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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGGAAGTAGTAAATCGGCTCACTACTGCAGTAGTTTTACCACCAGGATTTGTTCATGACTATATCTCAAACTGTATTCGATCATGTGAAGACATTAAGgtctggttcttaaccatgcattccatcttttctggtagatcaacatcttttgataatcatggtaacatgattccaacatcagttctctctcttttttggg...

Basic information

species Zea mays
transcript GRMZM2G011575_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011575_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os11g13694.1 (Oryza sativa), 5'ss of exon 10
AATGGAAGTAGTAAATCGGCTCACTACTGCAGTAGTTTTACCACCAGGATTTGTTCATGACTATATCTCAAACTGTATTCGATCATGTGAAGACATTAAGgtctggttcttaaccatgcattccatcttttctggtagatcaacatcttttgataatcatggtaacatgattccaacatcagttctctctcttttttggg--
||||||||| |||||  |||||||||| ||||||| | |||||||||||||  |||||||||| |||||||||||||||||||||||| || |||||||||| ||         | |   ||   |      |   || | | ||||||  |||  |  | || |||||| ||  |    |  | | |  |    |      
AATGGAAGTTGTAAACAGGCTCACTACAGCAGTAGATCTACCACCAGGATTCATTCATGACTACATCTCAAACTGTATTCGATCATGTCAAAACATTAAGgtttgtgaaagtctcttttctttactagacattcagaggtgatcatcttg-gatggtt-tagtgacatgactcatattatatgtttataacaaagtcaaacc
















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|24765764|gb|CA400923.1|CA400923
EST:     TTGTTCATGACTATATCTCAAACTGTATTCGATCATGTGAAGACATTAAG                         GACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAG
genomic: TTGTTCATGACTATATCTCAAACTGTATTCGATCATGTGAAGACATTAAGgtctggttct ... ttgtttgcagGACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAG
EST: gi|148930025|gb|EE285908.2|EE285908
EST:     TTGTTCATGACTATATCTCAAACTGTATTCGATCATGTGAAGACATTAAG                         GACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAG
genomic: TTGTTCATGACTATATCTCAAACTGTATTCGATCATGTGAAGACATTAAGgtctggttct ... ttgtttgcagGACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAG
EST: gi|211108201|gb|FL028207.1|FL028207
EST:     TTGTTCATGACTATATCTCAAACTGTATTCGATCATGTGAAGACATTAAG                         GACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAG
genomic: TTGTTCATGACTATATCTCAAACTGTATTCGATCATGTGAAGACATTAAGgtctggttct ... ttgtttgcagGACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAG
EST: gi|89251017|gb|DY622803.1|DY622803
EST:     AAGACATTAAG                         GACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAG
genomic: AAGACATTAAGgtctggttct ... ttgtttgcagGACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAG
EST: gi|211108200|gb|FL028206.1|FL028206
EST:     TTGTTCATGACTATATCTCAAACTGTATTCGATCATGTGAAGACATTAAG                         GACAAGTATATGCAAAATAGACTAGTGAAGACTAGTATGTGTTTTTCTACA
genomic: TTGTTCATGACTATATCTCAAACTGTATTCGATCATGTGAAGACATTAAGgtctggttct ... ttgtttgcagGACAAGTATATGCAAAATAGACTAGTGA-GACTAGTATGTGTTTTTCTACA
EST: gi|113701502|gb|EE679006.1|EE679006
EST:     TTGTTCATGACTATATCTCAAACTGTATTCGATCATGTGAAGACATTAAG                         GACAAGTATATGCAAAATAGACTAGTGAGATTAGTATGTGTTTTTCTACAG
genomic: TTGTTCATGACTATATCTCAAACTGTATTCGATCATGTGAAGACATTAAGgtctggttct ... ttgtttgcagGACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAG
EST: gi|40303841|gb|CK348228.1|CK348228
EST:     TTGTTCATGACTATATCTCAAACTGTATTCGATCATGTGAAGACATTAAG                         GACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAG
genomic: TTGTTCATGACTATATCTCAAACTGTATTCGATCATGTGAAGACATTAAGgtctggttct ... ttgtttgcagGACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAG
EST: gi|71769411|gb|DR967348.1|DR967348
EST:     TTGTTCATGACTATATCTCAAACTGTATTCGATCATGTGAAGACATTAAG                         GACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAG
genomic: TTGTTCATGACTATATCTCAAACTGTATTCGATCATGTGAAGACATTAAGgtctggttct ... ttgtttgcagGACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAG
EST: gi|91049014|gb|EB159432.1|EB159432
EST:     TTGTTCATGACTATATCTCAAACTGTATTCGATCATGTGAAGACATTAAG                         GACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAG
genomic: TTGTTCATGACTATATCTCAAACTGTATTCGATCATGTGAAGACATTAAGgtctggttct ... ttgtttgcagGACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAG
EST: gi|74239167|gb|DT647081.1|DT647081
EST:     CTATATCTCAAACTGTATTCGATCATGTGAAGACATTAAG                         GACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAG
genomic: CTATATCTCAAACTGTATTCGATCATGTGAAGACATTAAGgtctggttct ... ttgtttgcagGACAAGTATATGCAAAATAGACTAGTGAGACTAGTATGTGTTTTTCTACAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGGAAGTAGTAAATCGGCTCACTACTGCAGTAGTTTTACCACCAGGATTTGTTCATGACTATATCTCAAACTGTATTCGATCATGTGAAGACATTAAGgtctggttcttaaccatgcattccatcttttctggtagatcaacatcttttgataatcatggtaacatgattccaacatcagttctctctcttttttggg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tctctctc