcttccacagGCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
EST: gi|91050418|gb|EB160836.1|EB160836
EST:     CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGG                         GCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
genomic: CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGGgtgagtcatg ... gcttccacagGCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
EST: gi|116817956|gb|EC860887.1|EC860887
EST:     CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGG                         GCCACTACGTCCCCCAGTTGGCAAGGAAGATTGTCGAGTACAACGAGGCCT
genomic: CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGGgtgagtcatg ... gcttccacagGCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
EST: gi|29946821|gb|CB816342.1|CB816342
EST:     CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGG                         GCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
genomic: CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGGgtgagtcatg ... gcttccacagGCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
EST: gi|101395266|gb|EB819563.1|EB819563
EST:     CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGG                         GCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
genomic: CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGGgtgagtcatg ... gcttccacagGCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
EST: gi|71775053|gb|DR972931.1|DR972931
EST:     CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGG                         GCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
genomic: CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGGgtgagtcatg ... gcttccacagGCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
EST: gi|76020009|gb|DT947179.1|DT947179
EST:     CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGG                         GCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
genomic: CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGGgtgagtcatg ... gcttccacagGCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
EST: gi|93014934|gb|EB640454.1|EB640454
EST:     CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGG                         GCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT
genomic: CCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGGgtgagtcatg ... gcttccacagGCCACTACGTCCCCCAGTTGGCAAGGAAGATCGTCGAGTACAACGAGGCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCAAGACGCGCTGCAGTTCCTGGTCAGCTGGATGTCACGGTTCCCGCAGTACCGGCACCGAGATTTCTACATCGCCGGAGAAAGCTACGCGGgtgagtcatgtcactcgctgccattgctgatccacagggacacacaccagctagctgtccaagagttttctttttttttatgcttcaatctgttcactttgcttgcttccacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA