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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAGgtagataaaccactgcaagatgctgaagtgaattattcaaacatttcaaaaaaatattgtatgtgctgttttgagtatcattgctctgtaacttgagtgc...

Basic information

species Zea mays
transcript GRMZM5G830874_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G830874_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g08270.3 (Oryza sativa), 5'ss of exon 4
CAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAGgtagataaacc--actgcaagatgctgaagtgaattattcaaacatttcaaaaaaatattgtatgtgctgttttgagtatcattgctctgtaac--ttgagtgc---
||| ||  | |||||||||||||||||||| |||||||||||||||||| || |||||  |||| ||||||||  |||  |   |||    ||| || || |  ||| || | | |||| ||||  | ||| | |||||   | |||| ||  ||| |   |||   ||||  |    
CAAACATGTTTTTGGAATCAAAGGATGAAGCTCATGATTTTGCAAGCCTACGGCATGCGCTTCTGGAACAGgtgcatatgctctacttttcgatactaaatt--attgtt-acatattttaaaaccaaattat-tgtgca--tgtgagcat-gttgttaaataaatattgacagtatt
















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|32913918|gb|CF018730.1|CF018730
EST:     AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAG                         GAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
genomic: AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAGgtagataaac ... tacattgcagGAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
EST: gi|211376348|gb|FL146641.1|FL146641
EST:     AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAG                         GAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
genomic: AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAGgtagataaac ... tacattgcagGAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
EST: gi|94474874|gb|EB703832.1|EB703832
EST:     AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAG                         GAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
genomic: AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAGgtagataaac ... tacattgcagGAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
EST: gi|211291209|gb|FL443498.1|FL443498
EST:     AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAG                         GAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
genomic: AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAGgtagataaac ... tacattgcagGAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
EST: gi|71418229|gb|DR804377.1|DR804377
EST:     AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAG                         GAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA
genomic: AGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAGgtagataaac ... tacattgcagGAGCTATACAGTATACAAAGCCTGTTGGCTCAGGAGAAGGCTAGAGAAACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAGCACATATTTGGAATCAAAGGATGAAGTTCATGATTTTGCAAGCCTGCGACATGCAGTTCTTGAACAGgtagataaaccactgcaagatgctgaagtgaattattcaaacatttcaaaaaaatattgtatgtgctgttttgagtatcattgctctgtaacttgagtgc

- - - - - - - - - -  AGGATG