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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttcttactaaccctagtacttggtctctcttgtggctgtaattggcctacctacctaattaagctgtcaagtcactttcagttattattttttt...

Basic information

species Zea mays
transcript GRMZM2G093359_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G093359_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g10310.3 (Oryza sativa), 5'ss of exon 5
AGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttcttactaaccct---------agtacttggtctctcttgtggctgtaattggcctacctacctaattaagctgtcaagtc---actttcagttattattttttt-------------------------------------------------------------------------------------------
||| ||||| |||||||||||| | ||    |||||||||||||| ||| |||||||||||||||| |||||||||||||| ||||||| ||||           |||| ||||| | |||||   |||| |||| | |||||     ||     ||| || |     || |  ||| | ||| |  |                                                                                           
AGGGCAAGGCCATCCAACAGGAGATTCTCGACCTTATTTTGGTCCTTCTAAGAAGCTTGATTTTGAACTTGAGATGgttagtttcttacaaacctcttgactcacagtatttggtat-tcttg-aactgttattgacatacctgttgcat--gtttgttaaatttgagctgttggttgtcattgtggtataaaatctggccgtatgtaattagttatagatattttcatttcccctggatcaaatatatcataacgctttgttggcttgttgctttcag
















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|149090120|gb|EE179418.2|EE179418
EST:     CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGGTC-AGGAAATGAATTAGGCAAACCAATTGATATTCA
genomic: CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgttttcagGCTGCCATTGTTGG-TCCAGGAAATGAATTAGGCAAACCAATTGATAT-CA
EST: gi|149089319|gb|EE178541.2|EE178541
EST:     CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGAAATGAATTANGCAAACCAATTGATATCAAT
genomic: CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgttttcagGCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAAT
EST: gi|149008951|gb|EE041170.2|EE041170
EST:     CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAAT
genomic: CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgttttcagGCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAAT
EST: gi|12046552|gb|BF728691.1|BF728691
EST:     CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAAT
genomic: CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgttttcagGCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAAT
EST: gi|78180016|gb|DV550389.1|DV550389
EST:     CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAAT
genomic: CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgttttcagGCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAAT
EST: gi|6973663|gb|AW438237.1|AW438237
EST:     CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAAT
genomic: CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgttttcagGCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAAT
EST: gi|149094603|gb|EE180134.2|EE180134
EST:     CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAAT
genomic: CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgttttcagGCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAAT
EST: gi|101398071|gb|EB820910.1|EB820910
EST:     CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGAAATGAATTAAGCAAACCAATTGATATCAAT
genomic: CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgttttcagGCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAAT
EST: gi|31350712|gb|CD435069.1|CD435069
EST:     CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAAT
genomic: CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgttttcagGCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAAT
EST: gi|31355275|gb|CD439632.1|CD439632
EST:     CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAAT
genomic: CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgttttcagGCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAAT
EST: gi|71424525|gb|DR806344.1|DR806344
EST:     CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGAAATGAATTAAGCAAACCAATTGATATCAAT
genomic: CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgttttcagGCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAAT
EST: gi|149106513|gb|EE188405.2|EE188405
EST:     CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATG                         GCTGCCATTGTTGGTCCAGGAAATGAATTANGCAAACCAATTGATATCAAT
genomic: CCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttct ... ttgttttcagGCTGCCATTGTTGGTCCAGGAAATGAATTAGGCAAACCAATTGATATCAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGACAAGGACATCCAACAGGAAACTCCGCTCCTTATTTTGGTCCCTCTCAGAAGCTTGATTTTGAGCTTGAGATGgttagcttcttactaaccctagtacttggtctctcttgtggctgtaattggcctacctacctaattaagctgtcaagtcactttcagttattattttttt

- - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG